Multiple sequence alignment - TraesCS4A01G072000

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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 TraesCS4A01G072000 chr4A 100.000 2941 0 0 1 2941 69512094 69509154 0.000000e+00 5432.0
1 TraesCS4A01G072000 chr4A 95.583 2943 126 4 1 2941 69524797 69521857 0.000000e+00 4711.0
2 TraesCS4A01G072000 chr4D 94.633 2944 152 5 1 2941 388251823 388248883 0.000000e+00 4556.0
3 TraesCS4A01G072000 chr4B 93.938 1600 93 3 909 2508 476571615 476570020 0.000000e+00 2414.0
4 TraesCS4A01G072000 chr4B 88.991 872 90 6 1 871 476572482 476571616 0.000000e+00 1074.0
5 TraesCS4A01G072000 chr4B 92.742 124 9 0 2818 2941 476570013 476569890 2.330000e-41 180.0
6 TraesCS4A01G072000 chr3D 89.009 1574 144 6 947 2508 78096968 78098524 0.000000e+00 1921.0
7 TraesCS4A01G072000 chr3D 88.762 1575 145 10 947 2508 77999275 78000830 0.000000e+00 1899.0
8 TraesCS4A01G072000 chr3A 89.576 1439 131 5 956 2381 91285685 91284253 0.000000e+00 1808.0
9 TraesCS4A01G072000 chr7D 90.998 1322 106 4 947 2256 177169153 177170473 0.000000e+00 1770.0
10 TraesCS4A01G072000 chr7D 96.732 306 8 2 2508 2812 381970753 381970449 2.620000e-140 508.0
11 TraesCS4A01G072000 chr7A 89.864 1322 121 3 947 2256 181169024 181170344 0.000000e+00 1687.0
12 TraesCS4A01G072000 chr7A 89.486 1322 126 8 947 2256 181014945 181016265 0.000000e+00 1659.0
13 TraesCS4A01G072000 chr2B 97.059 306 7 2 2508 2812 391164016 391164320 5.620000e-142 514.0
14 TraesCS4A01G072000 chr2B 96.753 308 8 2 2506 2812 112844208 112844514 2.020000e-141 512.0
15 TraesCS4A01G072000 chr2B 75.377 199 40 7 478 671 211708080 211708274 1.450000e-13 87.9
16 TraesCS4A01G072000 chr7B 96.743 307 8 2 2508 2813 716835559 716835254 7.270000e-141 510.0
17 TraesCS4A01G072000 chr7B 96.732 306 8 2 2508 2812 742992453 742992757 2.620000e-140 508.0
18 TraesCS4A01G072000 chr7B 78.947 133 23 5 424 552 746377113 746376982 5.220000e-13 86.1
19 TraesCS4A01G072000 chr5A 96.743 307 8 2 2508 2813 19245831 19245526 7.270000e-141 510.0
20 TraesCS4A01G072000 chr5A 79.570 279 42 12 283 551 656715118 656714845 5.010000e-43 185.0
21 TraesCS4A01G072000 chr6D 96.732 306 8 2 2508 2812 124520535 124520839 2.620000e-140 508.0
22 TraesCS4A01G072000 chr6D 78.571 168 36 0 502 669 120862013 120862180 8.620000e-21 111.0
23 TraesCS4A01G072000 chr5D 81.690 284 46 4 389 669 545237344 545237624 6.340000e-57 231.0
24 TraesCS4A01G072000 chr3B 74.419 387 83 14 286 662 75326693 75326313 5.080000e-33 152.0
25 TraesCS4A01G072000 chr3B 85.938 128 18 0 2814 2941 124118855 124118728 1.420000e-28 137.0
26 TraesCS4A01G072000 chr1A 74.250 400 82 17 283 670 559625350 559625740 6.570000e-32 148.0
27 TraesCS4A01G072000 chr6B 87.719 57 7 0 613 669 16999683 16999627 1.890000e-07 67.6


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 TraesCS4A01G072000 chr4A 69509154 69512094 2940 True 5432.000000 5432 100.000000 1 2941 1 chr4A.!!$R1 2940
1 TraesCS4A01G072000 chr4A 69521857 69524797 2940 True 4711.000000 4711 95.583000 1 2941 1 chr4A.!!$R2 2940
2 TraesCS4A01G072000 chr4D 388248883 388251823 2940 True 4556.000000 4556 94.633000 1 2941 1 chr4D.!!$R1 2940
3 TraesCS4A01G072000 chr4B 476569890 476572482 2592 True 1222.666667 2414 91.890333 1 2941 3 chr4B.!!$R1 2940
4 TraesCS4A01G072000 chr3D 78096968 78098524 1556 False 1921.000000 1921 89.009000 947 2508 1 chr3D.!!$F2 1561
5 TraesCS4A01G072000 chr3D 77999275 78000830 1555 False 1899.000000 1899 88.762000 947 2508 1 chr3D.!!$F1 1561
6 TraesCS4A01G072000 chr3A 91284253 91285685 1432 True 1808.000000 1808 89.576000 956 2381 1 chr3A.!!$R1 1425
7 TraesCS4A01G072000 chr7D 177169153 177170473 1320 False 1770.000000 1770 90.998000 947 2256 1 chr7D.!!$F1 1309
8 TraesCS4A01G072000 chr7A 181169024 181170344 1320 False 1687.000000 1687 89.864000 947 2256 1 chr7A.!!$F2 1309
9 TraesCS4A01G072000 chr7A 181014945 181016265 1320 False 1659.000000 1659 89.486000 947 2256 1 chr7A.!!$F1 1309

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
639 641 0.179043 TTGTCAAGCTGCCGGTGTTA 60.179 50.0 1.9 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2140 0.254747 TACCCCTACATTGCTGCCAC 59.745 55.0 0.0 0.0 0.0 5.01 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
247 249 0.326618 CTTCCTTCCTCTAGGCCCCA 60.327 60.000 0.00 0.00 35.15 4.96
275 277 0.391661 GCCTCAGTTTGGCGATGAGA 60.392 55.000 6.88 0.00 42.48 3.27
296 298 1.002624 GATTCAAGGCCGTGGTGGA 60.003 57.895 19.08 0.25 42.00 4.02
318 320 0.606401 ATGTTGGTGGACGGCAAGAG 60.606 55.000 0.00 0.00 0.00 2.85
363 365 2.719705 AGGTGGTGAGGATTTTTGGGTA 59.280 45.455 0.00 0.00 0.00 3.69
377 379 6.410222 TTTTTGGGTAGGGAGAAATCCATA 57.590 37.500 0.00 0.00 0.00 2.74
442 444 2.163509 GTTCCTTCTTGAAGGGCTTCC 58.836 52.381 24.20 8.51 40.38 3.46
475 477 1.344087 CCCCACTACCCTCCATGTACT 60.344 57.143 0.00 0.00 0.00 2.73
600 602 0.886490 CATCTCCATAGGGCGCAACC 60.886 60.000 10.83 1.02 37.93 3.77
601 603 1.344953 ATCTCCATAGGGCGCAACCA 61.345 55.000 10.83 0.00 42.05 3.67
621 623 4.039124 ACCATTGCCGATCTTCTTTGTTTT 59.961 37.500 0.00 0.00 0.00 2.43
639 641 0.179043 TTGTCAAGCTGCCGGTGTTA 60.179 50.000 1.90 0.00 0.00 2.41
1106 1122 1.419012 TGATGAGATGGATGACCTGCC 59.581 52.381 0.00 0.00 37.04 4.85
1347 1363 8.248253 TCATTAACGTGATATGTAGTGTGTTCT 58.752 33.333 0.00 0.00 0.00 3.01
1505 1522 8.103305 AGTTAATTACATATGGGTCAGCTATGG 58.897 37.037 7.80 0.00 0.00 2.74
1544 1561 8.020819 TGCACACTTTGTTCTTAAATAGTATGC 58.979 33.333 0.00 0.00 0.00 3.14
1617 1635 7.586349 ACTATTGTATTCCCCTCATGAACATT 58.414 34.615 0.00 0.00 0.00 2.71
1630 1648 8.588472 CCCTCATGAACATTGTATCATACTCTA 58.412 37.037 0.00 0.00 34.61 2.43
1722 1740 7.070571 AGACCCAAAATTGTTGGATAGAAAACA 59.929 33.333 7.22 0.00 42.06 2.83
2010 2028 8.431910 ACTATAGTTTTACTTGGTTCCTCAGA 57.568 34.615 0.00 0.00 0.00 3.27
2079 2097 8.617809 GGTCGCTTGTTTATTTATTTCCATAGA 58.382 33.333 0.00 0.00 0.00 1.98
2122 2140 0.792640 GGCACGAGATATGGCAATCG 59.207 55.000 11.54 11.54 42.03 3.34
2398 2416 7.012327 GCAACATAAAGTGGTATGAGAGCATTA 59.988 37.037 0.00 0.00 37.99 1.90
2460 2478 4.742201 CCACCTCACGCACTCCCG 62.742 72.222 0.00 0.00 0.00 5.14
2636 2654 8.088981 ACTCAGTTCATATCTGTAAGTTCGTTT 58.911 33.333 0.00 0.00 34.86 3.60
2889 2908 2.325583 TGGTCTCCCGCATGAATTAC 57.674 50.000 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 28 4.394712 CACCGCCCAGAGACCACC 62.395 72.222 0.00 0.0 0.00 4.61
77 79 2.182030 GCTCGTGAAGTCCCCTCG 59.818 66.667 0.00 0.0 0.00 4.63
217 219 2.372172 GAGGAAGGAAGAGGGAACAACA 59.628 50.000 0.00 0.0 0.00 3.33
247 249 2.961062 GCCAAACTGAGGCCATTGATAT 59.039 45.455 5.01 0.0 46.50 1.63
275 277 1.176527 CACCACGGCCTTGAATCAAT 58.823 50.000 11.54 0.0 0.00 2.57
296 298 2.672996 GCCGTCCACCAACATGCT 60.673 61.111 0.00 0.0 0.00 3.79
318 320 0.029567 CGATCCGAGTGCTCCACTAC 59.970 60.000 0.00 0.0 45.44 2.73
363 365 3.772025 CGAGCCTATATGGATTTCTCCCT 59.228 47.826 0.00 0.0 41.29 4.20
377 379 4.530857 GGTGCCGCACGAGCCTAT 62.531 66.667 17.13 0.0 37.52 2.57
395 397 2.111043 CACAGGCGACACCACCTT 59.889 61.111 0.00 0.0 43.14 3.50
442 444 1.840198 GTGGGGAGGGGGTATACCG 60.840 68.421 15.80 0.0 41.60 4.02
539 541 1.570813 CGAAGCATCGCATACCAAGA 58.429 50.000 0.00 0.0 42.96 3.02
600 602 4.984161 ACAAAACAAAGAAGATCGGCAATG 59.016 37.500 0.00 0.0 0.00 2.82
601 603 5.200368 ACAAAACAAAGAAGATCGGCAAT 57.800 34.783 0.00 0.0 0.00 3.56
621 623 0.602638 CTAACACCGGCAGCTTGACA 60.603 55.000 0.00 0.0 0.00 3.58
639 641 7.284034 TGAGAGAAAGAAAGAGAAACAAATGCT 59.716 33.333 0.00 0.0 0.00 3.79
684 686 6.862209 TGGCGCTGATTACTTCAATAATTTT 58.138 32.000 7.64 0.0 32.78 1.82
776 778 9.968870 CTAGACCAAGATGTAATTAAGTAGACC 57.031 37.037 0.00 0.0 0.00 3.85
795 797 6.143206 TCATCCATATGAGTTTCCTAGACCA 58.857 40.000 3.65 0.0 37.20 4.02
940 943 7.343833 CCCCTATGTAGAACTGAAGGTTAACTA 59.656 40.741 5.42 0.0 38.41 2.24
1544 1561 3.402110 TGCTACAATGTTCAGTGGAGTG 58.598 45.455 12.87 0.0 0.00 3.51
1657 1675 6.543430 TGCCCTGCATTTATTAATTTCAGT 57.457 33.333 0.00 0.0 31.71 3.41
1713 1731 8.225603 TCAGTTTTCAGCTTCTTGTTTTCTAT 57.774 30.769 0.00 0.0 0.00 1.98
1722 1740 3.938963 TGACGTTCAGTTTTCAGCTTCTT 59.061 39.130 0.00 0.0 0.00 2.52
1811 1829 2.929592 GCGTTGGAACTCCGAAGTATGT 60.930 50.000 1.54 0.0 39.43 2.29
1956 1974 1.402968 CGGAATGAATGTTGGCTCAGG 59.597 52.381 0.00 0.0 0.00 3.86
2079 2097 2.758979 CCCACGTAGTAACCATGAGAGT 59.241 50.000 0.00 0.0 41.61 3.24
2122 2140 0.254747 TACCCCTACATTGCTGCCAC 59.745 55.000 0.00 0.0 0.00 5.01
2186 2204 0.963962 AGAGACAAAGACGGGCGTTA 59.036 50.000 0.00 0.0 0.00 3.18
2336 2354 6.071672 CGATGGTAGAGGTATCTCATGAATGT 60.072 42.308 5.64 0.0 42.34 2.71
2398 2416 2.686118 GCCTTGGCTCCAGAAGATGATT 60.686 50.000 4.11 0.0 0.00 2.57
2636 2654 6.957920 TTCTTTGAACCTTGTCAATGATCA 57.042 33.333 0.00 0.0 39.81 2.92
2776 2795 7.234355 ACTTTTGGAAGTTTGAGTGAGGATAT 58.766 34.615 0.00 0.0 43.48 1.63
2822 2841 5.235850 TCCTTCACCAAGTATTGCACTTA 57.764 39.130 0.00 0.0 46.04 2.24
2889 2908 4.744137 TGTGACAAAAATTCTCATTTGGCG 59.256 37.500 5.56 0.0 45.51 5.69


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

AutoCloner maintained by Alex Coulton.