Multiple sequence alignment - TraesCS4A01G435400

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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 TraesCS4A01G435400 chr4A 100.000 2057 0 0 805 2861 705572674 705570618 0.000000e+00 3799.0
1 TraesCS4A01G435400 chr4A 100.000 271 0 0 1 271 705573478 705573208 4.260000e-138 501.0
2 TraesCS4A01G435400 chr3A 98.299 2058 31 2 805 2861 11577334 11579388 0.000000e+00 3603.0
3 TraesCS4A01G435400 chr3A 97.575 2062 26 4 805 2861 457924934 457926976 0.000000e+00 3509.0
4 TraesCS4A01G435400 chr3A 99.492 197 1 0 75 271 11577136 11577332 2.710000e-95 359.0
5 TraesCS4A01G435400 chr3A 98.477 197 3 0 75 271 457924736 457924932 5.870000e-92 348.0
6 TraesCS4A01G435400 chr7A 97.618 2057 30 1 805 2861 345261490 345263527 0.000000e+00 3509.0
7 TraesCS4A01G435400 chr7A 97.970 197 4 0 75 271 345261292 345261488 2.730000e-90 342.0
8 TraesCS4A01G435400 chr7A 89.091 55 4 2 1 53 220907421 220907367 1.840000e-07 67.6
9 TraesCS4A01G435400 chr2B 97.618 2057 30 9 805 2861 571946413 571948450 0.000000e+00 3509.0
10 TraesCS4A01G435400 chr2B 97.970 197 4 0 75 271 571946215 571946411 2.730000e-90 342.0
11 TraesCS4A01G435400 chr2B 94.949 198 9 1 75 271 90434083 90434280 2.770000e-80 309.0
12 TraesCS4A01G435400 chr1B 97.569 2057 29 3 805 2861 322392824 322394859 0.000000e+00 3502.0
13 TraesCS4A01G435400 chr1B 98.985 197 2 0 75 271 322392626 322392822 1.260000e-93 353.0
14 TraesCS4A01G435400 chr1B 90.196 51 4 1 1 50 188181539 188181589 6.620000e-07 65.8
15 TraesCS4A01G435400 chr6B 97.674 1978 27 1 805 2782 568189567 568191525 0.000000e+00 3380.0
16 TraesCS4A01G435400 chr6B 98.515 202 2 1 70 271 568189365 568189565 3.510000e-94 355.0
17 TraesCS4A01G435400 chr3B 94.319 2077 71 23 805 2861 139621540 139623589 0.000000e+00 3138.0
18 TraesCS4A01G435400 chr1A 98.324 1432 20 1 805 2232 113882383 113883814 0.000000e+00 2508.0
19 TraesCS4A01G435400 chr1A 93.501 754 26 15 2101 2832 113883618 113884370 0.000000e+00 1099.0
20 TraesCS4A01G435400 chr1A 92.857 294 2 2 2101 2394 507991274 507991548 2.650000e-110 409.0
21 TraesCS4A01G435400 chr4B 97.666 1328 20 7 805 2129 134586480 134585161 0.000000e+00 2270.0
22 TraesCS4A01G435400 chr4B 95.926 761 12 1 2101 2861 134585244 134584503 0.000000e+00 1216.0
23 TraesCS4A01G435400 chr4B 98.049 205 3 1 67 271 134586685 134586482 3.510000e-94 355.0
24 TraesCS4A01G435400 chr2A 94.924 197 10 0 75 271 98570012 98570208 2.770000e-80 309.0
25 TraesCS4A01G435400 chr3D 92.157 51 3 1 1 50 481394876 481394826 1.420000e-08 71.3
26 TraesCS4A01G435400 chr7D 95.455 44 1 1 8 50 556998428 556998385 5.110000e-08 69.4


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 TraesCS4A01G435400 chr4A 705570618 705573478 2860 True 2150.000000 3799 100.000000 1 2861 2 chr4A.!!$R1 2860
1 TraesCS4A01G435400 chr3A 11577136 11579388 2252 False 1981.000000 3603 98.895500 75 2861 2 chr3A.!!$F1 2786
2 TraesCS4A01G435400 chr3A 457924736 457926976 2240 False 1928.500000 3509 98.026000 75 2861 2 chr3A.!!$F2 2786
3 TraesCS4A01G435400 chr7A 345261292 345263527 2235 False 1925.500000 3509 97.794000 75 2861 2 chr7A.!!$F1 2786
4 TraesCS4A01G435400 chr2B 571946215 571948450 2235 False 1925.500000 3509 97.794000 75 2861 2 chr2B.!!$F2 2786
5 TraesCS4A01G435400 chr1B 322392626 322394859 2233 False 1927.500000 3502 98.277000 75 2861 2 chr1B.!!$F2 2786
6 TraesCS4A01G435400 chr6B 568189365 568191525 2160 False 1867.500000 3380 98.094500 70 2782 2 chr6B.!!$F1 2712
7 TraesCS4A01G435400 chr3B 139621540 139623589 2049 False 3138.000000 3138 94.319000 805 2861 1 chr3B.!!$F1 2056
8 TraesCS4A01G435400 chr1A 113882383 113884370 1987 False 1803.500000 2508 95.912500 805 2832 2 chr1A.!!$F2 2027
9 TraesCS4A01G435400 chr4B 134584503 134586685 2182 True 1280.333333 2270 97.213667 67 2861 3 chr4B.!!$R1 2794

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
844 845 0.685785 TCGCCCTCTCTCTCTGCATT 60.686 55.000 0.00 0.0 0.00 3.56 F
1058 1062 2.532715 ACACCATGGAGCAGGGGT 60.533 61.111 21.47 0.0 39.88 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1723 0.393132 GGCCTTCCTTTCTTCCCTCG 60.393 60.000 0.0 0.0 0.00 4.63 R
2653 2725 1.072331 GAAGAGGTGAAGGAGCCACAA 59.928 52.381 0.0 0.0 36.31 3.33 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
35 36 9.905713 TTATATTGTAGCTCATCTTTTCTTGGT 57.094 29.630 0.00 0.0 0.00 3.67
38 39 7.615582 TTGTAGCTCATCTTTTCTTGGTATG 57.384 36.000 0.00 0.0 0.00 2.39
39 40 6.711277 TGTAGCTCATCTTTTCTTGGTATGT 58.289 36.000 0.00 0.0 0.00 2.29
40 41 6.595326 TGTAGCTCATCTTTTCTTGGTATGTG 59.405 38.462 0.00 0.0 0.00 3.21
41 42 5.564550 AGCTCATCTTTTCTTGGTATGTGT 58.435 37.500 0.00 0.0 0.00 3.72
42 43 5.413833 AGCTCATCTTTTCTTGGTATGTGTG 59.586 40.000 0.00 0.0 0.00 3.82
43 44 5.412594 GCTCATCTTTTCTTGGTATGTGTGA 59.587 40.000 0.00 0.0 0.00 3.58
44 45 6.094603 GCTCATCTTTTCTTGGTATGTGTGAT 59.905 38.462 0.00 0.0 0.00 3.06
45 46 7.381766 TCATCTTTTCTTGGTATGTGTGATG 57.618 36.000 0.00 0.0 0.00 3.07
46 47 6.942005 TCATCTTTTCTTGGTATGTGTGATGT 59.058 34.615 0.00 0.0 32.21 3.06
47 48 7.448161 TCATCTTTTCTTGGTATGTGTGATGTT 59.552 33.333 0.00 0.0 32.21 2.71
48 49 8.729756 CATCTTTTCTTGGTATGTGTGATGTTA 58.270 33.333 0.00 0.0 0.00 2.41
49 50 8.094798 TCTTTTCTTGGTATGTGTGATGTTAC 57.905 34.615 0.00 0.0 0.00 2.50
50 51 7.936847 TCTTTTCTTGGTATGTGTGATGTTACT 59.063 33.333 0.00 0.0 0.00 2.24
51 52 8.458573 TTTTCTTGGTATGTGTGATGTTACTT 57.541 30.769 0.00 0.0 0.00 2.24
52 53 9.562408 TTTTCTTGGTATGTGTGATGTTACTTA 57.438 29.630 0.00 0.0 0.00 2.24
53 54 9.733556 TTTCTTGGTATGTGTGATGTTACTTAT 57.266 29.630 0.00 0.0 0.00 1.73
62 63 9.890629 ATGTGTGATGTTACTTATATTGTGAGT 57.109 29.630 0.00 0.0 0.00 3.41
844 845 0.685785 TCGCCCTCTCTCTCTGCATT 60.686 55.000 0.00 0.0 0.00 3.56
1046 1050 4.648626 GCAGCAGGCAGGACACCA 62.649 66.667 0.00 0.0 43.97 4.17
1058 1062 2.532715 ACACCATGGAGCAGGGGT 60.533 61.111 21.47 0.0 39.88 4.95
1608 1616 3.788227 TGTGCTTATCTGAAGTGGGTT 57.212 42.857 0.00 0.0 0.00 4.11
1715 1723 3.494332 AGGATGCTGAAATTATGAGGCC 58.506 45.455 0.00 0.0 0.00 5.19
2235 2296 8.940768 AAGCAAAATTCAGTTAACTTAAGCAA 57.059 26.923 5.07 0.0 0.00 3.91
2236 2297 8.940768 AGCAAAATTCAGTTAACTTAAGCAAA 57.059 26.923 5.07 0.0 0.00 3.68
2237 2298 9.377312 AGCAAAATTCAGTTAACTTAAGCAAAA 57.623 25.926 5.07 0.0 0.00 2.44
2459 2531 3.290710 ACAGCACTTGAACACCAGATTT 58.709 40.909 0.00 0.0 0.00 2.17
2653 2725 1.067060 GGCGCCTTCTTCTTGTTTTGT 59.933 47.619 22.15 0.0 0.00 2.83
2763 2835 1.990160 TTTCTGCCACCCTCAACGGT 61.990 55.000 0.00 0.0 36.18 4.83
2764 2836 1.122632 TTCTGCCACCCTCAACGGTA 61.123 55.000 0.00 0.0 33.67 4.02
2838 2910 3.118738 ACAACAGTCTCTTTCAGGTCGTT 60.119 43.478 0.00 0.0 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.905713 ACCAAGAAAAGATGAGCTACAATATAA 57.094 29.630 0.00 0.00 0.00 0.98
12 13 9.330063 CATACCAAGAAAAGATGAGCTACAATA 57.670 33.333 0.00 0.00 0.00 1.90
13 14 7.831193 ACATACCAAGAAAAGATGAGCTACAAT 59.169 33.333 0.00 0.00 0.00 2.71
14 15 7.119699 CACATACCAAGAAAAGATGAGCTACAA 59.880 37.037 0.00 0.00 0.00 2.41
15 16 6.595326 CACATACCAAGAAAAGATGAGCTACA 59.405 38.462 0.00 0.00 0.00 2.74
16 17 6.595716 ACACATACCAAGAAAAGATGAGCTAC 59.404 38.462 0.00 0.00 0.00 3.58
17 18 6.595326 CACACATACCAAGAAAAGATGAGCTA 59.405 38.462 0.00 0.00 0.00 3.32
18 19 5.413833 CACACATACCAAGAAAAGATGAGCT 59.586 40.000 0.00 0.00 0.00 4.09
19 20 5.412594 TCACACATACCAAGAAAAGATGAGC 59.587 40.000 0.00 0.00 0.00 4.26
20 21 7.120285 ACATCACACATACCAAGAAAAGATGAG 59.880 37.037 0.00 0.00 34.73 2.90
21 22 6.942005 ACATCACACATACCAAGAAAAGATGA 59.058 34.615 0.00 0.00 34.73 2.92
22 23 7.149569 ACATCACACATACCAAGAAAAGATG 57.850 36.000 0.00 0.00 36.24 2.90
23 24 7.765695 AACATCACACATACCAAGAAAAGAT 57.234 32.000 0.00 0.00 0.00 2.40
24 25 7.936847 AGTAACATCACACATACCAAGAAAAGA 59.063 33.333 0.00 0.00 0.00 2.52
25 26 8.099364 AGTAACATCACACATACCAAGAAAAG 57.901 34.615 0.00 0.00 0.00 2.27
26 27 8.458573 AAGTAACATCACACATACCAAGAAAA 57.541 30.769 0.00 0.00 0.00 2.29
27 28 9.733556 ATAAGTAACATCACACATACCAAGAAA 57.266 29.630 0.00 0.00 0.00 2.52
36 37 9.890629 ACTCACAATATAAGTAACATCACACAT 57.109 29.630 0.00 0.00 0.00 3.21
51 52 9.733556 ACTCCACAATTTGTTACTCACAATATA 57.266 29.630 0.00 0.00 45.17 0.86
52 53 8.635765 ACTCCACAATTTGTTACTCACAATAT 57.364 30.769 0.00 0.00 45.17 1.28
53 54 8.458573 AACTCCACAATTTGTTACTCACAATA 57.541 30.769 0.00 0.00 45.17 1.90
54 55 6.959639 ACTCCACAATTTGTTACTCACAAT 57.040 33.333 0.00 0.00 45.17 2.71
55 56 6.767524 AACTCCACAATTTGTTACTCACAA 57.232 33.333 0.00 0.00 44.11 3.33
56 57 7.867305 TTAACTCCACAATTTGTTACTCACA 57.133 32.000 0.00 0.00 0.00 3.58
57 58 9.821662 GTATTAACTCCACAATTTGTTACTCAC 57.178 33.333 0.00 0.00 0.00 3.51
58 59 9.005777 GGTATTAACTCCACAATTTGTTACTCA 57.994 33.333 0.00 0.00 0.00 3.41
59 60 9.005777 TGGTATTAACTCCACAATTTGTTACTC 57.994 33.333 0.00 0.00 0.00 2.59
60 61 8.927675 TGGTATTAACTCCACAATTTGTTACT 57.072 30.769 0.00 0.00 0.00 2.24
195 196 1.945522 CCAAATGTCGCGTCCACAA 59.054 52.632 5.77 0.00 0.00 3.33
844 845 3.461831 AGGGATTTACGAATGGGGAATCA 59.538 43.478 0.00 0.00 0.00 2.57
1046 1050 2.607750 ACGACACCCCTGCTCCAT 60.608 61.111 0.00 0.00 0.00 3.41
1058 1062 2.197605 TGGCTTGAGGACGACGACA 61.198 57.895 0.00 0.00 0.00 4.35
1608 1616 0.776810 TCCCCTGCCATTCTTTGTCA 59.223 50.000 0.00 0.00 0.00 3.58
1647 1655 4.500375 GCCACATTCTCTTCAGCAAGTTTT 60.500 41.667 0.00 0.00 0.00 2.43
1715 1723 0.393132 GGCCTTCCTTTCTTCCCTCG 60.393 60.000 0.00 0.00 0.00 4.63
2229 2290 9.944663 CAGTGTTAAGTTAACTGATTTTGCTTA 57.055 29.630 22.87 0.00 43.22 3.09
2230 2291 7.435192 GCAGTGTTAAGTTAACTGATTTTGCTT 59.565 33.333 22.87 0.00 43.22 3.91
2231 2292 6.918022 GCAGTGTTAAGTTAACTGATTTTGCT 59.082 34.615 22.87 8.32 43.22 3.91
2232 2293 6.695278 TGCAGTGTTAAGTTAACTGATTTTGC 59.305 34.615 22.87 20.25 43.22 3.68
2233 2294 8.627487 TTGCAGTGTTAAGTTAACTGATTTTG 57.373 30.769 22.87 13.75 43.22 2.44
2234 2295 9.816354 ATTTGCAGTGTTAAGTTAACTGATTTT 57.184 25.926 22.87 0.00 43.22 1.82
2235 2296 9.816354 AATTTGCAGTGTTAAGTTAACTGATTT 57.184 25.926 22.87 0.00 43.22 2.17
2236 2297 9.816354 AAATTTGCAGTGTTAAGTTAACTGATT 57.184 25.926 22.87 9.61 43.22 2.57
2237 2298 9.463443 GAAATTTGCAGTGTTAAGTTAACTGAT 57.537 29.630 22.87 9.04 43.22 2.90
2238 2299 8.462811 TGAAATTTGCAGTGTTAAGTTAACTGA 58.537 29.630 22.87 0.00 43.22 3.41
2239 2300 8.627487 TGAAATTTGCAGTGTTAAGTTAACTG 57.373 30.769 22.87 16.10 43.37 3.16
2240 2301 8.466798 ACTGAAATTTGCAGTGTTAAGTTAACT 58.533 29.630 22.87 1.12 44.39 2.24
2241 2302 8.628882 ACTGAAATTTGCAGTGTTAAGTTAAC 57.371 30.769 17.26 17.26 44.39 2.01
2244 2305 9.301153 CTTAACTGAAATTTGCAGTGTTAAGTT 57.699 29.630 10.86 10.98 45.27 2.66
2245 2306 8.466798 ACTTAACTGAAATTTGCAGTGTTAAGT 58.533 29.630 19.96 19.96 45.27 2.24
2246 2307 8.856490 ACTTAACTGAAATTTGCAGTGTTAAG 57.144 30.769 19.08 19.08 45.27 1.85
2459 2531 5.675684 TGTTGAACTGCTGTATCTATGGA 57.324 39.130 0.00 0.00 0.00 3.41
2526 2598 7.063593 AGATGCAGAAGAGTAGTTAGGTATGA 58.936 38.462 0.00 0.00 0.00 2.15
2653 2725 1.072331 GAAGAGGTGAAGGAGCCACAA 59.928 52.381 0.00 0.00 36.31 3.33
2763 2835 4.666397 TGCTCGTTGCGCCGGTTA 62.666 61.111 4.18 0.00 46.63 2.85
2838 2910 3.587095 CGGTCTACGCCTCTGACA 58.413 61.111 0.00 0.00 34.82 3.58


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

AutoCloner maintained by Alex Coulton.