Multiple sequence alignment - TraesCS4A01G279400

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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 TraesCS4A01G279400 chr4A 100.000 3933 0 0 1 3933 586725830 586729762 0.000000e+00 7263.0
1 TraesCS4A01G279400 chr4A 95.408 4007 102 26 3 3933 456472662 456476662 0.000000e+00 6305.0
2 TraesCS4A01G279400 chr4A 82.870 683 81 24 3264 3927 742884584 742885249 7.330000e-162 580.0
3 TraesCS4A01G279400 chr4D 92.178 2378 125 22 706 3044 14560149 14562504 0.000000e+00 3304.0
4 TraesCS4A01G279400 chr4D 91.108 2103 108 28 990 3043 14832006 14829934 0.000000e+00 2774.0
5 TraesCS4A01G279400 chr4D 85.985 949 89 20 1016 1935 14523131 14524064 0.000000e+00 976.0
6 TraesCS4A01G279400 chr4D 87.835 822 63 15 3126 3933 14562810 14563608 0.000000e+00 929.0
7 TraesCS4A01G279400 chr4D 91.195 318 13 10 708 1023 14522183 14522487 6.080000e-113 418.0
8 TraesCS4A01G279400 chr4D 85.441 261 20 12 706 953 14832333 14832078 5.040000e-64 255.0
9 TraesCS4A01G279400 chr4D 92.908 141 9 1 2026 2166 14525432 14525571 1.850000e-48 204.0
10 TraesCS4A01G279400 chr4D 81.119 143 12 3 406 548 394550904 394550777 2.500000e-17 100.0
11 TraesCS4A01G279400 chr4B 91.929 2354 124 23 706 3018 24666272 24663944 0.000000e+00 3234.0
12 TraesCS4A01G279400 chr3B 89.330 1359 74 28 706 2009 452746437 452747779 0.000000e+00 1640.0
13 TraesCS4A01G279400 chr3B 94.052 891 53 0 2028 2918 452754391 452755281 0.000000e+00 1352.0
14 TraesCS4A01G279400 chr3B 94.370 675 31 2 1 668 670159780 670160454 0.000000e+00 1029.0
15 TraesCS4A01G279400 chr3B 93.935 676 33 2 1 668 749318192 749317517 0.000000e+00 1014.0
16 TraesCS4A01G279400 chr3B 87.752 694 67 15 3250 3933 505039403 505038718 0.000000e+00 795.0
17 TraesCS4A01G279400 chr3B 80.704 710 99 31 3247 3933 192027743 192027049 5.830000e-143 518.0
18 TraesCS4A01G279400 chr3B 80.484 702 106 24 3251 3933 687589556 687588867 3.510000e-140 508.0
19 TraesCS4A01G279400 chr3B 92.179 179 12 2 490 668 547054578 547054402 6.520000e-63 252.0
20 TraesCS4A01G279400 chr3B 83.333 138 13 9 3124 3256 827300683 827300815 6.900000e-23 119.0
21 TraesCS4A01G279400 chr3B 83.333 138 13 9 3124 3256 827812834 827812966 6.900000e-23 119.0
22 TraesCS4A01G279400 chr3B 82.857 140 12 10 3124 3256 827244845 827244979 8.930000e-22 115.0
23 TraesCS4A01G279400 chr3B 82.857 140 12 10 3124 3256 827755698 827755832 8.930000e-22 115.0
24 TraesCS4A01G279400 chr3B 97.059 34 0 1 2001 2033 452747786 452747819 5.490000e-04 56.5
25 TraesCS4A01G279400 chr6D 96.257 668 25 0 1 668 386061019 386061686 0.000000e+00 1096.0
26 TraesCS4A01G279400 chr6D 83.498 709 85 23 3243 3933 202260798 202260104 1.990000e-177 632.0
27 TraesCS4A01G279400 chr6D 83.234 167 25 3 2372 2537 429945116 429944952 2.450000e-32 150.0
28 TraesCS4A01G279400 chr6D 76.647 167 26 10 2365 2525 141591117 141591276 3.260000e-11 80.5
29 TraesCS4A01G279400 chr7D 87.427 684 69 11 3255 3933 116791215 116790544 0.000000e+00 771.0
30 TraesCS4A01G279400 chr7D 93.269 312 21 0 357 668 483879548 483879237 9.960000e-126 460.0
31 TraesCS4A01G279400 chr7A 85.387 698 76 18 3256 3933 86149209 86149900 0.000000e+00 701.0
32 TraesCS4A01G279400 chr6A 83.077 715 86 22 3243 3933 309869315 309870018 5.580000e-173 617.0
33 TraesCS4A01G279400 chr6A 77.246 167 25 10 2365 2525 186529699 186529858 7.000000e-13 86.1
34 TraesCS4A01G279400 chr3A 94.226 381 21 1 287 666 638490037 638490417 7.330000e-162 580.0
35 TraesCS4A01G279400 chr3A 81.218 591 110 1 79 668 509510234 509509644 3.560000e-130 475.0
36 TraesCS4A01G279400 chr2B 85.816 564 47 13 3371 3933 69660130 69660661 5.700000e-158 568.0
37 TraesCS4A01G279400 chr2D 82.601 546 77 8 3401 3933 26349442 26348902 2.140000e-127 466.0
38 TraesCS4A01G279400 chr2D 79.012 162 26 7 2412 2569 584898264 584898421 1.930000e-18 104.0
39 TraesCS4A01G279400 chr1D 92.857 210 14 1 389 598 197743687 197743895 1.780000e-78 303.0
40 TraesCS4A01G279400 chrUn 83.491 212 31 4 3725 3933 331542883 331543093 1.120000e-45 195.0
41 TraesCS4A01G279400 chrUn 83.491 212 31 4 3725 3933 397699839 397700049 1.120000e-45 195.0
42 TraesCS4A01G279400 chrUn 82.353 136 18 6 3124 3256 33372715 33372583 3.210000e-21 113.0
43 TraesCS4A01G279400 chrUn 82.353 136 18 6 3124 3256 33664596 33664464 3.210000e-21 113.0
44 TraesCS4A01G279400 chrUn 82.353 136 18 6 3124 3256 426273394 426273262 3.210000e-21 113.0
45 TraesCS4A01G279400 chr3D 88.158 152 18 0 51 202 388437219 388437068 8.680000e-42 182.0
46 TraesCS4A01G279400 chr3D 98.507 67 1 0 2 68 598307167 598307101 6.900000e-23 119.0


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 TraesCS4A01G279400 chr4A 586725830 586729762 3932 False 7263.000000 7263 100.000000 1 3933 1 chr4A.!!$F2 3932
1 TraesCS4A01G279400 chr4A 456472662 456476662 4000 False 6305.000000 6305 95.408000 3 3933 1 chr4A.!!$F1 3930
2 TraesCS4A01G279400 chr4A 742884584 742885249 665 False 580.000000 580 82.870000 3264 3927 1 chr4A.!!$F3 663
3 TraesCS4A01G279400 chr4D 14560149 14563608 3459 False 2116.500000 3304 90.006500 706 3933 2 chr4D.!!$F2 3227
4 TraesCS4A01G279400 chr4D 14829934 14832333 2399 True 1514.500000 2774 88.274500 706 3043 2 chr4D.!!$R2 2337
5 TraesCS4A01G279400 chr4D 14522183 14525571 3388 False 532.666667 976 90.029333 708 2166 3 chr4D.!!$F1 1458
6 TraesCS4A01G279400 chr4B 24663944 24666272 2328 True 3234.000000 3234 91.929000 706 3018 1 chr4B.!!$R1 2312
7 TraesCS4A01G279400 chr3B 452754391 452755281 890 False 1352.000000 1352 94.052000 2028 2918 1 chr3B.!!$F1 890
8 TraesCS4A01G279400 chr3B 670159780 670160454 674 False 1029.000000 1029 94.370000 1 668 1 chr3B.!!$F2 667
9 TraesCS4A01G279400 chr3B 749317517 749318192 675 True 1014.000000 1014 93.935000 1 668 1 chr3B.!!$R5 667
10 TraesCS4A01G279400 chr3B 452746437 452747819 1382 False 848.250000 1640 93.194500 706 2033 2 chr3B.!!$F7 1327
11 TraesCS4A01G279400 chr3B 505038718 505039403 685 True 795.000000 795 87.752000 3250 3933 1 chr3B.!!$R2 683
12 TraesCS4A01G279400 chr3B 192027049 192027743 694 True 518.000000 518 80.704000 3247 3933 1 chr3B.!!$R1 686
13 TraesCS4A01G279400 chr3B 687588867 687589556 689 True 508.000000 508 80.484000 3251 3933 1 chr3B.!!$R4 682
14 TraesCS4A01G279400 chr6D 386061019 386061686 667 False 1096.000000 1096 96.257000 1 668 1 chr6D.!!$F2 667
15 TraesCS4A01G279400 chr6D 202260104 202260798 694 True 632.000000 632 83.498000 3243 3933 1 chr6D.!!$R1 690
16 TraesCS4A01G279400 chr7D 116790544 116791215 671 True 771.000000 771 87.427000 3255 3933 1 chr7D.!!$R1 678
17 TraesCS4A01G279400 chr7A 86149209 86149900 691 False 701.000000 701 85.387000 3256 3933 1 chr7A.!!$F1 677
18 TraesCS4A01G279400 chr6A 309869315 309870018 703 False 617.000000 617 83.077000 3243 3933 1 chr6A.!!$F2 690
19 TraesCS4A01G279400 chr3A 509509644 509510234 590 True 475.000000 475 81.218000 79 668 1 chr3A.!!$R1 589
20 TraesCS4A01G279400 chr2B 69660130 69660661 531 False 568.000000 568 85.816000 3371 3933 1 chr2B.!!$F1 562
21 TraesCS4A01G279400 chr2D 26348902 26349442 540 True 466.000000 466 82.601000 3401 3933 1 chr2D.!!$R1 532

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
235 236 1.375853 GCACCAATAGACCGCATGCA 61.376 55.000 19.57 0.0 0.0 3.96 F
771 788 1.532868 GCAGAATGGCATACATCCGAC 59.467 52.381 0.00 0.0 39.4 4.79 F
2078 4207 1.301401 CGCCACTTCAAGGTCCGAA 60.301 57.895 0.00 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 4166 0.393537 CAGCCCATCCAGAACCTGAC 60.394 60.000 0.0 0.0 32.44 3.51 R
2252 4381 1.383664 CCAGCTCCTCCATCTGGGA 60.384 63.158 0.0 0.0 45.89 4.37 R
3520 5924 1.890979 GCTCAGGCATGGTCCATCG 60.891 63.158 0.0 0.0 38.54 3.84 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
196 197 7.702348 CCTTTAGATAAAAGCAAGGGAAAATCG 59.298 37.037 0.00 0.00 42.85 3.34
235 236 1.375853 GCACCAATAGACCGCATGCA 61.376 55.000 19.57 0.00 0.00 3.96
462 470 2.766263 TGTCGTTGGCTATCCAGAGAAT 59.234 45.455 0.00 0.00 44.53 2.40
571 580 7.761704 GCATCGCTTATCAAGGAGATTAGATAA 59.238 37.037 0.00 0.00 35.84 1.75
655 672 5.291128 TGATAGTTTAGCTAAGTTTGCTCGC 59.709 40.000 15.20 7.21 41.46 5.03
771 788 1.532868 GCAGAATGGCATACATCCGAC 59.467 52.381 0.00 0.00 39.40 4.79
1169 1925 2.202623 GCGCGTCGAGTCCATCTT 60.203 61.111 8.43 0.00 0.00 2.40
1453 2209 4.754667 GAGACAACGCGGGGGTCC 62.755 72.222 12.47 5.56 31.99 4.46
1765 2538 8.733857 AACTTTCGATTTGTGAGATTTCATTC 57.266 30.769 0.00 0.00 35.39 2.67
1771 2544 6.259608 CGATTTGTGAGATTTCATTCCTAGCT 59.740 38.462 0.00 0.00 35.39 3.32
1910 2707 6.652900 TGGGTTTTCCTTCTTTTTGAGTTTTG 59.347 34.615 0.00 0.00 40.46 2.44
1918 2718 8.368668 TCCTTCTTTTTGAGTTTTGTTTTACCA 58.631 29.630 0.00 0.00 0.00 3.25
2033 4162 3.382083 AGTGGGTTGGTGTTTCTTTCT 57.618 42.857 0.00 0.00 0.00 2.52
2037 4166 3.194542 TGGGTTGGTGTTTCTTTCTGTTG 59.805 43.478 0.00 0.00 0.00 3.33
2078 4207 1.301401 CGCCACTTCAAGGTCCGAA 60.301 57.895 0.00 0.00 0.00 4.30
2628 4766 3.318555 CGAGATCGAGCAGTGCGC 61.319 66.667 10.00 9.50 43.02 6.09
2794 4932 2.125147 ATGGACGATGGTGCCACG 60.125 61.111 0.00 10.16 33.93 4.94
2799 4937 2.047274 CGATGGTGCCACGGAGTT 60.047 61.111 0.00 0.00 41.61 3.01
3109 5454 2.030335 TCAATTTCCGCATCGTGATTCG 59.970 45.455 0.00 0.00 41.41 3.34
3186 5561 4.525912 AGAATGTGGGATGAAACTTTGC 57.474 40.909 0.00 0.00 0.00 3.68
3418 5814 8.618702 ATGTCATGATGAGATAATGGACTTTC 57.381 34.615 2.93 0.00 27.64 2.62
3803 6223 6.253946 ACAGATCCCCTAATAAAACCTCTG 57.746 41.667 0.00 0.00 35.04 3.35
3831 6253 2.402378 CGGCGGTTTATTTTGTTCGTTG 59.598 45.455 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 197 5.583854 GGTGCCTGTATCATATGTGATGATC 59.416 44.000 14.66 6.27 44.62 2.92
235 236 6.385759 TCCATGTGGGTACAGTACTTATGAAT 59.614 38.462 10.62 0.00 40.79 2.57
462 470 1.536766 CGATTGCAACTGGAAGCTCAA 59.463 47.619 0.00 0.00 37.60 3.02
571 580 5.355071 ACACGATTCATGAATGCACATAAGT 59.645 36.000 25.37 9.22 0.00 2.24
655 672 8.410141 ACTCAATTCGAGAATCTACCTTCTAAG 58.590 37.037 10.61 0.00 45.45 2.18
1150 1906 2.278857 GATGGACTCGACGCGCAT 60.279 61.111 5.73 0.00 0.00 4.73
1169 1925 2.796193 CCCTCATCGTGGCCATCGA 61.796 63.158 25.43 25.43 41.45 3.59
1209 1965 1.065928 CTCCACATACTCGCCGACC 59.934 63.158 0.00 0.00 0.00 4.79
1387 2143 4.397417 GGAGTTGATGTAGTAGTACACGGT 59.603 45.833 12.62 0.00 42.06 4.83
1771 2544 3.785887 AGGGTGGCTCAACTTAATATGGA 59.214 43.478 0.00 0.00 0.00 3.41
2033 4162 1.073763 CCCATCCAGAACCTGACAACA 59.926 52.381 0.00 0.00 32.44 3.33
2037 4166 0.393537 CAGCCCATCCAGAACCTGAC 60.394 60.000 0.00 0.00 32.44 3.51
2078 4207 3.675619 GAACGCACGGCCCTATGGT 62.676 63.158 0.00 0.00 0.00 3.55
2200 4329 3.857854 TAGACGACGGAGCGCGAC 61.858 66.667 12.10 1.97 32.81 5.19
2252 4381 1.383664 CCAGCTCCTCCATCTGGGA 60.384 63.158 0.00 0.00 45.89 4.37
2287 4416 2.282745 AGGAACTGCTTGCCAGCC 60.283 61.111 7.41 0.00 46.74 4.85
2298 4427 2.050269 CTGACGACCCACAGGAACT 58.950 57.895 0.00 0.00 43.88 3.01
2788 4926 2.029964 GGTTCGAACTCCGTGGCA 59.970 61.111 26.32 0.00 39.75 4.92
2794 4932 1.079336 CGGGGAAGGTTCGAACTCC 60.079 63.158 26.32 24.10 0.00 3.85
3126 5481 5.065704 TGTGCTGCAAAGTTTGAAGTTAA 57.934 34.783 22.18 8.21 38.65 2.01
3520 5924 1.890979 GCTCAGGCATGGTCCATCG 60.891 63.158 0.00 0.00 38.54 3.84
3671 6078 7.548075 ACAACTTACTATGGGTTCGTTTCTATG 59.452 37.037 0.00 0.00 0.00 2.23
3675 6082 5.467735 ACACAACTTACTATGGGTTCGTTTC 59.532 40.000 0.00 0.00 25.52 2.78
3803 6223 2.295394 AAATAAACCGCCGCGTACGC 62.295 55.000 29.83 29.83 38.22 4.42


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

AutoCloner maintained by Alex Coulton.