Multiple sequence alignment - TraesCS4B01G369700

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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 TraesCS4B01G369700 chr4B 100.000 2390 0 0 1 2390 655112407 655110018 0.000000e+00 4414.0
1 TraesCS4B01G369700 chr4B 95.923 883 35 1 1 883 655084427 655083546 0.000000e+00 1430.0
2 TraesCS4B01G369700 chr4B 99.470 755 3 1 1637 2390 5372864 5373618 0.000000e+00 1371.0
3 TraesCS4B01G369700 chr4B 96.588 762 25 1 878 1638 655078013 655077252 0.000000e+00 1262.0
4 TraesCS4B01G369700 chr4B 92.500 760 33 5 902 1638 654731982 654731224 0.000000e+00 1066.0
5 TraesCS4B01G369700 chr4B 94.087 389 21 2 1 389 654921432 654921046 7.360000e-165 590.0
6 TraesCS4B01G369700 chr4B 94.087 389 20 2 1 389 655032644 655032259 2.650000e-164 588.0
7 TraesCS4B01G369700 chr4B 93.830 389 22 2 1 389 654996898 654996512 3.420000e-163 584.0
8 TraesCS4B01G369700 chr4B 93.316 389 24 2 1 389 654961776 654961390 7.410000e-160 573.0
9 TraesCS4B01G369700 chr4B 81.460 685 103 17 1 666 654757740 654757061 7.520000e-150 540.0
10 TraesCS4B01G369700 chr4B 93.197 147 9 1 1492 1638 654806009 654805864 5.170000e-52 215.0
11 TraesCS4B01G369700 chr4B 85.417 144 20 1 2 144 655086207 655086064 5.320000e-32 148.0
12 TraesCS4B01G369700 chr4B 84.828 145 21 1 1 144 654998675 654998531 6.890000e-31 145.0
13 TraesCS4B01G369700 chr4B 84.828 145 21 1 1 144 655034420 655034276 6.890000e-31 145.0
14 TraesCS4B01G369700 chr4B 93.443 61 3 1 1578 1638 654778802 654778743 3.270000e-14 89.8
15 TraesCS4B01G369700 chr5B 99.470 755 3 1 1637 2390 48316274 48315520 0.000000e+00 1371.0
16 TraesCS4B01G369700 chr2A 99.470 755 3 1 1637 2390 144033693 144034447 0.000000e+00 1371.0
17 TraesCS4B01G369700 chr2A 99.338 755 4 1 1637 2390 602799676 602798922 0.000000e+00 1365.0
18 TraesCS4B01G369700 chr2A 99.338 755 4 1 1637 2390 676079640 676078886 0.000000e+00 1365.0
19 TraesCS4B01G369700 chr2A 98.952 763 8 0 1628 2390 687328419 687327657 0.000000e+00 1365.0
20 TraesCS4B01G369700 chr6B 99.079 760 7 0 1631 2390 339383028 339383787 0.000000e+00 1365.0
21 TraesCS4B01G369700 chr1B 99.338 755 4 1 1637 2390 451910459 451911213 0.000000e+00 1365.0
22 TraesCS4B01G369700 chr1B 99.338 755 4 1 1637 2390 655769504 655770258 0.000000e+00 1365.0
23 TraesCS4B01G369700 chrUn 86.821 736 71 10 916 1638 154542509 154543231 0.000000e+00 798.0
24 TraesCS4B01G369700 chrUn 88.456 667 68 4 973 1638 154567850 154568508 0.000000e+00 797.0
25 TraesCS4B01G369700 chrUn 86.685 736 72 10 916 1638 201369063 201369785 0.000000e+00 793.0
26 TraesCS4B01G369700 chrUn 86.549 736 72 11 916 1638 279543201 279543922 0.000000e+00 785.0
27 TraesCS4B01G369700 chrUn 86.413 736 74 10 916 1638 189575688 189574966 0.000000e+00 782.0
28 TraesCS4B01G369700 chrUn 88.138 666 66 6 973 1638 189561931 189561279 0.000000e+00 780.0
29 TraesCS4B01G369700 chrUn 86.141 736 76 10 916 1638 363336781 363337503 0.000000e+00 771.0
30 TraesCS4B01G369700 chrUn 79.877 810 109 35 1 791 154566902 154567676 5.810000e-151 544.0
31 TraesCS4B01G369700 chrUn 80.025 811 98 32 1 794 189562893 189562130 2.090000e-150 542.0
32 TraesCS4B01G369700 chrUn 80.050 807 98 31 1 791 189576581 189575822 7.520000e-150 540.0
33 TraesCS4B01G369700 chrUn 79.901 806 100 31 1 791 346445781 346445023 3.500000e-148 534.0
34 TraesCS4B01G369700 chrUn 79.750 800 111 31 1 791 201368172 201368929 1.260000e-147 532.0
35 TraesCS4B01G369700 chrUn 79.678 807 101 31 1 791 377346555 377345796 7.570000e-145 523.0
36 TraesCS4B01G369700 chrUn 87.245 392 42 6 407 791 363336257 363336647 7.840000e-120 440.0


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 TraesCS4B01G369700 chr4B 655110018 655112407 2389 True 4414.0 4414 100.0000 1 2390 1 chr4B.!!$R8 2389
1 TraesCS4B01G369700 chr4B 5372864 5373618 754 False 1371.0 1371 99.4700 1637 2390 1 chr4B.!!$F1 753
2 TraesCS4B01G369700 chr4B 655077252 655078013 761 True 1262.0 1262 96.5880 878 1638 1 chr4B.!!$R7 760
3 TraesCS4B01G369700 chr4B 654731224 654731982 758 True 1066.0 1066 92.5000 902 1638 1 chr4B.!!$R1 736
4 TraesCS4B01G369700 chr4B 655083546 655086207 2661 True 789.0 1430 90.6700 1 883 2 chr4B.!!$R11 882
5 TraesCS4B01G369700 chr4B 654757061 654757740 679 True 540.0 540 81.4600 1 666 1 chr4B.!!$R2 665
6 TraesCS4B01G369700 chr4B 655032259 655034420 2161 True 366.5 588 89.4575 1 389 2 chr4B.!!$R10 388
7 TraesCS4B01G369700 chr4B 654996512 654998675 2163 True 364.5 584 89.3290 1 389 2 chr4B.!!$R9 388
8 TraesCS4B01G369700 chr5B 48315520 48316274 754 True 1371.0 1371 99.4700 1637 2390 1 chr5B.!!$R1 753
9 TraesCS4B01G369700 chr2A 144033693 144034447 754 False 1371.0 1371 99.4700 1637 2390 1 chr2A.!!$F1 753
10 TraesCS4B01G369700 chr2A 602798922 602799676 754 True 1365.0 1365 99.3380 1637 2390 1 chr2A.!!$R1 753
11 TraesCS4B01G369700 chr2A 676078886 676079640 754 True 1365.0 1365 99.3380 1637 2390 1 chr2A.!!$R2 753
12 TraesCS4B01G369700 chr2A 687327657 687328419 762 True 1365.0 1365 98.9520 1628 2390 1 chr2A.!!$R3 762
13 TraesCS4B01G369700 chr6B 339383028 339383787 759 False 1365.0 1365 99.0790 1631 2390 1 chr6B.!!$F1 759
14 TraesCS4B01G369700 chr1B 451910459 451911213 754 False 1365.0 1365 99.3380 1637 2390 1 chr1B.!!$F1 753
15 TraesCS4B01G369700 chr1B 655769504 655770258 754 False 1365.0 1365 99.3380 1637 2390 1 chr1B.!!$F2 753
16 TraesCS4B01G369700 chrUn 154542509 154543231 722 False 798.0 798 86.8210 916 1638 1 chrUn.!!$F1 722
17 TraesCS4B01G369700 chrUn 279543201 279543922 721 False 785.0 785 86.5490 916 1638 1 chrUn.!!$F2 722
18 TraesCS4B01G369700 chrUn 154566902 154568508 1606 False 670.5 797 84.1665 1 1638 2 chrUn.!!$F3 1637
19 TraesCS4B01G369700 chrUn 201368172 201369785 1613 False 662.5 793 83.2175 1 1638 2 chrUn.!!$F4 1637
20 TraesCS4B01G369700 chrUn 189561279 189562893 1614 True 661.0 780 84.0815 1 1638 2 chrUn.!!$R3 1637
21 TraesCS4B01G369700 chrUn 189574966 189576581 1615 True 661.0 782 83.2315 1 1638 2 chrUn.!!$R4 1637
22 TraesCS4B01G369700 chrUn 363336257 363337503 1246 False 605.5 771 86.6930 407 1638 2 chrUn.!!$F5 1231
23 TraesCS4B01G369700 chrUn 346445023 346445781 758 True 534.0 534 79.9010 1 791 1 chrUn.!!$R1 790
24 TraesCS4B01G369700 chrUn 377345796 377346555 759 True 523.0 523 79.6780 1 791 1 chrUn.!!$R2 790

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
792 2615 0.109781 ATTTTGTTGGCTAGCGCACG 60.11 50.0 11.47 0.0 38.1 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 3522 4.030913 TGTTGTTTTGATACAAACCCCCA 58.969 39.13 0.0 0.0 39.54 4.96 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
47 1830 1.221414 GCATCCGATTGTGCTAGGAC 58.779 55.000 7.56 7.56 38.30 3.85
146 1930 4.960938 TCTGAGACATAACTTGTGCTTGT 58.039 39.130 0.00 0.00 39.18 3.16
191 1975 2.442413 GGCCCAGTAATTGTGTTAGCA 58.558 47.619 0.00 0.00 0.00 3.49
234 2019 8.574251 TGGAAGCTTGTATATACATGTTTGTT 57.426 30.769 25.41 15.82 35.84 2.83
516 2331 3.814842 CACCAACGACCATGCATGTATAT 59.185 43.478 24.58 7.75 0.00 0.86
562 2377 1.439543 AGTTGACTTCTCCTGCCCTT 58.560 50.000 0.00 0.00 0.00 3.95
580 2395 6.306199 TGCCCTTCAATTAGTATGCATATGT 58.694 36.000 10.16 3.27 0.00 2.29
597 2412 5.049749 GCATATGTTATACGTGTCCATGCAA 60.050 40.000 4.29 0.00 36.97 4.08
715 2537 1.133945 TCTGTGTGCAGGGCTTGTTTA 60.134 47.619 0.00 0.00 42.78 2.01
792 2615 0.109781 ATTTTGTTGGCTAGCGCACG 60.110 50.000 11.47 0.00 38.10 5.34
803 2626 1.934220 TAGCGCACGGAGGTTCAGAG 61.934 60.000 11.47 0.00 0.00 3.35
1056 2947 1.545428 GGCCTGAACTTGATGGTCACA 60.545 52.381 0.00 0.00 37.49 3.58
1123 3014 2.264480 CGCCTCCATCGACCAACA 59.736 61.111 0.00 0.00 0.00 3.33
1504 3396 5.039920 TCTATATGTCTTGTGCATGCCTT 57.960 39.130 16.68 0.00 0.00 4.35
1524 3416 4.095483 CCTTGGTTCTCTGTCATGCATTAC 59.905 45.833 3.98 3.98 0.00 1.89
1559 3451 2.760650 TGCAGTGATCACTAGGTAGGTG 59.239 50.000 27.44 14.56 40.20 4.00
1560 3452 3.024547 GCAGTGATCACTAGGTAGGTGA 58.975 50.000 27.44 0.00 45.84 4.02
1561 3453 3.067461 GCAGTGATCACTAGGTAGGTGAG 59.933 52.174 27.44 12.37 45.14 3.51
1562 3454 4.274147 CAGTGATCACTAGGTAGGTGAGT 58.726 47.826 27.44 0.00 45.14 3.41
1563 3455 5.437946 CAGTGATCACTAGGTAGGTGAGTA 58.562 45.833 27.44 0.00 45.14 2.59
1564 3456 5.886474 CAGTGATCACTAGGTAGGTGAGTAA 59.114 44.000 27.44 0.00 45.14 2.24
1592 3490 2.013400 TGCGTGAAAGTGTGTCATGTT 58.987 42.857 0.00 0.00 34.96 2.71
1623 3522 6.951198 TGTCCAAATAAATGACCCATGTAACT 59.049 34.615 0.00 0.00 0.00 2.24
1962 3861 3.416156 GATGTTGGACAAGCTTCTCCTT 58.584 45.455 19.96 4.48 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 1830 2.205074 CCTAGCATTGTAGGCGTCAAG 58.795 52.381 0.00 0.00 33.33 3.02
146 1930 2.297315 GCACCATGTCGATCTCCATAGA 59.703 50.000 0.00 0.00 35.80 1.98
223 2007 6.370442 CCGATAGAAGGTTCAACAAACATGTA 59.630 38.462 0.00 0.00 37.80 2.29
405 2211 7.354025 TGTTCATCATGCATGTGAAATTTTC 57.646 32.000 29.58 21.95 33.22 2.29
463 2271 3.620427 TCCACGCACTGGTTTATACAT 57.380 42.857 0.00 0.00 41.52 2.29
516 2331 0.110295 TTCCACAGCTAGCTTTGGCA 59.890 50.000 35.41 27.01 42.08 4.92
580 2395 3.620427 ACCTTGCATGGACACGTATAA 57.380 42.857 24.48 0.00 0.00 0.98
597 2412 8.130671 TGTAGTTGCTACTTAGTTTGATACCT 57.869 34.615 6.03 0.00 37.78 3.08
715 2537 3.195396 ACTTGATGGGCATGCGTATTTTT 59.805 39.130 12.44 0.00 0.00 1.94
792 2615 4.578105 CCTTTATTGATGCTCTGAACCTCC 59.422 45.833 0.00 0.00 0.00 4.30
803 2626 6.091713 ACGTGTACACTTACCTTTATTGATGC 59.908 38.462 23.01 0.00 0.00 3.91
1504 3396 3.008923 TGGTAATGCATGACAGAGAACCA 59.991 43.478 16.28 9.27 31.06 3.67
1559 3451 4.207841 ACTTTCACGCACTTACGTTTACTC 59.792 41.667 0.00 0.00 45.75 2.59
1560 3452 4.026310 CACTTTCACGCACTTACGTTTACT 60.026 41.667 0.00 0.00 45.75 2.24
1561 3453 4.198584 CACTTTCACGCACTTACGTTTAC 58.801 43.478 0.00 0.00 45.75 2.01
1562 3454 3.864583 ACACTTTCACGCACTTACGTTTA 59.135 39.130 0.00 0.00 45.75 2.01
1563 3455 2.674357 ACACTTTCACGCACTTACGTTT 59.326 40.909 0.00 0.00 45.75 3.60
1564 3456 2.029970 CACACTTTCACGCACTTACGTT 59.970 45.455 0.00 0.00 45.75 3.99
1592 3490 4.282195 GGGTCATTTATTTGGACACCACAA 59.718 41.667 0.00 0.00 30.78 3.33
1623 3522 4.030913 TGTTGTTTTGATACAAACCCCCA 58.969 39.130 0.00 0.00 39.54 4.96
1770 3669 4.286910 GAGTATCGACAAAGAGCTAGCTG 58.713 47.826 24.99 11.34 0.00 4.24


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

AutoCloner maintained by Alex Coulton.