Multiple sequence alignment - TraesCS5B01G084200

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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 TraesCS5B01G084200 chr5B 100.000 3250 0 0 1 3250 106811508 106808259 0.000000e+00 6002.0
1 TraesCS5B01G084200 chr5B 88.632 519 53 5 989 1506 643123495 643122982 7.650000e-176 627.0
2 TraesCS5B01G084200 chr5B 86.510 467 31 13 2797 3234 643122890 643122427 4.880000e-133 484.0
3 TraesCS5B01G084200 chr5B 87.387 222 16 5 236 446 307172798 307173018 9.010000e-61 244.0
4 TraesCS5B01G084200 chr5B 96.629 89 3 0 2657 2745 643122972 643122884 7.260000e-32 148.0
5 TraesCS5B01G084200 chr7B 94.440 2302 70 29 989 3250 723722089 723719806 0.000000e+00 3489.0
6 TraesCS5B01G084200 chr7B 95.920 1005 26 3 1 992 723726438 723725436 0.000000e+00 1615.0
7 TraesCS5B01G084200 chr7B 88.610 518 55 2 989 1506 112123496 112124009 7.650000e-176 627.0
8 TraesCS5B01G084200 chr7B 87.539 321 25 6 2932 3240 725660513 725660196 1.110000e-94 357.0
9 TraesCS5B01G084200 chr7B 93.991 233 12 1 760 992 723021262 723021032 5.160000e-93 351.0
10 TraesCS5B01G084200 chr7B 86.174 311 33 7 2932 3234 220331058 220330750 8.690000e-86 327.0
11 TraesCS5B01G084200 chr7B 97.753 89 2 0 2657 2745 112124019 112124107 1.560000e-33 154.0
12 TraesCS5B01G084200 chr7B 100.000 30 0 0 1519 1548 723721499 723721470 4.530000e-04 56.5
13 TraesCS5B01G084200 chr4A 96.915 1264 27 6 1789 3049 691304016 691305270 0.000000e+00 2108.0
14 TraesCS5B01G084200 chr4A 95.821 1005 27 3 1 992 691297359 691298361 0.000000e+00 1609.0
15 TraesCS5B01G084200 chr4A 96.044 809 27 2 989 1797 691301510 691302313 0.000000e+00 1312.0
16 TraesCS5B01G084200 chr4A 88.417 518 51 4 989 1506 696176049 696176557 1.660000e-172 616.0
17 TraesCS5B01G084200 chr4A 96.774 186 3 2 1 186 740147172 740147354 1.130000e-79 307.0
18 TraesCS5B01G084200 chr4A 95.556 90 3 1 2657 2745 696176567 696176656 3.380000e-30 143.0
19 TraesCS5B01G084200 chr6A 90.883 1393 94 14 989 2354 584479399 584480785 0.000000e+00 1838.0
20 TraesCS5B01G084200 chr6A 90.677 901 46 13 2352 3234 584480888 584481768 0.000000e+00 1164.0
21 TraesCS5B01G084200 chr6A 88.288 222 14 5 236 446 96780654 96780874 4.160000e-64 255.0
22 TraesCS5B01G084200 chr6A 87.556 225 16 5 236 449 540793230 540793007 1.940000e-62 250.0
23 TraesCS5B01G084200 chr7D 94.097 559 18 5 447 992 27248720 27248164 0.000000e+00 835.0
24 TraesCS5B01G084200 chr7D 86.174 311 34 5 2932 3234 5299579 5299270 8.690000e-86 327.0
25 TraesCS5B01G084200 chr2A 92.844 559 25 5 447 992 753428602 753429158 0.000000e+00 797.0
26 TraesCS5B01G084200 chr2A 87.838 222 15 5 236 446 758743932 758744152 1.940000e-62 250.0
27 TraesCS5B01G084200 chr3B 88.269 520 53 5 989 1506 809803903 809804416 1.660000e-172 616.0
28 TraesCS5B01G084200 chr3B 88.224 518 55 3 989 1506 799206245 799205734 5.960000e-172 614.0
29 TraesCS5B01G084200 chr3B 86.724 467 30 13 2797 3234 809804508 809804971 1.050000e-134 490.0
30 TraesCS5B01G084200 chr3B 93.133 233 14 1 757 989 18217396 18217626 1.120000e-89 340.0
31 TraesCS5B01G084200 chr3B 93.133 233 12 4 757 989 521512523 521512751 4.020000e-89 339.0
32 TraesCS5B01G084200 chr3B 84.865 185 15 7 1546 1718 597106167 597105984 1.200000e-39 174.0
33 TraesCS5B01G084200 chr3B 96.629 89 3 0 2657 2745 799205724 799205636 7.260000e-32 148.0
34 TraesCS5B01G084200 chr3B 96.629 89 3 0 2657 2745 809804426 809804514 7.260000e-32 148.0
35 TraesCS5B01G084200 chr1B 88.031 518 58 3 989 1506 676112071 676111558 7.710000e-171 610.0
36 TraesCS5B01G084200 chr1B 97.753 89 2 0 2657 2745 676111548 676111460 1.560000e-33 154.0
37 TraesCS5B01G084200 chr1D 90.196 306 16 4 2938 3234 470474358 470474658 1.410000e-103 387.0
38 TraesCS5B01G084200 chr1D 88.444 225 14 5 236 449 364837947 364837724 8.940000e-66 261.0
39 TraesCS5B01G084200 chr6B 88.424 311 26 4 2932 3234 100934588 100934896 1.840000e-97 366.0
40 TraesCS5B01G084200 chrUn 93.991 233 12 1 757 989 249742243 249742473 5.160000e-93 351.0
41 TraesCS5B01G084200 chr6D 85.531 311 36 5 2932 3234 25945192 25945501 1.880000e-82 316.0
42 TraesCS5B01G084200 chr6D 83.226 310 29 7 2932 3234 426498089 426498382 2.490000e-66 263.0
43 TraesCS5B01G084200 chr6D 87.611 226 15 6 236 449 430514821 430514597 1.940000e-62 250.0
44 TraesCS5B01G084200 chr4B 85.531 311 36 6 2932 3234 100832721 100832412 1.880000e-82 316.0
45 TraesCS5B01G084200 chr5D 82.903 310 30 4 2932 3234 64304034 64303741 1.160000e-64 257.0
46 TraesCS5B01G084200 chr5D 93.590 78 4 1 1 77 543470706 543470783 7.370000e-22 115.0
47 TraesCS5B01G084200 chr1A 87.556 225 16 5 236 449 513712600 513712377 1.940000e-62 250.0
48 TraesCS5B01G084200 chr2B 82.182 275 33 12 646 906 189016459 189016731 4.220000e-54 222.0
49 TraesCS5B01G084200 chr3D 86.486 185 12 6 1546 1718 560270413 560270596 1.190000e-44 191.0
50 TraesCS5B01G084200 chr3D 86.592 179 12 5 1552 1718 492105748 492105570 1.540000e-43 187.0
51 TraesCS5B01G084200 chr3D 85.795 176 18 6 1546 1718 4363908 4363737 2.580000e-41 180.0
52 TraesCS5B01G084200 chr5A 85.405 185 14 6 1546 1718 422246820 422246637 2.580000e-41 180.0


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 TraesCS5B01G084200 chr5B 106808259 106811508 3249 True 6002.000000 6002 100.000000 1 3250 1 chr5B.!!$R1 3249
1 TraesCS5B01G084200 chr5B 643122427 643123495 1068 True 419.666667 627 90.590333 989 3234 3 chr5B.!!$R2 2245
2 TraesCS5B01G084200 chr7B 723719806 723726438 6632 True 1720.166667 3489 96.786667 1 3250 3 chr7B.!!$R4 3249
3 TraesCS5B01G084200 chr7B 112123496 112124107 611 False 390.500000 627 93.181500 989 2745 2 chr7B.!!$F1 1756
4 TraesCS5B01G084200 chr4A 691297359 691305270 7911 False 1676.333333 2108 96.260000 1 3049 3 chr4A.!!$F2 3048
5 TraesCS5B01G084200 chr4A 696176049 696176656 607 False 379.500000 616 91.986500 989 2745 2 chr4A.!!$F3 1756
6 TraesCS5B01G084200 chr6A 584479399 584481768 2369 False 1501.000000 1838 90.780000 989 3234 2 chr6A.!!$F2 2245
7 TraesCS5B01G084200 chr7D 27248164 27248720 556 True 835.000000 835 94.097000 447 992 1 chr7D.!!$R2 545
8 TraesCS5B01G084200 chr2A 753428602 753429158 556 False 797.000000 797 92.844000 447 992 1 chr2A.!!$F1 545
9 TraesCS5B01G084200 chr3B 809803903 809804971 1068 False 418.000000 616 90.540667 989 3234 3 chr3B.!!$F3 2245
10 TraesCS5B01G084200 chr3B 799205636 799206245 609 True 381.000000 614 92.426500 989 2745 2 chr3B.!!$R2 1756
11 TraesCS5B01G084200 chr1B 676111460 676112071 611 True 382.000000 610 92.892000 989 2745 2 chr1B.!!$R1 1756

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
472 473 1.211457 GGCATGGAAGACAGAGATGGT 59.789 52.381 0.0 0.0 0.00 3.55 F
1236 4604 3.483869 GAGCTCGCCTCCCCCAAT 61.484 66.667 0.0 0.0 34.35 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1358 4726 0.601046 CTTGCTCTGGACGCACTTCA 60.601 55.000 0.00 0.0 37.07 3.02 R
2281 7418 2.065799 ACCTTGGTTGAGGATTCCACT 58.934 47.619 5.29 0.0 39.25 4.00 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
93 94 4.816385 TCTCACTTGCTGGTCTTGTTAAAG 59.184 41.667 0.00 0.00 34.45 1.85
244 245 2.757314 TGTTTTCACTGTGTGCAATGGA 59.243 40.909 7.79 0.00 32.98 3.41
336 337 2.496899 TGGTCCTTTGCTTGGATCTC 57.503 50.000 0.00 0.00 35.79 2.75
371 372 6.260050 TCGTTGCTTTTCTACTTCAAACTGAT 59.740 34.615 0.00 0.00 0.00 2.90
472 473 1.211457 GGCATGGAAGACAGAGATGGT 59.789 52.381 0.00 0.00 0.00 3.55
611 612 5.128919 GGAGTATCAGGTTGCTGAAATGAT 58.871 41.667 0.00 0.00 36.88 2.45
1236 4604 3.483869 GAGCTCGCCTCCCCCAAT 61.484 66.667 0.00 0.00 34.35 3.16
1238 4606 4.883354 GCTCGCCTCCCCCAATGG 62.883 72.222 0.00 0.00 0.00 3.16
1357 4725 0.319555 TGACAAGAAGAAGCCGACGG 60.320 55.000 10.29 10.29 0.00 4.79
1358 4726 0.319641 GACAAGAAGAAGCCGACGGT 60.320 55.000 16.73 0.00 0.00 4.83
1446 4814 4.956075 ACATATGAGATTTTTGTGGGGGTC 59.044 41.667 10.38 0.00 0.00 4.46
1449 4817 2.445145 TGAGATTTTTGTGGGGGTCTGA 59.555 45.455 0.00 0.00 0.00 3.27
1619 5021 3.186001 GCTTAATGATCTCTGCATCACCG 59.814 47.826 0.00 0.00 35.57 4.94
1681 5083 5.297569 ACTGAACTTTTCCTGAGTAAGCT 57.702 39.130 0.00 0.00 0.00 3.74
1718 5120 6.868622 ACTGCTATCTTGTTAGGTGAGTAAG 58.131 40.000 0.00 0.00 0.00 2.34
1766 5168 7.040686 GGAAACAAGTGTTGTAGTGGTCAATAT 60.041 37.037 0.00 0.00 44.59 1.28
1802 6915 6.963117 TCATCCCCTCTTTTAGTTTTCCTA 57.037 37.500 0.00 0.00 0.00 2.94
1803 6916 7.337826 TCATCCCCTCTTTTAGTTTTCCTAA 57.662 36.000 0.00 0.00 33.77 2.69
1946 7059 9.339850 GTCTAATTAGAAATAACTCCCCCTTTC 57.660 37.037 16.73 0.00 33.47 2.62
2105 7219 3.784338 CACAACCAACCATTGCCATATC 58.216 45.455 0.00 0.00 0.00 1.63
2239 7376 1.674057 CCTCTCTTCCCGTGCAGTT 59.326 57.895 0.00 0.00 0.00 3.16
2281 7418 2.224843 ACTGCAACATCCATGAACTCCA 60.225 45.455 0.00 0.00 0.00 3.86
2315 7452 0.320374 CAAGGTTCGCCAGTACCTGA 59.680 55.000 0.00 0.00 45.76 3.86
2401 7643 2.545742 CCTTTACCAGCCACAACTTTGC 60.546 50.000 0.00 0.00 0.00 3.68
2750 8005 4.771577 TGATGTGGTGGTGATTTGCTTTAT 59.228 37.500 0.00 0.00 0.00 1.40
3146 8437 4.571984 TCATGTAACAGCCAGAATCGAATG 59.428 41.667 0.00 0.00 0.00 2.67
3161 8452 6.309737 AGAATCGAATGTTAACCGTGTTCTAC 59.690 38.462 16.12 0.00 32.46 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 6.076981 AGAACAATGAGGAATGTCAAACAC 57.923 37.500 0.00 0.00 0.00 3.32
336 337 4.058817 AGAAAAGCAACGACTCAACCTAG 58.941 43.478 0.00 0.00 0.00 3.02
472 473 0.179702 CTTGAGGATGCAGGCTGCTA 59.820 55.000 36.50 24.27 45.31 3.49
489 490 3.763897 CACCCCTTTAGCAAGCATTACTT 59.236 43.478 0.00 0.00 40.05 2.24
947 961 5.880332 GGTAGATATTTCTGCAGTGTGGAAA 59.120 40.000 14.67 7.07 36.40 3.13
949 963 4.716784 AGGTAGATATTTCTGCAGTGTGGA 59.283 41.667 14.67 0.00 36.40 4.02
1153 4519 2.109834 TGGTCATCCCACTTCCAATTGT 59.890 45.455 4.43 0.00 38.72 2.71
1165 4531 0.106967 GCCTTCTCCTTGGTCATCCC 60.107 60.000 0.00 0.00 0.00 3.85
1204 4572 3.036429 GCTCCGCCTCCCACTTGAT 62.036 63.158 0.00 0.00 0.00 2.57
1236 4604 1.006571 GAGGTTGAAGTCGTCGCCA 60.007 57.895 0.00 0.00 0.00 5.69
1238 4606 0.784778 CTTGAGGTTGAAGTCGTCGC 59.215 55.000 0.00 0.00 0.00 5.19
1357 4725 0.880278 TTGCTCTGGACGCACTTCAC 60.880 55.000 0.00 0.00 37.07 3.18
1358 4726 0.601046 CTTGCTCTGGACGCACTTCA 60.601 55.000 0.00 0.00 37.07 3.02
1446 4814 2.988010 TTCATTCAGATCGGGGTCAG 57.012 50.000 0.00 0.00 0.00 3.51
1449 4817 3.652057 ACATTTCATTCAGATCGGGGT 57.348 42.857 0.00 0.00 0.00 4.95
1619 5021 5.371115 TGGCTTTGTATCTGCACTTTTAC 57.629 39.130 0.00 0.00 0.00 2.01
1681 5083 7.730084 ACAAGATAGCAGTAGCAAATCATCTA 58.270 34.615 0.00 0.00 45.49 1.98
1766 5168 3.711704 GAGGGGATGAACTAACATGAGGA 59.288 47.826 0.00 0.00 0.00 3.71
1802 6915 8.318412 ACCAACAAAATTGAAGTTTAGAAGGTT 58.682 29.630 0.00 0.00 0.00 3.50
1803 6916 7.847096 ACCAACAAAATTGAAGTTTAGAAGGT 58.153 30.769 0.00 0.00 0.00 3.50
2105 7219 4.397481 TGTGAGCTCTGATGGTAATCTG 57.603 45.455 16.19 0.00 33.61 2.90
2281 7418 2.065799 ACCTTGGTTGAGGATTCCACT 58.934 47.619 5.29 0.00 39.25 4.00
2315 7452 2.325583 TTGAGACAAGGCAAACGACT 57.674 45.000 0.00 0.00 0.00 4.18
2834 8089 6.048732 TGTTATGTATGGCAAGAGAACTGA 57.951 37.500 0.00 0.00 0.00 3.41
3146 8437 3.732212 ACTTGGGTAGAACACGGTTAAC 58.268 45.455 0.00 0.00 0.00 2.01
3161 8452 6.040729 TGCAATGACATTATATCCAACTTGGG 59.959 38.462 8.01 0.00 38.32 4.12


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

AutoCloner maintained by Alex Coulton.