Multiple sequence alignment - TraesCS4A01G424500

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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 TraesCS4A01G424500 chr4A 100.000 4249 0 0 1 4249 695803956 695808204 0.000000e+00 7847.0
1 TraesCS4A01G424500 chr4A 99.365 4249 27 0 1 4249 695870257 695874505 0.000000e+00 7697.0
2 TraesCS4A01G424500 chr4A 96.128 2505 94 3 635 3137 625885787 625883284 0.000000e+00 4085.0
3 TraesCS4A01G424500 chr4A 84.727 1722 232 16 1424 3127 625895583 625893875 0.000000e+00 1694.0
4 TraesCS4A01G424500 chr4A 81.451 1558 233 38 1424 2945 695981747 695980210 0.000000e+00 1225.0
5 TraesCS4A01G424500 chr4A 94.033 419 22 3 3832 4249 614697886 614698302 2.160000e-177 632.0
6 TraesCS4A01G424500 chr4A 86.765 544 38 18 116 636 625886770 625886238 3.680000e-160 575.0
7 TraesCS4A01G424500 chr4A 96.522 115 3 1 3658 3772 1520078 1519965 5.610000e-44 189.0
8 TraesCS4A01G424500 chr4A 97.500 80 2 0 1 80 588655516 588655595 2.060000e-28 137.0
9 TraesCS4A01G424500 chr4A 94.937 79 4 0 1188 1266 625885298 625885220 1.600000e-24 124.0
10 TraesCS4A01G424500 chr4A 94.937 79 4 0 1188 1266 695805080 695805158 1.600000e-24 124.0
11 TraesCS4A01G424500 chr4A 82.394 142 11 7 3369 3499 625883360 625883222 1.250000e-20 111.0
12 TraesCS4A01G424500 chr4A 86.905 84 8 2 3369 3452 695873317 695873397 1.630000e-14 91.6
13 TraesCS4A01G424500 chr5B 96.609 2507 84 1 635 3141 557109610 557112115 0.000000e+00 4157.0
14 TraesCS4A01G424500 chr5B 95.893 2508 95 5 635 3141 684755150 684752650 0.000000e+00 4054.0
15 TraesCS4A01G424500 chr5B 81.529 1543 238 29 1424 2945 684879957 684881473 0.000000e+00 1227.0
16 TraesCS4A01G424500 chr5B 87.458 590 27 18 82 636 684756182 684755605 1.670000e-178 636.0
17 TraesCS4A01G424500 chr5B 80.470 553 63 18 90 636 557108137 557108650 8.620000e-102 381.0
18 TraesCS4A01G424500 chr5B 90.104 192 18 1 3139 3329 567426995 567427186 9.120000e-62 248.0
19 TraesCS4A01G424500 chr5B 91.018 167 15 0 762 928 557109793 557109959 4.270000e-55 226.0
20 TraesCS4A01G424500 chr5B 90.419 167 16 0 819 985 557109736 557109902 1.990000e-53 220.0
21 TraesCS4A01G424500 chr5B 98.780 82 1 0 1 82 115412612 115412693 3.420000e-31 147.0
22 TraesCS4A01G424500 chr5B 88.696 115 13 0 757 871 557109845 557109959 1.590000e-29 141.0
23 TraesCS4A01G424500 chr5B 92.708 96 5 1 1 96 482500863 482500956 2.060000e-28 137.0
24 TraesCS4A01G424500 chr5B 96.203 79 3 0 1125 1203 684754598 684754520 3.450000e-26 130.0
25 TraesCS4A01G424500 chr5B 85.586 111 10 5 3369 3479 557112035 557112139 1.250000e-20 111.0
26 TraesCS4A01G424500 chr5D 96.336 2511 80 7 635 3141 543333008 543335510 0.000000e+00 4117.0
27 TraesCS4A01G424500 chr5D 81.210 1554 227 43 1424 2945 543411921 543410401 0.000000e+00 1192.0
28 TraesCS4A01G424500 chr5D 85.106 423 22 8 224 636 543332167 543332558 1.110000e-105 394.0
29 TraesCS4A01G424500 chr5D 80.160 499 91 6 1629 2123 543271595 543272089 2.410000e-97 366.0
30 TraesCS4A01G424500 chr5D 81.633 294 28 16 3378 3660 543335439 543335717 1.990000e-53 220.0
31 TraesCS4A01G424500 chr5D 96.203 79 3 0 1125 1203 543333560 543333638 3.450000e-26 130.0
32 TraesCS4A01G424500 chr2D 94.621 725 36 3 635 1358 474251731 474251009 0.000000e+00 1120.0
33 TraesCS4A01G424500 chr2D 93.617 188 12 0 3141 3328 567635234 567635047 9.000000e-72 281.0
34 TraesCS4A01G424500 chr2D 88.770 187 21 0 3141 3327 536907387 536907573 3.300000e-56 230.0
35 TraesCS4A01G424500 chr2D 83.256 215 19 13 436 636 474252621 474252410 9.390000e-42 182.0
36 TraesCS4A01G424500 chr3D 93.713 668 39 3 691 1358 119547983 119548647 0.000000e+00 998.0
37 TraesCS4A01G424500 chr3D 89.583 192 14 5 3141 3329 595079178 595078990 5.490000e-59 239.0
38 TraesCS4A01G424500 chr3D 82.870 216 20 12 435 636 119531688 119531900 1.210000e-40 178.0
39 TraesCS4A01G424500 chr3D 95.455 88 4 0 1 88 134495924 134496011 1.590000e-29 141.0
40 TraesCS4A01G424500 chr3D 93.220 59 4 0 635 693 119541531 119541589 2.100000e-13 87.9
41 TraesCS4A01G424500 chr4D 96.912 421 11 2 3830 4249 85613369 85613788 0.000000e+00 704.0
42 TraesCS4A01G424500 chr4D 95.402 87 3 1 1 87 80087136 80087051 2.060000e-28 137.0
43 TraesCS4A01G424500 chr1A 95.422 415 17 2 3836 4249 298125628 298125215 0.000000e+00 660.0
44 TraesCS4A01G424500 chr1A 94.699 415 20 2 3836 4249 258856856 258857269 0.000000e+00 643.0
45 TraesCS4A01G424500 chr7A 94.749 419 19 3 3832 4249 603953324 603953740 0.000000e+00 649.0
46 TraesCS4A01G424500 chr7A 96.386 83 3 0 1 83 671502292 671502374 2.060000e-28 137.0
47 TraesCS4A01G424500 chr3A 94.175 412 22 2 3839 4249 36486811 36487221 1.000000e-175 627.0
48 TraesCS4A01G424500 chr3A 93.080 289 19 1 3962 4249 530482573 530482285 5.080000e-114 422.0
49 TraesCS4A01G424500 chr3A 89.418 189 20 0 3140 3328 738717233 738717421 5.490000e-59 239.0
50 TraesCS4A01G424500 chr3A 95.614 114 5 0 3662 3775 468643140 468643027 2.610000e-42 183.0
51 TraesCS4A01G424500 chr3A 89.524 105 8 2 1 104 182282873 182282975 3.450000e-26 130.0
52 TraesCS4A01G424500 chr1B 92.661 436 13 6 3831 4249 429962172 429961739 1.010000e-170 610.0
53 TraesCS4A01G424500 chr1B 94.253 87 5 0 1 87 430146288 430146374 2.670000e-27 134.0
54 TraesCS4A01G424500 chr6A 94.038 369 20 2 3882 4249 26777774 26778141 3.710000e-155 558.0
55 TraesCS4A01G424500 chr6B 90.526 190 18 0 3139 3328 184761020 184761209 7.050000e-63 252.0
56 TraesCS4A01G424500 chr6B 90.526 190 17 1 3141 3329 697994902 697994713 2.540000e-62 250.0
57 TraesCS4A01G424500 chr5A 89.340 197 20 1 3135 3330 41873481 41873677 3.280000e-61 246.0
58 TraesCS4A01G424500 chr5A 95.690 116 5 0 3659 3774 299272898 299273013 2.020000e-43 187.0
59 TraesCS4A01G424500 chr7D 95.690 116 5 0 3662 3777 30960181 30960296 2.020000e-43 187.0
60 TraesCS4A01G424500 chr7D 95.652 115 5 0 3661 3775 621738348 621738234 7.260000e-43 185.0
61 TraesCS4A01G424500 chr2B 95.690 116 5 0 3662 3777 693737130 693737245 2.020000e-43 187.0
62 TraesCS4A01G424500 chr2A 93.443 122 7 1 3659 3780 102329263 102329383 3.380000e-41 180.0
63 TraesCS4A01G424500 chr2A 91.406 128 10 1 3659 3785 679980342 679980215 1.570000e-39 174.0


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 TraesCS4A01G424500 chr4A 695803956 695808204 4248 False 3985.500000 7847 97.468500 1 4249 2 chr4A.!!$F3 4248
1 TraesCS4A01G424500 chr4A 695870257 695874505 4248 False 3894.300000 7697 93.135000 1 4249 2 chr4A.!!$F4 4248
2 TraesCS4A01G424500 chr4A 625893875 625895583 1708 True 1694.000000 1694 84.727000 1424 3127 1 chr4A.!!$R2 1703
3 TraesCS4A01G424500 chr4A 695980210 695981747 1537 True 1225.000000 1225 81.451000 1424 2945 1 chr4A.!!$R3 1521
4 TraesCS4A01G424500 chr4A 625883222 625886770 3548 True 1223.750000 4085 90.056000 116 3499 4 chr4A.!!$R4 3383
5 TraesCS4A01G424500 chr5B 684752650 684756182 3532 True 1606.666667 4054 93.184667 82 3141 3 chr5B.!!$R1 3059
6 TraesCS4A01G424500 chr5B 684879957 684881473 1516 False 1227.000000 1227 81.529000 1424 2945 1 chr5B.!!$F4 1521
7 TraesCS4A01G424500 chr5B 557108137 557112139 4002 False 872.666667 4157 88.799667 90 3479 6 chr5B.!!$F5 3389
8 TraesCS4A01G424500 chr5D 543332167 543335717 3550 False 1215.250000 4117 89.819500 224 3660 4 chr5D.!!$F2 3436
9 TraesCS4A01G424500 chr5D 543410401 543411921 1520 True 1192.000000 1192 81.210000 1424 2945 1 chr5D.!!$R1 1521
10 TraesCS4A01G424500 chr2D 474251009 474252621 1612 True 651.000000 1120 88.938500 436 1358 2 chr2D.!!$R2 922
11 TraesCS4A01G424500 chr3D 119547983 119548647 664 False 998.000000 998 93.713000 691 1358 1 chr3D.!!$F3 667

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
1678 3000 1.005748 GTGGCAAGCTTCCAAAGGC 60.006 57.895 16.19 9.24 35.01 4.35 F
2322 3653 0.323178 CTGAAGGCTGCCAAGGATGT 60.323 55.000 22.65 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3089 4444 1.795768 TTCAGACCGTGTGCATCTTC 58.204 50.0 0.0 0.0 0.0 2.87 R
4093 5457 0.312102 GTGTCTTCAGCCAACAAGCC 59.688 55.0 0.0 0.0 0.0 4.35 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
1678 3000 1.005748 GTGGCAAGCTTCCAAAGGC 60.006 57.895 16.19 9.24 35.01 4.35
1729 3051 1.880027 GAAAACCATGTTGGCGAGAGT 59.120 47.619 0.00 0.00 42.67 3.24
1769 3100 2.562912 CCATTCTTTGCGCGCAGT 59.437 55.556 34.25 15.76 0.00 4.40
1817 3148 2.594131 GGTGTTGGGCCTAAAAGAGTT 58.406 47.619 1.74 0.00 0.00 3.01
1885 3216 3.785486 TCATCGATGAGATTGACACCAC 58.215 45.455 23.99 0.00 37.52 4.16
2322 3653 0.323178 CTGAAGGCTGCCAAGGATGT 60.323 55.000 22.65 0.00 0.00 3.06
2367 3698 7.255381 GGATCACATTGAATATTCCAAGGACAG 60.255 40.741 12.90 5.78 0.00 3.51
3089 4444 8.686397 TTACTTGCATGCATACAAATGTAAAG 57.314 30.769 23.37 13.35 35.38 1.85
3129 4492 8.531146 TCTGAATTTCTCTGGTTTTTGTTTCTT 58.469 29.630 0.00 0.00 0.00 2.52
3200 4563 2.378547 TGCAGAAAACCACCTAATCCCT 59.621 45.455 0.00 0.00 0.00 4.20
3222 4585 6.365050 CCTAATTTTGTGCAAAAATCACTGC 58.635 36.000 13.13 0.00 42.71 4.40
3679 5043 2.606378 ACTACTCCCTCCGTTCACTTT 58.394 47.619 0.00 0.00 0.00 2.66
3735 5099 7.872163 TGTTTTGCACATTGTCTGAAATATC 57.128 32.000 0.00 0.00 0.00 1.63
3766 5130 8.049721 AGGTCTTATAAAAATGAACAGAGGGAG 58.950 37.037 0.00 0.00 0.00 4.30
3804 5168 0.756815 CTAGGCAAAAGGGATGGGCC 60.757 60.000 0.00 0.00 44.92 5.80
4022 5386 3.629398 CCTTTCAATCAGTGCTATCACCC 59.371 47.826 0.00 0.00 44.16 4.61
4093 5457 2.290464 AGAACCTGACCGATCGTAGAG 58.710 52.381 15.09 5.98 43.63 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
934 2219 5.641636 GGAGAAAACAAGTTGCCAAAAGAAA 59.358 36.000 1.81 0.00 0.00 2.52
1609 2927 4.449068 GCATGATAGGTTACCAACTCGATG 59.551 45.833 3.51 5.42 0.00 3.84
1678 3000 2.633509 GGGCCAGCAAGCAGAACAG 61.634 63.158 4.39 0.00 0.00 3.16
1769 3100 2.989253 TCCTCGAAGTCGCTGCCA 60.989 61.111 0.00 0.00 39.60 4.92
1817 3148 1.827969 GCTTCACTGAAGAGCTCCCTA 59.172 52.381 20.98 0.00 41.71 3.53
1885 3216 4.060038 CTTGCCTTTGCCCAGCGG 62.060 66.667 0.00 0.00 36.33 5.52
2322 3653 1.403647 CCATCGTAACAGCTTCCGACA 60.404 52.381 0.00 0.00 31.43 4.35
2367 3698 0.954449 CTCGCTGCCCATCATGATCC 60.954 60.000 4.86 0.00 0.00 3.36
2852 4201 2.222445 GCGCCGTGATAATATTTTCCGT 59.778 45.455 0.00 0.00 0.00 4.69
3089 4444 1.795768 TTCAGACCGTGTGCATCTTC 58.204 50.000 0.00 0.00 0.00 2.87
3129 4492 5.178096 TGCAATTCACTCCTCCATAAGAA 57.822 39.130 0.00 0.00 0.00 2.52
3200 4563 5.521735 ACGCAGTGATTTTTGCACAAAATTA 59.478 32.000 9.21 11.51 42.51 1.40
3679 5043 7.857734 TTGAGTTGTCTGAAATGACTTACAA 57.142 32.000 0.00 0.00 37.79 2.41
3848 5212 2.730090 CGCAATGAAAGTAGCCAAGCTG 60.730 50.000 0.00 0.00 40.10 4.24
4022 5386 0.316522 ATCGATGCTGGGAGATGTCG 59.683 55.000 0.00 0.00 0.00 4.35
4093 5457 0.312102 GTGTCTTCAGCCAACAAGCC 59.688 55.000 0.00 0.00 0.00 4.35
4185 5549 0.321671 GCACTTCAGGTAGGCTCACA 59.678 55.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.