Multiple sequence alignment - TraesCS4B01G270300

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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 TraesCS4B01G270300 chr4B 100.000 3594 0 0 1 3594 546578199 546581792 0.000000e+00 6637
1 TraesCS4B01G270300 chr4B 99.741 1545 4 0 1 1545 546600373 546601917 0.000000e+00 2832
2 TraesCS4B01G270300 chr4B 99.857 1396 0 1 1751 3144 546602190 546603585 0.000000e+00 2566
3 TraesCS4B01G270300 chr4B 84.892 1112 138 18 1498 2601 546673644 546674733 0.000000e+00 1096
4 TraesCS4B01G270300 chr4B 78.643 1400 227 58 1228 2586 546023506 546024874 0.000000e+00 863
5 TraesCS4B01G270300 chr4B 100.000 396 0 0 1 396 546595643 546596038 0.000000e+00 732
6 TraesCS4B01G270300 chr4B 93.779 434 25 2 1 432 315063292 315063725 0.000000e+00 651
7 TraesCS4B01G270300 chr4B 93.750 432 27 0 1 432 413503152 413503583 0.000000e+00 649
8 TraesCS4B01G270300 chr4B 88.281 128 15 0 1228 1355 545179249 545179376 1.730000e-33 154
9 TraesCS4B01G270300 chr4A 88.305 2112 111 41 576 2631 26634227 26632196 0.000000e+00 2407
10 TraesCS4B01G270300 chr4A 88.305 2112 111 41 576 2631 26636969 26634938 0.000000e+00 2407
11 TraesCS4B01G270300 chr4A 88.305 2112 111 41 576 2631 26649526 26647495 0.000000e+00 2407
12 TraesCS4B01G270300 chr4A 87.337 845 84 10 2764 3594 618277147 618276312 0.000000e+00 946
13 TraesCS4B01G270300 chr4A 86.525 141 19 0 1228 1368 29302933 29303073 4.800000e-34 156
14 TraesCS4B01G270300 chr4D 92.784 1178 59 8 1480 2640 441058069 441059237 0.000000e+00 1681
15 TraesCS4B01G270300 chr4D 91.087 920 33 21 549 1437 441057171 441058072 0.000000e+00 1199
16 TraesCS4B01G270300 chr4D 82.300 1113 139 27 1498 2602 441064263 441065325 0.000000e+00 911
17 TraesCS4B01G270300 chr4D 83.333 390 52 6 3216 3594 166531605 166531218 7.390000e-92 348
18 TraesCS4B01G270300 chr4D 86.777 121 16 0 1228 1348 440044922 440045042 6.260000e-28 135
19 TraesCS4B01G270300 chrUn 87.083 960 105 12 1657 2608 286309746 286308798 0.000000e+00 1068
20 TraesCS4B01G270300 chrUn 87.083 960 105 12 1657 2608 286316029 286315081 0.000000e+00 1068
21 TraesCS4B01G270300 chrUn 87.083 960 105 12 1657 2608 295780526 295781474 0.000000e+00 1068
22 TraesCS4B01G270300 chrUn 85.166 391 45 6 3216 3594 441810773 441811162 4.350000e-104 388
23 TraesCS4B01G270300 chr6D 89.112 845 75 9 2765 3594 35026970 35026128 0.000000e+00 1035
24 TraesCS4B01G270300 chr3D 88.848 825 79 5 2783 3594 13601508 13602332 0.000000e+00 1002
25 TraesCS4B01G270300 chr3D 87.678 844 90 6 2765 3594 561715395 561714552 0.000000e+00 970
26 TraesCS4B01G270300 chr5A 87.947 838 92 6 2764 3594 121115966 121116801 0.000000e+00 979
27 TraesCS4B01G270300 chr5A 86.714 843 96 6 2765 3594 618310675 618311514 0.000000e+00 922
28 TraesCS4B01G270300 chr5A 85.458 557 59 8 1 543 550145773 550146321 8.710000e-156 560
29 TraesCS4B01G270300 chr5A 83.797 395 54 3 3210 3594 415574307 415574701 2.040000e-97 366
30 TraesCS4B01G270300 chr7B 87.173 842 91 8 2765 3594 201536360 201535524 0.000000e+00 941
31 TraesCS4B01G270300 chr7B 93.779 434 25 2 1 432 47693647 47694080 0.000000e+00 651
32 TraesCS4B01G270300 chr3B 86.951 843 95 8 2765 3594 173563643 173562803 0.000000e+00 933
33 TraesCS4B01G270300 chr3B 85.472 826 96 13 2783 3594 737346735 737347550 0.000000e+00 839
34 TraesCS4B01G270300 chr3B 93.750 432 26 1 1 432 39931221 39930791 0.000000e+00 647
35 TraesCS4B01G270300 chr7D 85.472 826 97 10 2782 3594 295116176 295115361 0.000000e+00 839
36 TraesCS4B01G270300 chr5B 93.519 432 28 0 1 432 682938927 682938496 0.000000e+00 643
37 TraesCS4B01G270300 chr5B 88.123 522 50 9 34 546 580512075 580512593 8.530000e-171 610
38 TraesCS4B01G270300 chr2D 93.333 435 25 4 1 432 458743161 458743594 1.090000e-179 640
39 TraesCS4B01G270300 chr2D 84.872 390 47 7 3216 3594 629843619 629843231 2.020000e-102 383
40 TraesCS4B01G270300 chr1B 90.886 395 26 3 3210 3594 268798531 268798137 4.110000e-144 521
41 TraesCS4B01G270300 chr1B 80.779 385 52 13 3215 3594 440478594 440478227 7.600000e-72 281
42 TraesCS4B01G270300 chr2B 84.910 391 46 6 3216 3594 43651073 43650684 2.020000e-102 383
43 TraesCS4B01G270300 chr6B 86.111 144 11 2 3460 3594 655107921 655107778 2.890000e-31 147


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 TraesCS4B01G270300 chr4B 546578199 546581792 3593 False 6637 6637 100.0000 1 3594 1 chr4B.!!$F5 3593
1 TraesCS4B01G270300 chr4B 546600373 546603585 3212 False 2699 2832 99.7990 1 3144 2 chr4B.!!$F8 3143
2 TraesCS4B01G270300 chr4B 546673644 546674733 1089 False 1096 1096 84.8920 1498 2601 1 chr4B.!!$F7 1103
3 TraesCS4B01G270300 chr4B 546023506 546024874 1368 False 863 863 78.6430 1228 2586 1 chr4B.!!$F4 1358
4 TraesCS4B01G270300 chr4A 26632196 26636969 4773 True 2407 2407 88.3050 576 2631 2 chr4A.!!$R3 2055
5 TraesCS4B01G270300 chr4A 26647495 26649526 2031 True 2407 2407 88.3050 576 2631 1 chr4A.!!$R1 2055
6 TraesCS4B01G270300 chr4A 618276312 618277147 835 True 946 946 87.3370 2764 3594 1 chr4A.!!$R2 830
7 TraesCS4B01G270300 chr4D 441057171 441059237 2066 False 1440 1681 91.9355 549 2640 2 chr4D.!!$F3 2091
8 TraesCS4B01G270300 chr4D 441064263 441065325 1062 False 911 911 82.3000 1498 2602 1 chr4D.!!$F2 1104
9 TraesCS4B01G270300 chrUn 286308798 286309746 948 True 1068 1068 87.0830 1657 2608 1 chrUn.!!$R1 951
10 TraesCS4B01G270300 chrUn 286315081 286316029 948 True 1068 1068 87.0830 1657 2608 1 chrUn.!!$R2 951
11 TraesCS4B01G270300 chrUn 295780526 295781474 948 False 1068 1068 87.0830 1657 2608 1 chrUn.!!$F1 951
12 TraesCS4B01G270300 chr6D 35026128 35026970 842 True 1035 1035 89.1120 2765 3594 1 chr6D.!!$R1 829
13 TraesCS4B01G270300 chr3D 13601508 13602332 824 False 1002 1002 88.8480 2783 3594 1 chr3D.!!$F1 811
14 TraesCS4B01G270300 chr3D 561714552 561715395 843 True 970 970 87.6780 2765 3594 1 chr3D.!!$R1 829
15 TraesCS4B01G270300 chr5A 121115966 121116801 835 False 979 979 87.9470 2764 3594 1 chr5A.!!$F1 830
16 TraesCS4B01G270300 chr5A 618310675 618311514 839 False 922 922 86.7140 2765 3594 1 chr5A.!!$F4 829
17 TraesCS4B01G270300 chr5A 550145773 550146321 548 False 560 560 85.4580 1 543 1 chr5A.!!$F3 542
18 TraesCS4B01G270300 chr7B 201535524 201536360 836 True 941 941 87.1730 2765 3594 1 chr7B.!!$R1 829
19 TraesCS4B01G270300 chr3B 173562803 173563643 840 True 933 933 86.9510 2765 3594 1 chr3B.!!$R2 829
20 TraesCS4B01G270300 chr3B 737346735 737347550 815 False 839 839 85.4720 2783 3594 1 chr3B.!!$F1 811
21 TraesCS4B01G270300 chr7D 295115361 295116176 815 True 839 839 85.4720 2782 3594 1 chr7D.!!$R1 812
22 TraesCS4B01G270300 chr5B 580512075 580512593 518 False 610 610 88.1230 34 546 1 chr5B.!!$F1 512

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
518 535 2.739287 CGCGTTTTACAGGCCGGA 60.739 61.111 10.86 0.0 32.16 5.14 F
1639 1718 3.565307 TGCTCTGTTCTTGGGTGAATTT 58.435 40.909 0.00 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1825 0.249398 GGAGTTGTAGCGGATGGTGT 59.751 55.0 0.0 0.0 0.00 4.16 R
3467 6392 0.319641 AAGAGAGAAACGACACCGCC 60.320 55.0 0.0 0.0 39.95 6.13 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
518 535 2.739287 CGCGTTTTACAGGCCGGA 60.739 61.111 10.86 0.00 32.16 5.14
1590 1666 5.367644 ACTGTGAGATATCCATCCAACATCA 59.632 40.000 0.00 0.00 30.65 3.07
1594 1670 8.608598 TGTGAGATATCCATCCAACATCAATAT 58.391 33.333 0.00 0.00 0.00 1.28
1639 1718 3.565307 TGCTCTGTTCTTGGGTGAATTT 58.435 40.909 0.00 0.00 0.00 1.82
1648 1727 6.549364 TGTTCTTGGGTGAATTTATCTGTGTT 59.451 34.615 0.00 0.00 0.00 3.32
1653 1732 4.142381 GGGTGAATTTATCTGTGTTGCTCC 60.142 45.833 0.00 0.00 0.00 4.70
3273 6196 0.465705 GGCTTGGTGATCGGATCTCA 59.534 55.000 18.16 13.31 0.00 3.27
3330 6253 2.616842 GACATGGTTGTCGGTGAAAACT 59.383 45.455 0.00 0.00 42.66 2.66
3358 6281 1.887242 GCAGATGATGGCGGCGTTA 60.887 57.895 9.37 0.32 0.00 3.18
3377 6301 4.362279 GTTATACGCCGTTACCTTGATGA 58.638 43.478 0.00 0.00 0.00 2.92
3397 6321 3.129813 TGAAGGCATCGTCGTGTAACTAT 59.870 43.478 0.00 0.00 31.75 2.12
3447 6372 4.814771 GGAACCCTATAATCTGGTGTTTCG 59.185 45.833 0.00 0.00 31.32 3.46
3554 6489 0.944311 GTCTTGCACGGAGCTTCGAA 60.944 55.000 24.16 3.83 45.94 3.71
3564 6499 1.202475 GGAGCTTCGAAGGAGATGTCC 60.202 57.143 25.77 0.00 44.33 4.02
3566 6501 2.102252 GAGCTTCGAAGGAGATGTCCAT 59.898 50.000 25.77 0.00 46.80 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
518 535 2.939760 TATCAGACCCCGCATCCCGT 62.940 60.000 0.00 0.00 34.38 5.28
1590 1666 4.867047 CAGAGCAAGTTCGTGTCTGATATT 59.133 41.667 10.16 0.00 37.43 1.28
1594 1670 1.681264 TCAGAGCAAGTTCGTGTCTGA 59.319 47.619 12.48 12.48 41.01 3.27
1639 1718 3.273434 GCATCAAGGAGCAACACAGATA 58.727 45.455 0.00 0.00 0.00 1.98
1648 1727 1.924939 TCCCCTGCATCAAGGAGCA 60.925 57.895 0.00 0.00 40.02 4.26
1653 1732 2.276740 GGGGTCCCCTGCATCAAG 59.723 66.667 21.13 0.00 41.34 3.02
1734 1825 0.249398 GGAGTTGTAGCGGATGGTGT 59.751 55.000 0.00 0.00 0.00 4.16
3189 6112 2.601398 AACGAGACGACGCGAGACA 61.601 57.895 15.93 0.00 41.48 3.41
3273 6196 3.007398 GCCGGAACTAGATGATGGATCTT 59.993 47.826 5.05 0.00 41.94 2.40
3344 6267 2.822306 CGTATAACGCCGCCATCAT 58.178 52.632 0.00 0.00 33.65 2.45
3358 6281 3.454375 CTTCATCAAGGTAACGGCGTAT 58.546 45.455 15.20 6.45 46.39 3.06
3377 6301 3.795623 ATAGTTACACGACGATGCCTT 57.204 42.857 0.00 0.00 0.00 4.35
3433 6358 4.459390 TTCGATCCGAAACACCAGATTA 57.541 40.909 0.00 0.00 43.00 1.75
3434 6359 3.328382 TTCGATCCGAAACACCAGATT 57.672 42.857 0.00 0.00 43.00 2.40
3445 6370 2.025584 CGCCATCGTTCGATCCGA 59.974 61.111 14.89 9.71 38.89 4.55
3447 6372 1.226859 TGTCGCCATCGTTCGATCC 60.227 57.895 4.67 0.00 37.06 3.36
3467 6392 0.319641 AAGAGAGAAACGACACCGCC 60.320 55.000 0.00 0.00 39.95 6.13
3554 6489 2.133520 AGGCATGAATGGACATCTCCT 58.866 47.619 0.00 0.00 37.48 3.69
3564 6499 1.012086 CTGTCGGTCAGGCATGAATG 58.988 55.000 0.92 0.00 40.23 2.67


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

AutoCloner maintained by Alex Coulton.