Multiple sequence alignment - TraesCS3A01G222600

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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 TraesCS3A01G222600 chr3A 100.000 2255 0 0 1 2255 416295595 416293341 0.000000e+00 4165.0
1 TraesCS3A01G222600 chr3A 95.421 2271 87 2 2 2255 416287742 416285472 0.000000e+00 3602.0
2 TraesCS3A01G222600 chr3A 87.515 857 89 18 1407 2255 575795221 575796067 0.000000e+00 974.0
3 TraesCS3A01G222600 chr3A 86.931 857 96 15 1407 2255 245566336 245565488 0.000000e+00 948.0
4 TraesCS3A01G222600 chr3A 82.717 1082 141 31 1201 2255 169736186 169735124 0.000000e+00 920.0
5 TraesCS3A01G222600 chr3A 82.468 1078 145 33 1202 2255 169724563 169723506 0.000000e+00 904.0
6 TraesCS3A01G222600 chr3A 82.500 1080 134 37 1201 2255 169710805 169709756 0.000000e+00 896.0
7 TraesCS3A01G222600 chr3A 84.314 612 78 15 2 607 9904919 9904320 1.160000e-162 582.0
8 TraesCS3A01G222600 chr3A 89.888 178 17 1 1197 1373 332907326 332907503 6.270000e-56 228.0
9 TraesCS3A01G222600 chr3A 87.200 125 14 2 1231 1354 643272543 643272420 8.400000e-30 141.0
10 TraesCS3A01G222600 chr3A 91.228 57 4 1 1257 1312 126859993 126859937 2.400000e-10 76.8
11 TraesCS3A01G222600 chr6A 90.970 897 71 9 1363 2255 582052303 582053193 0.000000e+00 1199.0
12 TraesCS3A01G222600 chr6A 87.822 854 92 11 1407 2253 130286921 130286073 0.000000e+00 990.0
13 TraesCS3A01G222600 chr2A 87.368 855 93 15 1407 2253 526829758 526828911 0.000000e+00 966.0
14 TraesCS3A01G222600 chr2A 87.296 858 90 19 1407 2253 526837500 526836651 0.000000e+00 963.0
15 TraesCS3A01G222600 chr2A 92.487 599 43 1 754 1352 358292640 358292044 0.000000e+00 856.0
16 TraesCS3A01G222600 chr2A 91.653 599 49 1 754 1352 358284743 358284146 0.000000e+00 828.0
17 TraesCS3A01G222600 chr2A 84.967 612 77 11 2 606 322066770 322066167 6.890000e-170 606.0
18 TraesCS3A01G222600 chr2A 90.769 455 38 3 754 1205 152876203 152876656 2.480000e-169 604.0
19 TraesCS3A01G222600 chr2A 89.648 454 41 4 754 1203 152983762 152984213 6.990000e-160 573.0
20 TraesCS3A01G222600 chr2A 88.814 447 45 3 754 1198 152989581 152990024 5.480000e-151 544.0
21 TraesCS3A01G222600 chr2A 87.583 451 43 5 757 1198 40406167 40405721 5.560000e-141 510.0
22 TraesCS3A01G222600 chr5A 86.860 860 95 18 1404 2255 282436227 282437076 0.000000e+00 946.0
23 TraesCS3A01G222600 chr5A 83.903 702 92 18 2 694 424406365 424405676 0.000000e+00 651.0
24 TraesCS3A01G222600 chr5A 83.618 702 94 18 2 694 424398868 424398179 6.790000e-180 640.0
25 TraesCS3A01G222600 chr5A 79.161 787 110 35 10 764 135264116 135263352 1.560000e-136 496.0
26 TraesCS3A01G222600 chr5A 78.643 796 114 38 2 764 274569330 274570102 5.630000e-131 477.0
27 TraesCS3A01G222600 chr5A 78.753 786 114 31 2 758 300743541 300744302 5.630000e-131 477.0
28 TraesCS3A01G222600 chr5A 78.680 788 114 36 10 764 135256422 135255656 2.030000e-130 475.0
29 TraesCS3A01G222600 chr5A 78.035 733 111 30 53 758 300736166 300736875 1.250000e-112 416.0
30 TraesCS3A01G222600 chr2B 86.860 860 96 17 1404 2253 93617696 93618548 0.000000e+00 946.0
31 TraesCS3A01G222600 chr1A 85.868 651 78 11 2 648 551719760 551720400 0.000000e+00 680.0
32 TraesCS3A01G222600 chr1A 83.232 656 94 13 2 647 394795370 394796019 2.490000e-164 588.0
33 TraesCS3A01G222600 chr7A 85.173 607 72 11 2 601 703432309 703432904 6.890000e-170 606.0
34 TraesCS3A01G222600 chr7A 82.703 688 95 15 2 678 396875923 396875249 6.940000e-165 590.0
35 TraesCS3A01G222600 chr7A 90.044 452 41 3 754 1203 273100030 273099581 1.160000e-162 582.0
36 TraesCS3A01G222600 chr7A 89.231 455 36 9 754 1205 273090411 273089967 7.040000e-155 556.0
37 TraesCS3A01G222600 chr7A 84.259 108 15 2 658 764 369131773 369131667 1.100000e-18 104.0
38 TraesCS3A01G222600 chr7A 92.727 55 2 2 710 764 309990951 309991003 6.680000e-11 78.7
39 TraesCS3A01G222600 chr4A 85.222 609 66 16 10 606 555447983 555448579 2.480000e-169 604.0
40 TraesCS3A01G222600 chr4A 80.928 776 108 27 2 764 612869317 612868569 5.400000e-161 577.0
41 TraesCS3A01G222600 chr3B 94.521 73 3 1 598 669 336118876 336118804 6.580000e-21 111.0
42 TraesCS3A01G222600 chr3B 89.157 83 4 5 600 678 256754965 256755046 5.130000e-17 99.0


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 TraesCS3A01G222600 chr3A 416293341 416295595 2254 True 4165 4165 100.000 1 2255 1 chr3A.!!$R8 2254
1 TraesCS3A01G222600 chr3A 416285472 416287742 2270 True 3602 3602 95.421 2 2255 1 chr3A.!!$R7 2253
2 TraesCS3A01G222600 chr3A 575795221 575796067 846 False 974 974 87.515 1407 2255 1 chr3A.!!$F2 848
3 TraesCS3A01G222600 chr3A 245565488 245566336 848 True 948 948 86.931 1407 2255 1 chr3A.!!$R6 848
4 TraesCS3A01G222600 chr3A 169735124 169736186 1062 True 920 920 82.717 1201 2255 1 chr3A.!!$R5 1054
5 TraesCS3A01G222600 chr3A 169723506 169724563 1057 True 904 904 82.468 1202 2255 1 chr3A.!!$R4 1053
6 TraesCS3A01G222600 chr3A 169709756 169710805 1049 True 896 896 82.500 1201 2255 1 chr3A.!!$R3 1054
7 TraesCS3A01G222600 chr3A 9904320 9904919 599 True 582 582 84.314 2 607 1 chr3A.!!$R1 605
8 TraesCS3A01G222600 chr6A 582052303 582053193 890 False 1199 1199 90.970 1363 2255 1 chr6A.!!$F1 892
9 TraesCS3A01G222600 chr6A 130286073 130286921 848 True 990 990 87.822 1407 2253 1 chr6A.!!$R1 846
10 TraesCS3A01G222600 chr2A 526828911 526829758 847 True 966 966 87.368 1407 2253 1 chr2A.!!$R5 846
11 TraesCS3A01G222600 chr2A 526836651 526837500 849 True 963 963 87.296 1407 2253 1 chr2A.!!$R6 846
12 TraesCS3A01G222600 chr2A 358292044 358292640 596 True 856 856 92.487 754 1352 1 chr2A.!!$R4 598
13 TraesCS3A01G222600 chr2A 358284146 358284743 597 True 828 828 91.653 754 1352 1 chr2A.!!$R3 598
14 TraesCS3A01G222600 chr2A 322066167 322066770 603 True 606 606 84.967 2 606 1 chr2A.!!$R2 604
15 TraesCS3A01G222600 chr5A 282436227 282437076 849 False 946 946 86.860 1404 2255 1 chr5A.!!$F2 851
16 TraesCS3A01G222600 chr5A 424405676 424406365 689 True 651 651 83.903 2 694 1 chr5A.!!$R4 692
17 TraesCS3A01G222600 chr5A 424398179 424398868 689 True 640 640 83.618 2 694 1 chr5A.!!$R3 692
18 TraesCS3A01G222600 chr5A 135263352 135264116 764 True 496 496 79.161 10 764 1 chr5A.!!$R2 754
19 TraesCS3A01G222600 chr5A 274569330 274570102 772 False 477 477 78.643 2 764 1 chr5A.!!$F1 762
20 TraesCS3A01G222600 chr5A 300743541 300744302 761 False 477 477 78.753 2 758 1 chr5A.!!$F4 756
21 TraesCS3A01G222600 chr5A 135255656 135256422 766 True 475 475 78.680 10 764 1 chr5A.!!$R1 754
22 TraesCS3A01G222600 chr5A 300736166 300736875 709 False 416 416 78.035 53 758 1 chr5A.!!$F3 705
23 TraesCS3A01G222600 chr2B 93617696 93618548 852 False 946 946 86.860 1404 2253 1 chr2B.!!$F1 849
24 TraesCS3A01G222600 chr1A 551719760 551720400 640 False 680 680 85.868 2 648 1 chr1A.!!$F2 646
25 TraesCS3A01G222600 chr1A 394795370 394796019 649 False 588 588 83.232 2 647 1 chr1A.!!$F1 645
26 TraesCS3A01G222600 chr7A 703432309 703432904 595 False 606 606 85.173 2 601 1 chr7A.!!$F2 599
27 TraesCS3A01G222600 chr7A 396875249 396875923 674 True 590 590 82.703 2 678 1 chr7A.!!$R4 676
28 TraesCS3A01G222600 chr4A 555447983 555448579 596 False 604 604 85.222 10 606 1 chr4A.!!$F1 596
29 TraesCS3A01G222600 chr4A 612868569 612869317 748 True 577 577 80.928 2 764 1 chr4A.!!$R1 762

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
382 417 0.106619 CAGTCCTCTACCTACCGCCT 60.107 60.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1387 0.245813 GGAACCGCTCCTTCGTACTT 59.754 55.0 0.0 0.0 41.61 2.24 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
35 37 7.753132 GCATTGCATCATCATGTTTTTCAAAAT 59.247 29.630 3.15 0.00 31.86 1.82
150 156 1.029681 AAGTGGCCGAAAAGTGTTCC 58.970 50.000 0.00 0.00 0.00 3.62
153 159 1.598685 GGCCGAAAAGTGTTCCCGA 60.599 57.895 0.00 0.00 0.00 5.14
290 298 1.332882 CGGTCTTTCGTCGGACGTTC 61.333 60.000 27.53 14.76 43.14 3.95
329 339 2.422127 GACGGGTTTCTCTCTCTCTCTG 59.578 54.545 0.00 0.00 0.00 3.35
382 417 0.106619 CAGTCCTCTACCTACCGCCT 60.107 60.000 0.00 0.00 0.00 5.52
512 559 6.526566 AACATCTACAAAACGTCTCTGTTC 57.473 37.500 0.00 0.00 0.00 3.18
518 565 7.361127 TCTACAAAACGTCTCTGTTCTCTTAG 58.639 38.462 0.00 0.00 0.00 2.18
521 568 7.486647 ACAAAACGTCTCTGTTCTCTTAGTTA 58.513 34.615 0.00 0.00 0.00 2.24
679 759 2.429930 CGCCACCCACTTTCTCCA 59.570 61.111 0.00 0.00 0.00 3.86
689 769 3.891366 CCCACTTTCTCCACAATTTCAGT 59.109 43.478 0.00 0.00 0.00 3.41
702 782 1.978455 TTTCAGTGCCACCCAGTCGT 61.978 55.000 0.00 0.00 0.00 4.34
908 991 0.822121 GCCCAGTCTTTGTTCCCGTT 60.822 55.000 0.00 0.00 0.00 4.44
917 1000 2.356673 GTTCCCGTTCCGCTCGTT 60.357 61.111 0.00 0.00 0.00 3.85
1047 1130 0.324943 ATGTTGGCTTCTACCAGCGT 59.675 50.000 0.00 0.00 43.37 5.07
1193 1276 2.127194 CGCTCGGATCCGTCGATC 60.127 66.667 32.09 18.89 43.73 3.69
1304 1387 1.335051 CGTTCTGTCTCTGTCGAGCAA 60.335 52.381 0.00 0.00 37.19 3.91
1307 1390 1.957177 TCTGTCTCTGTCGAGCAAAGT 59.043 47.619 0.00 0.00 37.19 2.66
1437 1532 3.025599 ATGGCCCATGGGTGAGCT 61.026 61.111 31.58 9.92 37.65 4.09
1438 1533 3.369410 ATGGCCCATGGGTGAGCTG 62.369 63.158 31.58 5.02 37.65 4.24
1803 1917 7.151976 GTGGAAAAATGCCTAGTTTAACATGT 58.848 34.615 0.00 0.00 0.00 3.21
1805 1919 8.207545 TGGAAAAATGCCTAGTTTAACATGTTT 58.792 29.630 17.78 0.51 33.66 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.955905 TGATGCAATGCGGATGATGG 59.044 50.000 0.00 0.0 0.00 3.51
35 37 2.046700 GACCCGGACGGATGCAAA 60.047 61.111 13.13 0.0 37.50 3.68
150 156 2.866065 GCCAACTTTCAACCCATTTCGG 60.866 50.000 0.00 0.0 0.00 4.30
153 159 3.742385 CATGCCAACTTTCAACCCATTT 58.258 40.909 0.00 0.0 0.00 2.32
329 339 2.684881 CAGGCTGAGAGAAGAGAGAGAC 59.315 54.545 9.42 0.0 0.00 3.36
382 417 0.178873 AGAGAGGTTAGGTTGGGCCA 60.179 55.000 0.00 0.0 40.61 5.36
521 568 3.838903 CGGATAAATAGGTTAGGGAGCCT 59.161 47.826 0.00 0.0 38.81 4.58
679 759 1.331214 CTGGGTGGCACTGAAATTGT 58.669 50.000 18.45 0.0 0.00 2.71
702 782 2.347490 GAAGGCAGGTGAAGGCGA 59.653 61.111 0.00 0.0 36.55 5.54
750 831 2.581354 GACGAGGAGCTGCATGGT 59.419 61.111 8.35 1.3 0.00 3.55
917 1000 2.640302 GGAGAGCAGAGGTCACGCA 61.640 63.158 0.00 0.0 31.89 5.24
950 1033 0.108138 AGCAGTACGAATCTGGTGGC 60.108 55.000 9.22 0.0 41.19 5.01
956 1039 0.460987 GGCTGCAGCAGTACGAATCT 60.461 55.000 37.63 0.0 44.36 2.40
1047 1130 1.306141 ACGAGGATGAGGAAGGGCA 60.306 57.895 0.00 0.0 0.00 5.36
1167 1250 3.077556 ATCCGAGCGGTGAAGGCT 61.078 61.111 8.96 0.0 45.00 4.58
1304 1387 0.245813 GGAACCGCTCCTTCGTACTT 59.754 55.000 0.00 0.0 41.61 2.24
1437 1532 1.228552 GTGCAAAAGGAGAGGGGCA 60.229 57.895 0.00 0.0 0.00 5.36
1438 1533 0.328258 TAGTGCAAAAGGAGAGGGGC 59.672 55.000 0.00 0.0 0.00 5.80
1696 1810 5.135383 AGCATTTTAGCATGGCATAAGAGA 58.865 37.500 0.00 0.0 36.85 3.10
1805 1919 9.405587 GAGTTATTAAACATGCAAAGCAAGTAA 57.594 29.630 0.02 0.0 39.58 2.24


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

AutoCloner maintained by Alex Coulton.