Multiple sequence alignment - TraesCS2A01G342000

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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 TraesCS2A01G342000 chr2A 100.000 3826 0 0 1 3826 578652630 578656455 0.000000e+00 7066
1 TraesCS2A01G342000 chr2A 82.973 740 103 14 2733 3456 757739842 757739110 0.000000e+00 647
2 TraesCS2A01G342000 chr2A 82.440 746 99 20 2738 3455 472863391 472862650 1.170000e-174 623
3 TraesCS2A01G342000 chr2A 81.338 284 51 2 90 372 738830963 738830681 2.970000e-56 230
4 TraesCS2A01G342000 chr4A 98.006 2959 44 4 513 3456 547186043 547189001 0.000000e+00 5123
5 TraesCS2A01G342000 chr4A 97.326 2917 57 10 512 3412 397611436 397608525 0.000000e+00 4935
6 TraesCS2A01G342000 chr4A 80.634 284 53 2 90 372 296351893 296352175 6.440000e-53 219
7 TraesCS2A01G342000 chr4A 80.282 284 54 2 90 372 293293181 293293463 2.990000e-51 213
8 TraesCS2A01G342000 chr6A 97.905 2959 47 4 513 3456 49916383 49919341 0.000000e+00 5107
9 TraesCS2A01G342000 chr6A 80.204 783 96 34 2721 3460 209128330 209127564 2.020000e-147 532
10 TraesCS2A01G342000 chr5B 83.494 1345 137 36 512 1800 710279980 710278665 0.000000e+00 1175
11 TraesCS2A01G342000 chr5B 88.498 739 60 12 1865 2589 710278412 710277685 0.000000e+00 870
12 TraesCS2A01G342000 chr7A 98.635 513 6 1 1 512 299285152 299285664 0.000000e+00 907
13 TraesCS2A01G342000 chr7A 98.047 512 10 0 1 512 545660382 545659871 0.000000e+00 891
14 TraesCS2A01G342000 chr7A 98.072 415 8 0 1 415 95929865 95929451 0.000000e+00 723
15 TraesCS2A01G342000 chr7A 98.378 370 5 1 3457 3826 545659873 545659505 0.000000e+00 649
16 TraesCS2A01G342000 chr7A 97.838 370 8 0 3457 3826 299285662 299286031 1.160000e-179 640
17 TraesCS2A01G342000 chr7A 97.568 370 9 0 3457 3826 95929400 95929031 5.390000e-178 634
18 TraesCS2A01G342000 chr7A 80.077 778 97 33 2721 3456 232502057 232502818 3.390000e-145 525
19 TraesCS2A01G342000 chr5D 88.038 744 75 8 1991 2724 33933731 33932992 0.000000e+00 869
20 TraesCS2A01G342000 chr2D 87.366 744 80 7 1991 2724 9359722 9358983 0.000000e+00 841
21 TraesCS2A01G342000 chr2D 83.576 755 93 16 2721 3454 649920318 649921062 0.000000e+00 678
22 TraesCS2A01G342000 chr2D 80.785 739 99 24 2738 3457 495247045 495246331 4.350000e-149 538
23 TraesCS2A01G342000 chr6D 87.097 744 82 8 1991 2724 75799440 75798701 0.000000e+00 830
24 TraesCS2A01G342000 chr3B 86.729 746 81 11 1991 2724 72588611 72587872 0.000000e+00 813
25 TraesCS2A01G342000 chr3B 80.079 758 103 32 2733 3456 767758813 767758070 1.580000e-143 520
26 TraesCS2A01G342000 chr3D 86.694 744 84 9 1991 2724 563813573 563814311 0.000000e+00 811
27 TraesCS2A01G342000 chr1B 86.878 724 76 10 1991 2705 2245741 2246454 0.000000e+00 793
28 TraesCS2A01G342000 chr2B 91.171 521 43 3 1 519 424020004 424020523 0.000000e+00 704
29 TraesCS2A01G342000 chr2B 82.216 731 91 24 2740 3456 134504304 134505009 9.150000e-166 593
30 TraesCS2A01G342000 chr2B 90.591 372 33 1 3457 3826 424020513 424020884 3.430000e-135 492
31 TraesCS2A01G342000 chr2B 80.407 541 80 20 2930 3453 6099826 6100357 4.640000e-104 388
32 TraesCS2A01G342000 chr7D 82.443 786 90 25 2721 3458 594004097 594003312 0.000000e+00 643
33 TraesCS2A01G342000 chr7B 82.101 771 94 25 2721 3456 641891751 641892512 1.510000e-173 619
34 TraesCS2A01G342000 chr6B 82.130 554 70 21 2739 3277 8460117 8460656 7.540000e-122 448
35 TraesCS2A01G342000 chr4B 88.235 153 18 0 91 243 207099990 207100142 2.350000e-42 183


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 TraesCS2A01G342000 chr2A 578652630 578656455 3825 False 7066.0 7066 100.0000 1 3826 1 chr2A.!!$F1 3825
1 TraesCS2A01G342000 chr2A 757739110 757739842 732 True 647.0 647 82.9730 2733 3456 1 chr2A.!!$R3 723
2 TraesCS2A01G342000 chr2A 472862650 472863391 741 True 623.0 623 82.4400 2738 3455 1 chr2A.!!$R1 717
3 TraesCS2A01G342000 chr4A 547186043 547189001 2958 False 5123.0 5123 98.0060 513 3456 1 chr4A.!!$F3 2943
4 TraesCS2A01G342000 chr4A 397608525 397611436 2911 True 4935.0 4935 97.3260 512 3412 1 chr4A.!!$R1 2900
5 TraesCS2A01G342000 chr6A 49916383 49919341 2958 False 5107.0 5107 97.9050 513 3456 1 chr6A.!!$F1 2943
6 TraesCS2A01G342000 chr6A 209127564 209128330 766 True 532.0 532 80.2040 2721 3460 1 chr6A.!!$R1 739
7 TraesCS2A01G342000 chr5B 710277685 710279980 2295 True 1022.5 1175 85.9960 512 2589 2 chr5B.!!$R1 2077
8 TraesCS2A01G342000 chr7A 299285152 299286031 879 False 773.5 907 98.2365 1 3826 2 chr7A.!!$F2 3825
9 TraesCS2A01G342000 chr7A 545659505 545660382 877 True 770.0 891 98.2125 1 3826 2 chr7A.!!$R2 3825
10 TraesCS2A01G342000 chr7A 95929031 95929865 834 True 678.5 723 97.8200 1 3826 2 chr7A.!!$R1 3825
11 TraesCS2A01G342000 chr7A 232502057 232502818 761 False 525.0 525 80.0770 2721 3456 1 chr7A.!!$F1 735
12 TraesCS2A01G342000 chr5D 33932992 33933731 739 True 869.0 869 88.0380 1991 2724 1 chr5D.!!$R1 733
13 TraesCS2A01G342000 chr2D 9358983 9359722 739 True 841.0 841 87.3660 1991 2724 1 chr2D.!!$R1 733
14 TraesCS2A01G342000 chr2D 649920318 649921062 744 False 678.0 678 83.5760 2721 3454 1 chr2D.!!$F1 733
15 TraesCS2A01G342000 chr2D 495246331 495247045 714 True 538.0 538 80.7850 2738 3457 1 chr2D.!!$R2 719
16 TraesCS2A01G342000 chr6D 75798701 75799440 739 True 830.0 830 87.0970 1991 2724 1 chr6D.!!$R1 733
17 TraesCS2A01G342000 chr3B 72587872 72588611 739 True 813.0 813 86.7290 1991 2724 1 chr3B.!!$R1 733
18 TraesCS2A01G342000 chr3B 767758070 767758813 743 True 520.0 520 80.0790 2733 3456 1 chr3B.!!$R2 723
19 TraesCS2A01G342000 chr3D 563813573 563814311 738 False 811.0 811 86.6940 1991 2724 1 chr3D.!!$F1 733
20 TraesCS2A01G342000 chr1B 2245741 2246454 713 False 793.0 793 86.8780 1991 2705 1 chr1B.!!$F1 714
21 TraesCS2A01G342000 chr2B 424020004 424020884 880 False 598.0 704 90.8810 1 3826 2 chr2B.!!$F3 3825
22 TraesCS2A01G342000 chr2B 134504304 134505009 705 False 593.0 593 82.2160 2740 3456 1 chr2B.!!$F2 716
23 TraesCS2A01G342000 chr2B 6099826 6100357 531 False 388.0 388 80.4070 2930 3453 1 chr2B.!!$F1 523
24 TraesCS2A01G342000 chr7D 594003312 594004097 785 True 643.0 643 82.4430 2721 3458 1 chr7D.!!$R1 737
25 TraesCS2A01G342000 chr7B 641891751 641892512 761 False 619.0 619 82.1010 2721 3456 1 chr7B.!!$F1 735
26 TraesCS2A01G342000 chr6B 8460117 8460656 539 False 448.0 448 82.1300 2739 3277 1 chr6B.!!$F1 538

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
630 635 0.098200 CTTCACGACGACCAGCGATA 59.902 55.000 0.00 0.0 44.57 2.92 F
1349 1389 1.505807 CAAATCGATGGTGGCGCAA 59.494 52.632 10.83 0.0 0.00 4.85 F
1644 1696 7.636150 ACTAATGCTATCTGCTTTGTCAATT 57.364 32.000 0.00 0.0 43.37 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2216 3.687125 AGTACGATGAGTCAGTCCTTCA 58.313 45.455 0.00 0.0 0.00 3.02 R
2233 2497 4.901197 TGCTGTCAAGTTTCCATACCTA 57.099 40.909 0.00 0.0 0.00 3.08 R
3568 3937 6.143551 TGGCTGGGTGATTGATCAATATAT 57.856 37.500 20.75 0.0 38.75 0.86 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
108 110 5.478679 CCCACCAACACAAAATTAGTCCATA 59.521 40.000 0.00 0.0 0.00 2.74
110 112 7.437748 CCACCAACACAAAATTAGTCCATAAA 58.562 34.615 0.00 0.0 0.00 1.40
509 511 6.974622 GCCACATGAAATAACACCAGATAAAG 59.025 38.462 0.00 0.0 0.00 1.85
510 512 6.974622 CCACATGAAATAACACCAGATAAAGC 59.025 38.462 0.00 0.0 0.00 3.51
580 585 1.014352 CGTTAGCAGTACAATGGGCC 58.986 55.000 0.00 0.0 0.00 5.80
630 635 0.098200 CTTCACGACGACCAGCGATA 59.902 55.000 0.00 0.0 44.57 2.92
892 900 5.350365 GGAACATCGTAGCAACATACAAGAA 59.650 40.000 0.00 0.0 0.00 2.52
1129 1168 8.566260 CAAAGAAATTAGATCCATCCAGCTTAG 58.434 37.037 0.00 0.0 0.00 2.18
1173 1212 2.481952 GACATCTTGGTGCTCTTGTGTC 59.518 50.000 0.00 0.0 0.00 3.67
1349 1389 1.505807 CAAATCGATGGTGGCGCAA 59.494 52.632 10.83 0.0 0.00 4.85
1644 1696 7.636150 ACTAATGCTATCTGCTTTGTCAATT 57.364 32.000 0.00 0.0 43.37 2.32
1968 2216 9.171877 ACAATTTTTGGTTGTTGTAATTCACAT 57.828 25.926 0.00 0.0 36.44 3.21
2485 2756 5.769484 TCAAGTATCTTCTACGGGATGAC 57.231 43.478 0.00 0.0 32.18 3.06
3568 3937 5.185056 GGCTTTCCTAAAAGAAGTTGCCATA 59.815 40.000 2.21 0.0 43.90 2.74
3802 4171 4.016444 GTCCATGCCTCCAAAATCAACTA 58.984 43.478 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 112 6.107901 TGTGGCTTATTTTGGTAGCATTTT 57.892 33.333 0.00 0.0 36.64 1.82
509 511 5.890424 TGGCCTAATTTTTAGTAGTGTGC 57.110 39.130 3.32 0.0 0.00 4.57
510 512 7.624360 TGATGGCCTAATTTTTAGTAGTGTG 57.376 36.000 3.32 0.0 0.00 3.82
580 585 0.029300 CAAAGTTGGACGTGTGGCTG 59.971 55.000 0.00 0.0 0.00 4.85
630 635 5.123805 ACGTTAAAAATAACAACGGGCAT 57.876 34.783 10.38 0.0 46.93 4.40
892 900 5.212745 CCTTCTATGAACTTAGGGAGAGGT 58.787 45.833 0.00 0.0 0.00 3.85
1129 1168 0.734889 CCTGGTCGATTCCATTGCAC 59.265 55.000 0.00 0.0 36.84 4.57
1173 1212 2.202932 CAGCGACGAAGGGGATGG 60.203 66.667 0.00 0.0 0.00 3.51
1349 1389 4.348486 TCAGATCTCAAGCTAACCTCACT 58.652 43.478 0.00 0.0 0.00 3.41
1394 1446 4.553323 GACTGTACGCTTACCTCTGAAAA 58.447 43.478 0.00 0.0 0.00 2.29
1644 1696 5.816777 TCGCTGTACATGATGAATCATTCAA 59.183 36.000 3.63 0.0 44.70 2.69
1662 1714 8.033038 TCACAGTTAACTTCTATTTATCGCTGT 58.967 33.333 5.07 0.0 33.32 4.40
1968 2216 3.687125 AGTACGATGAGTCAGTCCTTCA 58.313 45.455 0.00 0.0 0.00 3.02
2233 2497 4.901197 TGCTGTCAAGTTTCCATACCTA 57.099 40.909 0.00 0.0 0.00 3.08
3568 3937 6.143551 TGGCTGGGTGATTGATCAATATAT 57.856 37.500 20.75 0.0 38.75 0.86


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

AutoCloner maintained by Alex Coulton.