Multiple sequence alignment - TraesCS3D01G058000

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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 TraesCS3D01G058000 chr3D 100.000 2696 0 0 1 2696 24172346 24169651 0.000000e+00 4979.0
1 TraesCS3D01G058000 chr3D 93.031 861 49 8 176 1034 136756841 136757692 0.000000e+00 1247.0
2 TraesCS3D01G058000 chrUn 99.427 1570 9 0 1031 2600 93411669 93413238 0.000000e+00 2850.0
3 TraesCS3D01G058000 chrUn 99.614 1035 3 1 1 1034 44705818 44704784 0.000000e+00 1888.0
4 TraesCS3D01G058000 chrUn 92.567 861 52 7 176 1034 91550678 91551528 0.000000e+00 1225.0
5 TraesCS3D01G058000 chrUn 98.165 109 1 1 2588 2696 403668523 403668416 3.540000e-44 189.0
6 TraesCS3D01G058000 chrUn 98.165 109 1 1 2588 2696 455370227 455370120 3.540000e-44 189.0
7 TraesCS3D01G058000 chr2D 99.363 1571 7 3 1031 2600 635584591 635586159 0.000000e+00 2843.0
8 TraesCS3D01G058000 chr2D 98.600 1571 18 4 1031 2600 272795930 272797497 0.000000e+00 2776.0
9 TraesCS3D01G058000 chr2D 92.991 856 50 6 183 1034 108914804 108915653 0.000000e+00 1240.0
10 TraesCS3D01G058000 chr2D 98.165 109 1 1 2588 2696 272797116 272797009 3.540000e-44 189.0
11 TraesCS3D01G058000 chr2D 93.103 58 4 0 8 65 133052921 133052864 4.780000e-13 86.1
12 TraesCS3D01G058000 chr5D 99.045 1571 12 3 1031 2600 503216181 503214613 0.000000e+00 2815.0
13 TraesCS3D01G058000 chr5D 98.165 109 1 1 2588 2696 329123325 329123218 3.540000e-44 189.0
14 TraesCS3D01G058000 chr5D 98.165 109 1 1 2588 2696 503214996 503215103 3.540000e-44 189.0
15 TraesCS3D01G058000 chr5D 96.825 63 2 0 3 65 488189988 488189926 3.670000e-19 106.0
16 TraesCS3D01G058000 chr3B 98.791 1571 16 2 1031 2600 201524973 201523405 0.000000e+00 2793.0
17 TraesCS3D01G058000 chr6D 98.664 1572 16 3 1031 2600 168249502 168247934 0.000000e+00 2782.0
18 TraesCS3D01G058000 chr6D 98.165 109 1 1 2588 2696 168248318 168248425 3.540000e-44 189.0
19 TraesCS3D01G058000 chr6D 96.825 63 2 0 1 63 436726690 436726628 3.670000e-19 106.0
20 TraesCS3D01G058000 chr3A 98.217 1570 25 3 1031 2600 672912046 672913612 0.000000e+00 2741.0
21 TraesCS3D01G058000 chr4D 97.962 1570 27 5 1032 2600 19926759 19925194 0.000000e+00 2717.0
22 TraesCS3D01G058000 chr6A 97.774 1572 30 4 1031 2600 260118318 260119886 0.000000e+00 2704.0
23 TraesCS3D01G058000 chr6A 98.165 109 1 1 2588 2696 271186551 271186658 3.540000e-44 189.0
24 TraesCS3D01G058000 chr6B 93.224 856 47 10 184 1034 667789680 667788831 0.000000e+00 1249.0
25 TraesCS3D01G058000 chr5B 93.811 824 46 5 214 1034 166633846 166633025 0.000000e+00 1234.0
26 TraesCS3D01G058000 chr5B 92.424 66 3 2 1 65 669447742 669447678 2.860000e-15 93.5
27 TraesCS3D01G058000 chr7D 92.415 857 55 5 183 1034 43239732 43238881 0.000000e+00 1214.0
28 TraesCS3D01G058000 chr5A 93.604 813 49 3 221 1032 425541766 425542576 0.000000e+00 1210.0
29 TraesCS3D01G058000 chr4B 92.479 851 57 7 187 1034 286081559 286082405 0.000000e+00 1210.0
30 TraesCS3D01G058000 chr1D 98.165 109 1 1 2588 2696 459901148 459901041 3.540000e-44 189.0
31 TraesCS3D01G058000 chr1D 92.063 63 4 1 3 65 454204735 454204674 1.330000e-13 87.9
32 TraesCS3D01G058000 chr1A 98.165 109 1 1 2588 2696 584780222 584780329 3.540000e-44 189.0
33 TraesCS3D01G058000 chr7A 92.424 66 3 2 1 65 566981706 566981642 2.860000e-15 93.5
34 TraesCS3D01G058000 chr1B 92.063 63 4 1 3 65 624716566 624716505 1.330000e-13 87.9


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 TraesCS3D01G058000 chr3D 24169651 24172346 2695 True 4979 4979 100.000 1 2696 1 chr3D.!!$R1 2695
1 TraesCS3D01G058000 chr3D 136756841 136757692 851 False 1247 1247 93.031 176 1034 1 chr3D.!!$F1 858
2 TraesCS3D01G058000 chrUn 93411669 93413238 1569 False 2850 2850 99.427 1031 2600 1 chrUn.!!$F2 1569
3 TraesCS3D01G058000 chrUn 44704784 44705818 1034 True 1888 1888 99.614 1 1034 1 chrUn.!!$R1 1033
4 TraesCS3D01G058000 chrUn 91550678 91551528 850 False 1225 1225 92.567 176 1034 1 chrUn.!!$F1 858
5 TraesCS3D01G058000 chr2D 635584591 635586159 1568 False 2843 2843 99.363 1031 2600 1 chr2D.!!$F3 1569
6 TraesCS3D01G058000 chr2D 272795930 272797497 1567 False 2776 2776 98.600 1031 2600 1 chr2D.!!$F2 1569
7 TraesCS3D01G058000 chr2D 108914804 108915653 849 False 1240 1240 92.991 183 1034 1 chr2D.!!$F1 851
8 TraesCS3D01G058000 chr5D 503214613 503216181 1568 True 2815 2815 99.045 1031 2600 1 chr5D.!!$R3 1569
9 TraesCS3D01G058000 chr3B 201523405 201524973 1568 True 2793 2793 98.791 1031 2600 1 chr3B.!!$R1 1569
10 TraesCS3D01G058000 chr6D 168247934 168249502 1568 True 2782 2782 98.664 1031 2600 1 chr6D.!!$R1 1569
11 TraesCS3D01G058000 chr3A 672912046 672913612 1566 False 2741 2741 98.217 1031 2600 1 chr3A.!!$F1 1569
12 TraesCS3D01G058000 chr4D 19925194 19926759 1565 True 2717 2717 97.962 1032 2600 1 chr4D.!!$R1 1568
13 TraesCS3D01G058000 chr6A 260118318 260119886 1568 False 2704 2704 97.774 1031 2600 1 chr6A.!!$F1 1569
14 TraesCS3D01G058000 chr6B 667788831 667789680 849 True 1249 1249 93.224 184 1034 1 chr6B.!!$R1 850
15 TraesCS3D01G058000 chr5B 166633025 166633846 821 True 1234 1234 93.811 214 1034 1 chr5B.!!$R1 820
16 TraesCS3D01G058000 chr7D 43238881 43239732 851 True 1214 1214 92.415 183 1034 1 chr7D.!!$R1 851
17 TraesCS3D01G058000 chr5A 425541766 425542576 810 False 1210 1210 93.604 221 1032 1 chr5A.!!$F1 811
18 TraesCS3D01G058000 chr4B 286081559 286082405 846 False 1210 1210 92.479 187 1034 1 chr4B.!!$F1 847

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
432 437 3.371898 TCACACTGCTGAATTATCTTGCG 59.628 43.478 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 2633 6.964807 AGGCAATGTGATAAAGCATCAATA 57.035 33.333 0.0 0.0 45.28 1.9 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
432 437 3.371898 TCACACTGCTGAATTATCTTGCG 59.628 43.478 0.00 0.0 0.00 4.85
669 677 6.379133 ACATATGCAAAATTCAGGTGTCATCT 59.621 34.615 1.58 0.0 0.00 2.90
1264 1275 6.183360 CCAAAAAGAAATCGATACGATCCACA 60.183 38.462 0.00 0.0 46.30 4.17
2633 2655 9.865321 ATTATATTGATGCTTTATCACATTGCC 57.135 29.630 0.00 0.0 45.22 4.52
2634 2656 5.864418 ATTGATGCTTTATCACATTGCCT 57.136 34.783 0.00 0.0 45.22 4.75
2635 2657 5.664294 TTGATGCTTTATCACATTGCCTT 57.336 34.783 0.00 0.0 45.22 4.35
2636 2658 5.664294 TGATGCTTTATCACATTGCCTTT 57.336 34.783 0.00 0.0 40.82 3.11
2637 2659 6.040209 TGATGCTTTATCACATTGCCTTTT 57.960 33.333 0.00 0.0 40.82 2.27
2638 2660 7.167924 TGATGCTTTATCACATTGCCTTTTA 57.832 32.000 0.00 0.0 40.82 1.52
2639 2661 7.784037 TGATGCTTTATCACATTGCCTTTTAT 58.216 30.769 0.00 0.0 40.82 1.40
2640 2662 7.707464 TGATGCTTTATCACATTGCCTTTTATG 59.293 33.333 0.00 0.0 40.82 1.90
2641 2663 7.167924 TGCTTTATCACATTGCCTTTTATGA 57.832 32.000 0.00 0.0 0.00 2.15
2642 2664 7.784037 TGCTTTATCACATTGCCTTTTATGAT 58.216 30.769 0.00 0.0 0.00 2.45
2643 2665 7.707464 TGCTTTATCACATTGCCTTTTATGATG 59.293 33.333 0.00 0.0 0.00 3.07
2644 2666 7.707893 GCTTTATCACATTGCCTTTTATGATGT 59.292 33.333 0.00 0.0 0.00 3.06
2649 2671 9.754382 ATCACATTGCCTTTTATGATGTAATTC 57.246 29.630 0.00 0.0 30.39 2.17
2650 2672 8.747471 TCACATTGCCTTTTATGATGTAATTCA 58.253 29.630 0.00 0.0 30.39 2.57
2651 2673 9.537192 CACATTGCCTTTTATGATGTAATTCAT 57.463 29.630 0.00 0.0 39.60 2.57
2656 2678 9.066892 TGCCTTTTATGATGTAATTCATAGACC 57.933 33.333 0.00 0.0 39.20 3.85
2657 2679 9.066892 GCCTTTTATGATGTAATTCATAGACCA 57.933 33.333 0.00 0.0 39.20 4.02
2668 2690 9.374711 TGTAATTCATAGACCATACATAGTGGA 57.625 33.333 0.00 0.0 39.12 4.02
2671 2693 9.950496 AATTCATAGACCATACATAGTGGAATC 57.050 33.333 0.00 0.0 39.12 2.52
2672 2694 7.482169 TCATAGACCATACATAGTGGAATCC 57.518 40.000 0.00 0.0 39.12 3.01
2673 2695 7.248976 TCATAGACCATACATAGTGGAATCCT 58.751 38.462 0.00 0.0 39.12 3.24
2674 2696 8.398743 TCATAGACCATACATAGTGGAATCCTA 58.601 37.037 0.00 0.0 39.12 2.94
2675 2697 9.206690 CATAGACCATACATAGTGGAATCCTAT 57.793 37.037 0.00 0.0 39.12 2.57
2678 2700 9.427821 AGACCATACATAGTGGAATCCTATATC 57.572 37.037 0.00 0.0 39.12 1.63
2679 2701 9.427821 GACCATACATAGTGGAATCCTATATCT 57.572 37.037 0.00 0.0 39.12 1.98
2680 2702 9.790297 ACCATACATAGTGGAATCCTATATCTT 57.210 33.333 0.00 0.0 39.12 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
669 677 9.844790 CATTAGTGTGAATCTCAAATTGCTAAA 57.155 29.630 0.00 0.0 0.00 1.85
2607 2629 9.865321 GGCAATGTGATAAAGCATCAATATAAT 57.135 29.630 0.00 0.0 45.28 1.28
2608 2630 9.081204 AGGCAATGTGATAAAGCATCAATATAA 57.919 29.630 0.00 0.0 45.28 0.98
2609 2631 8.640063 AGGCAATGTGATAAAGCATCAATATA 57.360 30.769 0.00 0.0 45.28 0.86
2610 2632 7.534723 AGGCAATGTGATAAAGCATCAATAT 57.465 32.000 0.00 0.0 45.28 1.28
2611 2633 6.964807 AGGCAATGTGATAAAGCATCAATA 57.035 33.333 0.00 0.0 45.28 1.90
2612 2634 5.864418 AGGCAATGTGATAAAGCATCAAT 57.136 34.783 0.00 0.0 45.28 2.57
2613 2635 5.664294 AAGGCAATGTGATAAAGCATCAA 57.336 34.783 0.00 0.0 45.28 2.57
2614 2636 5.664294 AAAGGCAATGTGATAAAGCATCA 57.336 34.783 0.00 0.0 41.52 3.07
2615 2637 7.922278 TCATAAAAGGCAATGTGATAAAGCATC 59.078 33.333 0.00 0.0 0.00 3.91
2616 2638 7.784037 TCATAAAAGGCAATGTGATAAAGCAT 58.216 30.769 0.00 0.0 0.00 3.79
2617 2639 7.167924 TCATAAAAGGCAATGTGATAAAGCA 57.832 32.000 0.00 0.0 0.00 3.91
2618 2640 7.707893 ACATCATAAAAGGCAATGTGATAAAGC 59.292 33.333 0.00 0.0 0.00 3.51
2623 2645 9.754382 GAATTACATCATAAAAGGCAATGTGAT 57.246 29.630 0.00 0.0 33.01 3.06
2624 2646 8.747471 TGAATTACATCATAAAAGGCAATGTGA 58.253 29.630 0.00 0.0 33.01 3.58
2625 2647 8.929827 TGAATTACATCATAAAAGGCAATGTG 57.070 30.769 0.00 0.0 33.01 3.21
2630 2652 9.066892 GGTCTATGAATTACATCATAAAAGGCA 57.933 33.333 0.00 0.0 40.71 4.75
2631 2653 9.066892 TGGTCTATGAATTACATCATAAAAGGC 57.933 33.333 0.00 0.0 40.71 4.35
2642 2664 9.374711 TCCACTATGTATGGTCTATGAATTACA 57.625 33.333 0.00 0.0 38.47 2.41
2645 2667 9.950496 GATTCCACTATGTATGGTCTATGAATT 57.050 33.333 0.00 0.0 38.47 2.17
2646 2668 8.543774 GGATTCCACTATGTATGGTCTATGAAT 58.456 37.037 0.00 0.0 38.47 2.57
2647 2669 7.734865 AGGATTCCACTATGTATGGTCTATGAA 59.265 37.037 5.29 0.0 38.47 2.57
2648 2670 7.248976 AGGATTCCACTATGTATGGTCTATGA 58.751 38.462 5.29 0.0 38.47 2.15
2649 2671 7.487822 AGGATTCCACTATGTATGGTCTATG 57.512 40.000 5.29 0.0 38.47 2.23
2652 2674 9.427821 GATATAGGATTCCACTATGTATGGTCT 57.572 37.037 5.29 0.0 38.47 3.85
2653 2675 9.427821 AGATATAGGATTCCACTATGTATGGTC 57.572 37.037 5.29 0.0 38.47 4.02
2654 2676 9.790297 AAGATATAGGATTCCACTATGTATGGT 57.210 33.333 5.29 0.0 38.47 3.55


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

AutoCloner maintained by Alex Coulton.