Multiple sequence alignment - TraesCS3D01G432400

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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 TraesCS3D01G432400 chr3D 100.000 2607 0 0 1 2607 546203982 546201376 0.000000e+00 4815
1 TraesCS3D01G432400 chr3D 86.882 526 59 5 1 522 321947563 321947044 4.840000e-162 580
2 TraesCS3D01G432400 chr7D 95.764 1936 53 8 698 2604 95858552 95860487 0.000000e+00 3094
3 TraesCS3D01G432400 chr7D 83.502 594 86 8 1 584 552926801 552926210 6.350000e-151 544
4 TraesCS3D01G432400 chr7D 83.178 214 19 8 2393 2589 95860799 95861012 2.060000e-41 180
5 TraesCS3D01G432400 chr7D 81.667 180 25 6 2394 2567 636487638 636487815 2.700000e-30 143
6 TraesCS3D01G432400 chr1D 95.713 1936 56 8 698 2607 331879936 331881870 0.000000e+00 3090
7 TraesCS3D01G432400 chr1D 97.247 1816 42 6 742 2553 249755948 249757759 0.000000e+00 3070
8 TraesCS3D01G432400 chr1D 83.616 177 24 4 2434 2607 249757685 249757859 7.470000e-36 161
9 TraesCS3D01G432400 chr7A 94.015 1654 77 13 695 2330 51670404 51668755 0.000000e+00 2486
10 TraesCS3D01G432400 chr7A 87.619 315 16 6 2316 2607 51668719 51668405 6.910000e-91 344
11 TraesCS3D01G432400 chr5D 97.366 1291 29 4 1268 2553 481131154 481129864 0.000000e+00 2191
12 TraesCS3D01G432400 chr5D 82.039 206 26 7 2405 2607 481129961 481129764 5.770000e-37 165
13 TraesCS3D01G432400 chr3B 95.122 656 30 2 1 655 722593061 722592407 0.000000e+00 1033
14 TraesCS3D01G432400 chr3B 85.069 576 71 8 1 567 579456833 579456264 8.090000e-160 573
15 TraesCS3D01G432400 chr3A 90.476 714 47 4 1 698 682480844 682480136 0.000000e+00 922
16 TraesCS3D01G432400 chr6D 85.763 590 71 8 11 588 364097945 364097357 1.710000e-171 612
17 TraesCS3D01G432400 chr6D 84.337 581 75 10 1 568 350559184 350558607 2.930000e-154 555
18 TraesCS3D01G432400 chr6D 81.553 206 27 8 2369 2566 148163639 148163841 2.690000e-35 159
19 TraesCS3D01G432400 chr6D 80.000 225 30 8 2357 2567 80063985 80063762 4.490000e-33 152
20 TraesCS3D01G432400 chr5B 84.087 597 80 10 1 586 442366919 442366327 1.750000e-156 562
21 TraesCS3D01G432400 chr5A 83.866 595 83 9 1 584 17015709 17015117 2.930000e-154 555


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 TraesCS3D01G432400 chr3D 546201376 546203982 2606 True 4815.0 4815 100.0000 1 2607 1 chr3D.!!$R2 2606
1 TraesCS3D01G432400 chr3D 321947044 321947563 519 True 580.0 580 86.8820 1 522 1 chr3D.!!$R1 521
2 TraesCS3D01G432400 chr7D 95858552 95861012 2460 False 1637.0 3094 89.4710 698 2604 2 chr7D.!!$F2 1906
3 TraesCS3D01G432400 chr7D 552926210 552926801 591 True 544.0 544 83.5020 1 584 1 chr7D.!!$R1 583
4 TraesCS3D01G432400 chr1D 331879936 331881870 1934 False 3090.0 3090 95.7130 698 2607 1 chr1D.!!$F1 1909
5 TraesCS3D01G432400 chr1D 249755948 249757859 1911 False 1615.5 3070 90.4315 742 2607 2 chr1D.!!$F2 1865
6 TraesCS3D01G432400 chr7A 51668405 51670404 1999 True 1415.0 2486 90.8170 695 2607 2 chr7A.!!$R1 1912
7 TraesCS3D01G432400 chr5D 481129764 481131154 1390 True 1178.0 2191 89.7025 1268 2607 2 chr5D.!!$R1 1339
8 TraesCS3D01G432400 chr3B 722592407 722593061 654 True 1033.0 1033 95.1220 1 655 1 chr3B.!!$R2 654
9 TraesCS3D01G432400 chr3B 579456264 579456833 569 True 573.0 573 85.0690 1 567 1 chr3B.!!$R1 566
10 TraesCS3D01G432400 chr3A 682480136 682480844 708 True 922.0 922 90.4760 1 698 1 chr3A.!!$R1 697
11 TraesCS3D01G432400 chr6D 364097357 364097945 588 True 612.0 612 85.7630 11 588 1 chr6D.!!$R3 577
12 TraesCS3D01G432400 chr6D 350558607 350559184 577 True 555.0 555 84.3370 1 568 1 chr6D.!!$R2 567
13 TraesCS3D01G432400 chr5B 442366327 442366919 592 True 562.0 562 84.0870 1 586 1 chr5B.!!$R1 585
14 TraesCS3D01G432400 chr5A 17015117 17015709 592 True 555.0 555 83.8660 1 584 1 chr5A.!!$R1 583

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
935 967 0.250727 CACCCCGACCACACAAATCT 60.251 55.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2618 1.82509 TTTGCCATCATTCGCTCACT 58.175 45.0 0.0 0.0 0.0 3.41 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 36 1.888512 GGGCATTCTGAGTGCTTCAAA 59.111 47.619 21.95 0.00 42.16 2.69
71 74 3.243805 TGTTTGTGGAGTTGCAATGATGG 60.244 43.478 0.59 0.00 0.00 3.51
75 78 2.762327 GTGGAGTTGCAATGATGGGAAT 59.238 45.455 0.59 0.00 0.00 3.01
76 79 3.196254 GTGGAGTTGCAATGATGGGAATT 59.804 43.478 0.59 0.00 0.00 2.17
82 87 6.870769 AGTTGCAATGATGGGAATTAGAAAG 58.129 36.000 0.59 0.00 0.00 2.62
473 487 3.104512 AGTCCGGATTTGAGGTATGTGA 58.895 45.455 7.81 0.00 0.00 3.58
568 584 0.953471 TGACCGGATTTGCCAAGTCG 60.953 55.000 9.46 0.00 40.69 4.18
581 597 1.676006 CCAAGTCGGGATGTAAATGCC 59.324 52.381 0.00 0.00 0.00 4.40
590 606 4.444306 CGGGATGTAAATGCCCTAAAGAGA 60.444 45.833 0.00 0.00 39.79 3.10
659 690 2.957402 TCACCACTTGCCTCTTTGAT 57.043 45.000 0.00 0.00 0.00 2.57
669 700 8.522830 CCACTTGCCTCTTTGATATTTTAGAAA 58.477 33.333 0.00 0.00 0.00 2.52
800 832 2.102070 TGACGTAAATTCGTGGCCAT 57.898 45.000 9.72 0.00 44.21 4.40
811 843 1.819632 GTGGCCATGTCATCGGTCC 60.820 63.158 9.72 0.00 0.00 4.46
910 942 7.613551 TTTCTAGACTAGTCCACTCCTTTTT 57.386 36.000 19.38 0.00 0.00 1.94
935 967 0.250727 CACCCCGACCACACAAATCT 60.251 55.000 0.00 0.00 0.00 2.40
1024 1056 1.401931 CGGTAGTTCGAGAAAGCGGAA 60.402 52.381 6.65 0.00 0.00 4.30
1430 1463 0.391927 TATTCCGTTCACCTTGCGGG 60.392 55.000 0.00 0.00 44.97 6.13
1443 1476 3.948719 GCGGGGGTGTCTTGGTCA 61.949 66.667 0.00 0.00 0.00 4.02
1857 1895 4.587211 TTGTATGGTTTACGATCGCAAC 57.413 40.909 16.60 17.57 0.00 4.17
2142 2194 7.067372 TGGCATCTTCCATAAATGTTTCTACTG 59.933 37.037 0.00 0.00 0.00 2.74
2212 2264 8.649841 CATGGCAACTTTACAAAGATAACAATG 58.350 33.333 8.65 0.00 39.31 2.82
2428 2530 7.376435 GCCATGGCAAATTTACTTTTATTGT 57.624 32.000 32.08 0.00 41.49 2.71
2476 2601 7.722795 AACAACCATGGCAAATTTAGTTAAC 57.277 32.000 13.04 0.00 0.00 2.01
2477 2602 5.923684 ACAACCATGGCAAATTTAGTTAACG 59.076 36.000 13.04 0.00 0.00 3.18
2478 2603 5.968528 ACCATGGCAAATTTAGTTAACGA 57.031 34.783 13.04 0.00 0.00 3.85
2479 2604 6.334102 ACCATGGCAAATTTAGTTAACGAA 57.666 33.333 13.04 0.00 0.00 3.85
2480 2605 6.930731 ACCATGGCAAATTTAGTTAACGAAT 58.069 32.000 13.04 3.59 0.00 3.34
2481 2606 6.811170 ACCATGGCAAATTTAGTTAACGAATG 59.189 34.615 13.04 0.00 0.00 2.67
2482 2607 7.032580 CCATGGCAAATTTAGTTAACGAATGA 58.967 34.615 0.00 0.00 0.00 2.57
2483 2608 7.706179 CCATGGCAAATTTAGTTAACGAATGAT 59.294 33.333 0.00 0.00 0.00 2.45
2484 2609 8.533965 CATGGCAAATTTAGTTAACGAATGATG 58.466 33.333 1.80 9.49 0.00 3.07
2485 2610 7.032580 TGGCAAATTTAGTTAACGAATGATGG 58.967 34.615 1.80 0.17 0.00 3.51
2486 2611 7.033185 GGCAAATTTAGTTAACGAATGATGGT 58.967 34.615 1.80 0.00 0.00 3.55
2487 2612 8.185505 GGCAAATTTAGTTAACGAATGATGGTA 58.814 33.333 1.80 0.00 0.00 3.25
2488 2613 9.562583 GCAAATTTAGTTAACGAATGATGGTAA 57.437 29.630 1.80 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.360801 CACAAACAATTCCCCAACGAGT 59.639 45.455 0.00 0.00 0.00 4.18
71 74 3.426292 GCTGCCACGAACTTTCTAATTCC 60.426 47.826 0.00 0.00 0.00 3.01
75 78 2.143122 CAGCTGCCACGAACTTTCTAA 58.857 47.619 0.00 0.00 0.00 2.10
76 79 1.343142 TCAGCTGCCACGAACTTTCTA 59.657 47.619 9.47 0.00 0.00 2.10
82 87 0.950555 TGTCATCAGCTGCCACGAAC 60.951 55.000 9.47 1.92 0.00 3.95
246 253 3.493877 GCACCTGATGATCTCGAAGATTG 59.506 47.826 0.00 0.00 34.53 2.67
473 487 0.535780 CATATGTCATGCCCGGCAGT 60.536 55.000 18.96 3.38 43.65 4.40
568 584 5.048846 TCTCTTTAGGGCATTTACATCCC 57.951 43.478 0.00 0.00 40.36 3.85
581 597 8.722394 GTGGAGAAAGTGTTTTATCTCTTTAGG 58.278 37.037 0.00 0.00 38.64 2.69
590 606 6.293698 ACCGTTAGTGGAGAAAGTGTTTTAT 58.706 36.000 0.00 0.00 0.00 1.40
659 690 8.856103 GCCTAGCCCATGTTAATTTCTAAAATA 58.144 33.333 0.00 0.00 0.00 1.40
713 745 3.318839 TCTCCTAAAAACCTGACGTTCGA 59.681 43.478 0.00 0.00 31.78 3.71
800 832 1.338107 ACAGTTCAGGACCGATGACA 58.662 50.000 0.00 0.00 0.00 3.58
811 843 0.508641 CGTCCTTGCGAACAGTTCAG 59.491 55.000 13.82 7.33 0.00 3.02
841 873 1.137513 CGCGAGAGAAAAAGGTTCGT 58.862 50.000 0.00 0.00 34.05 3.85
910 942 1.766864 TGTGGTCGGGGTGGAAGAA 60.767 57.895 0.00 0.00 0.00 2.52
935 967 1.488812 CGATCTGGTTGGGGTGGAATA 59.511 52.381 0.00 0.00 0.00 1.75
1024 1056 3.842923 CCAGCATCCTCGAGCGGT 61.843 66.667 6.99 0.00 35.48 5.68
1081 1113 2.815308 CGCCCGCCTCTTAGACAT 59.185 61.111 0.00 0.00 0.00 3.06
1173 1206 1.734477 GCTGCGACTTTCTCGAGCA 60.734 57.895 7.81 0.00 46.14 4.26
1189 1222 2.182791 CACGCATCCTCGAGTGCT 59.817 61.111 21.45 9.37 39.16 4.40
1192 1225 4.498520 CGCCACGCATCCTCGAGT 62.499 66.667 12.31 0.00 0.00 4.18
1430 1463 2.067365 AGGTTTTGACCAAGACACCC 57.933 50.000 5.90 0.00 0.00 4.61
1435 1468 2.223386 CGCGAAAAGGTTTTGACCAAGA 60.223 45.455 0.00 0.00 0.00 3.02
1443 1476 1.566404 CAAAGCCGCGAAAAGGTTTT 58.434 45.000 8.23 0.00 41.76 2.43
1729 1764 4.271696 TGACAACTAAGGATGGACACTG 57.728 45.455 0.00 0.00 0.00 3.66
2142 2194 3.876242 AAATTTGCCATGCGACAAAAC 57.124 38.095 9.80 0.00 39.09 2.43
2428 2530 9.304731 GTTTGCTAATAATTGCAATCATCTTGA 57.695 29.630 13.38 0.00 46.55 3.02
2476 2601 6.019075 TCGCTCACTAAATTTACCATCATTCG 60.019 38.462 0.00 0.00 0.00 3.34
2477 2602 7.246674 TCGCTCACTAAATTTACCATCATTC 57.753 36.000 0.00 0.00 0.00 2.67
2478 2603 7.624360 TTCGCTCACTAAATTTACCATCATT 57.376 32.000 0.00 0.00 0.00 2.57
2479 2604 7.498900 TCATTCGCTCACTAAATTTACCATCAT 59.501 33.333 0.00 0.00 0.00 2.45
2480 2605 6.821160 TCATTCGCTCACTAAATTTACCATCA 59.179 34.615 0.00 0.00 0.00 3.07
2481 2606 7.246674 TCATTCGCTCACTAAATTTACCATC 57.753 36.000 0.00 0.00 0.00 3.51
2482 2607 7.255242 CCATCATTCGCTCACTAAATTTACCAT 60.255 37.037 0.00 0.00 0.00 3.55
2483 2608 6.038161 CCATCATTCGCTCACTAAATTTACCA 59.962 38.462 0.00 0.00 0.00 3.25
2484 2609 6.430451 CCATCATTCGCTCACTAAATTTACC 58.570 40.000 0.00 0.00 0.00 2.85
2485 2610 5.909610 GCCATCATTCGCTCACTAAATTTAC 59.090 40.000 0.00 0.00 0.00 2.01
2486 2611 5.588246 TGCCATCATTCGCTCACTAAATTTA 59.412 36.000 0.00 0.00 0.00 1.40
2487 2612 4.398988 TGCCATCATTCGCTCACTAAATTT 59.601 37.500 0.00 0.00 0.00 1.82
2488 2613 3.947196 TGCCATCATTCGCTCACTAAATT 59.053 39.130 0.00 0.00 0.00 1.82
2489 2614 3.544684 TGCCATCATTCGCTCACTAAAT 58.455 40.909 0.00 0.00 0.00 1.40
2490 2615 2.984562 TGCCATCATTCGCTCACTAAA 58.015 42.857 0.00 0.00 0.00 1.85
2491 2616 2.689553 TGCCATCATTCGCTCACTAA 57.310 45.000 0.00 0.00 0.00 2.24
2492 2617 2.689553 TTGCCATCATTCGCTCACTA 57.310 45.000 0.00 0.00 0.00 2.74
2493 2618 1.825090 TTTGCCATCATTCGCTCACT 58.175 45.000 0.00 0.00 0.00 3.41
2494 2619 2.857592 ATTTGCCATCATTCGCTCAC 57.142 45.000 0.00 0.00 0.00 3.51
2495 2620 3.872511 AAATTTGCCATCATTCGCTCA 57.127 38.095 0.00 0.00 0.00 4.26
2496 2621 4.925068 ACTAAATTTGCCATCATTCGCTC 58.075 39.130 0.00 0.00 0.00 5.03
2497 2622 4.989279 ACTAAATTTGCCATCATTCGCT 57.011 36.364 0.00 0.00 0.00 4.93
2498 2623 6.291060 CGTTAACTAAATTTGCCATCATTCGC 60.291 38.462 3.71 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.