Multiple sequence alignment - TraesCS3D01G020900

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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 TraesCS3D01G020900 chr3D 100.000 2873 0 0 1 2873 6990413 6993285 0.000000e+00 5306.0
1 TraesCS3D01G020900 chr3D 95.890 657 23 2 1659 2312 5544737 5545392 0.000000e+00 1061.0
2 TraesCS3D01G020900 chr3B 96.623 2902 67 6 1 2873 8504549 8507448 0.000000e+00 4787.0
3 TraesCS3D01G020900 chr3B 88.581 1734 113 44 654 2309 597427123 597428849 0.000000e+00 2026.0
4 TraesCS3D01G020900 chr3B 91.202 341 23 4 1974 2311 564172727 564173063 9.380000e-125 457.0
5 TraesCS3D01G020900 chr4D 93.077 1690 78 24 654 2310 459191680 459193363 0.000000e+00 2436.0
6 TraesCS3D01G020900 chr4D 86.928 153 19 1 2554 2706 483599819 483599668 1.370000e-38 171.0
7 TraesCS3D01G020900 chr1B 92.499 1693 67 12 655 2308 127026033 127024362 0.000000e+00 2368.0
8 TraesCS3D01G020900 chr1B 82.547 636 80 23 2 613 668080091 668080719 5.450000e-147 531.0
9 TraesCS3D01G020900 chr2D 92.582 1685 60 15 654 2306 631749236 631747585 0.000000e+00 2359.0
10 TraesCS3D01G020900 chr2D 90.476 1365 88 25 654 1982 469107597 469106239 0.000000e+00 1762.0
11 TraesCS3D01G020900 chr2B 95.824 1317 47 6 999 2312 677292569 677293880 0.000000e+00 2121.0
12 TraesCS3D01G020900 chr7B 88.793 1740 103 39 654 2315 551484382 551482657 0.000000e+00 2049.0
13 TraesCS3D01G020900 chr1A 90.896 1340 86 25 673 1982 461966429 461965096 0.000000e+00 1766.0
14 TraesCS3D01G020900 chr1A 94.634 615 30 2 2 613 556599237 556598623 0.000000e+00 950.0
15 TraesCS3D01G020900 chr1A 89.627 723 39 18 654 1346 35563666 35562950 0.000000e+00 887.0
16 TraesCS3D01G020900 chr1A 83.096 633 83 14 2 613 473039481 473040110 3.230000e-154 555.0
17 TraesCS3D01G020900 chr1A 88.010 417 31 6 2306 2706 556598628 556598215 2.590000e-130 475.0
18 TraesCS3D01G020900 chr7A 96.617 1064 30 4 999 2059 48781869 48782929 0.000000e+00 1760.0
19 TraesCS3D01G020900 chr7A 92.182 614 34 9 3 613 688307879 688308481 0.000000e+00 856.0
20 TraesCS3D01G020900 chr7A 96.845 317 9 1 1992 2308 48782925 48783240 1.960000e-146 529.0
21 TraesCS3D01G020900 chr7A 84.583 480 62 8 2 472 645909398 645908922 1.560000e-127 466.0
22 TraesCS3D01G020900 chr7A 84.179 335 13 14 2304 2633 688308475 688308774 3.620000e-74 289.0
23 TraesCS3D01G020900 chr7A 78.365 416 67 11 2306 2705 15683832 15684240 6.150000e-62 248.0
24 TraesCS3D01G020900 chr7A 87.500 120 15 0 2587 2706 7791488 7791607 3.860000e-29 139.0
25 TraesCS3D01G020900 chr7A 87.069 116 15 0 2590 2705 629754945 629754830 6.460000e-27 132.0
26 TraesCS3D01G020900 chrUn 91.369 1286 72 20 733 1982 96553413 96554695 0.000000e+00 1724.0
27 TraesCS3D01G020900 chr2A 89.969 1306 71 26 724 1982 57826331 57827623 0.000000e+00 1631.0
28 TraesCS3D01G020900 chr2A 83.443 610 67 18 32 613 516093221 516092618 1.170000e-148 536.0
29 TraesCS3D01G020900 chr2A 96.405 306 10 1 2003 2308 763971122 763970818 1.190000e-138 503.0
30 TraesCS3D01G020900 chr2A 81.625 283 40 8 2414 2695 516092386 516092115 1.040000e-54 224.0
31 TraesCS3D01G020900 chr7D 91.878 985 60 6 1328 2308 422343534 422344502 0.000000e+00 1358.0
32 TraesCS3D01G020900 chr7D 82.445 638 84 16 2 613 558927709 558928344 1.520000e-147 532.0
33 TraesCS3D01G020900 chr5D 84.038 639 72 15 2 613 43070909 43070274 3.190000e-164 588.0
34 TraesCS3D01G020900 chr5D 81.473 421 59 11 2302 2706 335861391 335861808 7.680000e-86 327.0
35 TraesCS3D01G020900 chr5D 86.076 158 21 1 2554 2710 311930821 311930664 4.920000e-38 169.0
36 TraesCS3D01G020900 chr5D 85.211 142 19 2 2554 2695 538541311 538541450 8.300000e-31 145.0
37 TraesCS3D01G020900 chr5B 83.360 631 78 19 2 613 341553406 341554028 2.500000e-155 558.0
38 TraesCS3D01G020900 chr5B 93.333 45 2 1 2828 2872 635902304 635902347 6.640000e-07 65.8
39 TraesCS3D01G020900 chr5A 83.096 633 83 14 2 613 568705463 568704834 3.230000e-154 555.0
40 TraesCS3D01G020900 chr3A 82.889 637 83 16 2 613 12458833 12458198 1.500000e-152 549.0
41 TraesCS3D01G020900 chr6B 80.492 569 71 23 2 538 227722995 227723555 1.600000e-107 399.0
42 TraesCS3D01G020900 chr4A 92.857 42 3 0 2831 2872 714353577 714353536 8.600000e-06 62.1
43 TraesCS3D01G020900 chr6D 97.059 34 1 0 2839 2872 433936987 433936954 1.110000e-04 58.4


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 TraesCS3D01G020900 chr3D 6990413 6993285 2872 False 5306.0 5306 100.0000 1 2873 1 chr3D.!!$F2 2872
1 TraesCS3D01G020900 chr3D 5544737 5545392 655 False 1061.0 1061 95.8900 1659 2312 1 chr3D.!!$F1 653
2 TraesCS3D01G020900 chr3B 8504549 8507448 2899 False 4787.0 4787 96.6230 1 2873 1 chr3B.!!$F1 2872
3 TraesCS3D01G020900 chr3B 597427123 597428849 1726 False 2026.0 2026 88.5810 654 2309 1 chr3B.!!$F3 1655
4 TraesCS3D01G020900 chr4D 459191680 459193363 1683 False 2436.0 2436 93.0770 654 2310 1 chr4D.!!$F1 1656
5 TraesCS3D01G020900 chr1B 127024362 127026033 1671 True 2368.0 2368 92.4990 655 2308 1 chr1B.!!$R1 1653
6 TraesCS3D01G020900 chr1B 668080091 668080719 628 False 531.0 531 82.5470 2 613 1 chr1B.!!$F1 611
7 TraesCS3D01G020900 chr2D 631747585 631749236 1651 True 2359.0 2359 92.5820 654 2306 1 chr2D.!!$R2 1652
8 TraesCS3D01G020900 chr2D 469106239 469107597 1358 True 1762.0 1762 90.4760 654 1982 1 chr2D.!!$R1 1328
9 TraesCS3D01G020900 chr2B 677292569 677293880 1311 False 2121.0 2121 95.8240 999 2312 1 chr2B.!!$F1 1313
10 TraesCS3D01G020900 chr7B 551482657 551484382 1725 True 2049.0 2049 88.7930 654 2315 1 chr7B.!!$R1 1661
11 TraesCS3D01G020900 chr1A 461965096 461966429 1333 True 1766.0 1766 90.8960 673 1982 1 chr1A.!!$R2 1309
12 TraesCS3D01G020900 chr1A 35562950 35563666 716 True 887.0 887 89.6270 654 1346 1 chr1A.!!$R1 692
13 TraesCS3D01G020900 chr1A 556598215 556599237 1022 True 712.5 950 91.3220 2 2706 2 chr1A.!!$R3 2704
14 TraesCS3D01G020900 chr1A 473039481 473040110 629 False 555.0 555 83.0960 2 613 1 chr1A.!!$F1 611
15 TraesCS3D01G020900 chr7A 48781869 48783240 1371 False 1144.5 1760 96.7310 999 2308 2 chr7A.!!$F3 1309
16 TraesCS3D01G020900 chr7A 688307879 688308774 895 False 572.5 856 88.1805 3 2633 2 chr7A.!!$F4 2630
17 TraesCS3D01G020900 chrUn 96553413 96554695 1282 False 1724.0 1724 91.3690 733 1982 1 chrUn.!!$F1 1249
18 TraesCS3D01G020900 chr2A 57826331 57827623 1292 False 1631.0 1631 89.9690 724 1982 1 chr2A.!!$F1 1258
19 TraesCS3D01G020900 chr2A 516092115 516093221 1106 True 380.0 536 82.5340 32 2695 2 chr2A.!!$R2 2663
20 TraesCS3D01G020900 chr7D 422343534 422344502 968 False 1358.0 1358 91.8780 1328 2308 1 chr7D.!!$F1 980
21 TraesCS3D01G020900 chr7D 558927709 558928344 635 False 532.0 532 82.4450 2 613 1 chr7D.!!$F2 611
22 TraesCS3D01G020900 chr5D 43070274 43070909 635 True 588.0 588 84.0380 2 613 1 chr5D.!!$R1 611
23 TraesCS3D01G020900 chr5B 341553406 341554028 622 False 558.0 558 83.3600 2 613 1 chr5B.!!$F1 611
24 TraesCS3D01G020900 chr5A 568704834 568705463 629 True 555.0 555 83.0960 2 613 1 chr5A.!!$R1 611
25 TraesCS3D01G020900 chr3A 12458198 12458833 635 True 549.0 549 82.8890 2 613 1 chr3A.!!$R1 611
26 TraesCS3D01G020900 chr6B 227722995 227723555 560 False 399.0 399 80.4920 2 538 1 chr6B.!!$F1 536

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
648 708 0.961019 GTCACCAGCTGGAATTTGCA 59.039 50.0 39.19 13.32 38.94 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2777 0.81441 TTGCAGAAACGCCAACGGTA 60.814 50.0 0.0 0.0 39.25 4.02 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
627 687 1.071071 CCTTAGGGTGTGTTCGGTTGA 59.929 52.381 0.00 0.00 0.00 3.18
648 708 0.961019 GTCACCAGCTGGAATTTGCA 59.039 50.000 39.19 13.32 38.94 4.08
1518 1635 4.743057 TGACGTTGATGATGAGGAGAAT 57.257 40.909 0.00 0.00 0.00 2.40
1522 1639 3.558829 CGTTGATGATGAGGAGAATGGTG 59.441 47.826 0.00 0.00 0.00 4.17
1998 2152 3.266510 TGTGAGAGACATGTATTGGCC 57.733 47.619 0.00 0.00 31.49 5.36
2431 2680 5.638530 TCCTGCCCAATATATGTACAACA 57.361 39.130 0.00 0.00 0.00 3.33
2546 2833 1.072173 TGCACTAGCCACAGACAATGT 59.928 47.619 0.00 0.00 40.18 2.71
2847 3265 1.594129 AGTACTACTCCCTCCGTCCT 58.406 55.000 0.00 0.00 0.00 3.85
2855 3273 2.167900 ACTCCCTCCGTCCTAAAATTCG 59.832 50.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
627 687 1.547372 GCAAATTCCAGCTGGTGACAT 59.453 47.619 31.58 16.52 41.51 3.06
648 708 1.276989 CTGCCCAGCCATCAAAATGTT 59.723 47.619 0.00 0.00 0.00 2.71
1111 1209 2.975410 TCTCATTCAAAACAGCAGCG 57.025 45.000 0.00 0.00 0.00 5.18
1518 1635 1.191489 TCTCGCCATTCACCTCACCA 61.191 55.000 0.00 0.00 0.00 4.17
1522 1639 1.936547 GTTGATCTCGCCATTCACCTC 59.063 52.381 0.00 0.00 0.00 3.85
1998 2152 1.067706 TGGCACATCCAAAAGCAATCG 60.068 47.619 0.00 0.00 43.21 3.34
2373 2621 2.815478 CCAGTTCTAATCAGCGACCTC 58.185 52.381 0.00 0.00 0.00 3.85
2431 2680 2.283824 GGTCCACCCGTCAGTGTAT 58.716 57.895 0.00 0.00 35.93 2.29
2493 2777 0.814410 TTGCAGAAACGCCAACGGTA 60.814 50.000 0.00 0.00 39.25 4.02
2729 3147 6.945938 TTTGAAATTTTACTGAACTCCCGA 57.054 33.333 0.00 0.00 0.00 5.14
2810 3228 4.929808 AGTACTTTTGAACTGGCATCTACG 59.070 41.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.