Multiple sequence alignment - TraesCS5A01G027600

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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 TraesCS5A01G027600 chr5A 100.000 3485 0 0 1 3485 23611561 23608077 0.000000e+00 6436.0
1 TraesCS5A01G027600 chr5A 98.901 910 7 1 2579 3485 483276588 483275679 0.000000e+00 1622.0
2 TraesCS5A01G027600 chr5D 97.984 2580 35 3 1 2578 30617433 30619997 0.000000e+00 4460.0
3 TraesCS5A01G027600 chr3A 96.415 1590 47 5 1 1587 692345338 692346920 0.000000e+00 2612.0
4 TraesCS5A01G027600 chr3A 99.116 905 8 0 2581 3485 91017013 91016109 0.000000e+00 1628.0
5 TraesCS5A01G027600 chr3A 98.681 910 11 1 2576 3485 277503239 277502331 0.000000e+00 1613.0
6 TraesCS5A01G027600 chr3A 94.975 995 50 0 1584 2578 692347223 692348217 0.000000e+00 1561.0
7 TraesCS5A01G027600 chr3A 90.909 99 8 1 853 950 26493779 26493681 7.850000e-27 132.0
8 TraesCS5A01G027600 chr6D 95.424 1617 64 4 1 1615 98090515 98092123 0.000000e+00 2567.0
9 TraesCS5A01G027600 chr6D 89.157 166 18 0 2334 2499 16667595 16667760 1.270000e-49 207.0
10 TraesCS5A01G027600 chr3D 99.224 902 7 0 2584 3485 496780412 496779511 0.000000e+00 1628.0
11 TraesCS5A01G027600 chr3D 93.651 63 4 0 1 63 33324816 33324878 1.030000e-15 95.3
12 TraesCS5A01G027600 chr1D 99.011 910 6 1 2579 3485 223524579 223523670 0.000000e+00 1628.0
13 TraesCS5A01G027600 chr1D 98.900 909 10 0 2577 3485 94050649 94051557 0.000000e+00 1624.0
14 TraesCS5A01G027600 chr1D 98.897 907 10 0 2579 3485 493220713 493219807 0.000000e+00 1620.0
15 TraesCS5A01G027600 chr1D 81.307 979 113 23 1616 2578 407296331 407297255 0.000000e+00 730.0
16 TraesCS5A01G027600 chr1D 91.200 125 11 0 2446 2570 4538335 4538211 1.660000e-38 171.0
17 TraesCS5A01G027600 chr1D 93.651 63 4 0 1 63 484189118 484189180 1.030000e-15 95.3
18 TraesCS5A01G027600 chr2A 98.901 910 7 1 2579 3485 624462226 624463135 0.000000e+00 1622.0
19 TraesCS5A01G027600 chr2A 98.686 913 9 1 2576 3485 19253317 19254229 0.000000e+00 1616.0
20 TraesCS5A01G027600 chr2A 85.098 255 32 3 993 1242 138143510 138143257 4.460000e-64 255.0
21 TraesCS5A01G027600 chr2A 93.056 144 10 0 127 270 509365173 509365030 9.800000e-51 211.0
22 TraesCS5A01G027600 chr3B 88.677 786 68 7 848 1615 672672706 672671924 0.000000e+00 939.0
23 TraesCS5A01G027600 chr3B 91.363 521 45 0 1686 2206 658558488 658557968 0.000000e+00 713.0
24 TraesCS5A01G027600 chr3B 86.312 263 32 3 373 633 747702963 747703223 2.050000e-72 283.0
25 TraesCS5A01G027600 chr3B 92.708 192 14 0 127 318 756654462 756654271 9.530000e-71 278.0
26 TraesCS5A01G027600 chr7A 85.798 683 64 9 953 1615 528294514 528293845 0.000000e+00 693.0
27 TraesCS5A01G027600 chr7A 90.099 101 9 1 850 950 528294703 528294604 2.820000e-26 130.0
28 TraesCS5A01G027600 chr5B 89.787 470 45 3 316 785 562105700 562105234 1.790000e-167 599.0
29 TraesCS5A01G027600 chr5B 91.919 99 7 1 853 950 65100978 65101076 1.690000e-28 137.0
30 TraesCS5A01G027600 chr5B 96.721 61 2 0 792 852 84732015 84731955 6.150000e-18 102.0
31 TraesCS5A01G027600 chr4B 91.315 426 37 0 316 741 527960132 527960557 1.800000e-162 582.0
32 TraesCS5A01G027600 chr4B 86.312 263 33 2 373 633 59873286 59873547 2.050000e-72 283.0
33 TraesCS5A01G027600 chr4B 90.104 192 16 1 127 318 14179412 14179224 2.690000e-61 246.0
34 TraesCS5A01G027600 chr7D 84.669 574 75 10 950 1514 561004951 561004382 8.450000e-156 560.0
35 TraesCS5A01G027600 chr7D 84.864 403 55 5 2181 2578 618033310 618032909 5.420000e-108 401.0
36 TraesCS5A01G027600 chr7D 92.929 99 6 1 853 950 159081320 159081222 3.630000e-30 143.0
37 TraesCS5A01G027600 chr2B 83.394 548 75 10 954 1491 234826355 234826896 8.690000e-136 494.0
38 TraesCS5A01G027600 chr2B 96.721 61 2 0 792 852 613039671 613039611 6.150000e-18 102.0
39 TraesCS5A01G027600 chr7B 86.265 415 54 3 954 1366 608904925 608904512 6.860000e-122 448.0
40 TraesCS5A01G027600 chr7B 87.805 205 23 1 373 575 60366993 60366789 4.500000e-59 239.0
41 TraesCS5A01G027600 chr7B 89.381 113 11 1 1269 1381 197700950 197701061 1.300000e-29 141.0
42 TraesCS5A01G027600 chr1B 79.236 602 71 28 1616 2202 547701776 547702338 1.530000e-98 370.0
43 TraesCS5A01G027600 chr1B 87.778 180 21 1 2334 2513 550223862 550223684 3.520000e-50 209.0
44 TraesCS5A01G027600 chr1B 90.625 64 4 2 136 197 570305928 570305991 2.230000e-12 84.2
45 TraesCS5A01G027600 chr6B 88.889 180 20 0 2334 2513 648198368 648198189 4.530000e-54 222.0
46 TraesCS5A01G027600 chr6B 87.778 180 22 0 2334 2513 563912440 563912261 9.800000e-51 211.0
47 TraesCS5A01G027600 chr2D 94.366 142 8 0 127 268 582153618 582153477 5.860000e-53 219.0
48 TraesCS5A01G027600 chr2D 92.000 125 10 0 2446 2570 220630646 220630770 3.570000e-40 176.0
49 TraesCS5A01G027600 chr2D 91.919 99 7 1 853 950 398665849 398665751 1.690000e-28 137.0
50 TraesCS5A01G027600 chr4A 92.361 144 11 0 127 270 435436975 435437118 4.560000e-49 206.0


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 TraesCS5A01G027600 chr5A 23608077 23611561 3484 True 6436.0 6436 100.0000 1 3485 1 chr5A.!!$R1 3484
1 TraesCS5A01G027600 chr5A 483275679 483276588 909 True 1622.0 1622 98.9010 2579 3485 1 chr5A.!!$R2 906
2 TraesCS5A01G027600 chr5D 30617433 30619997 2564 False 4460.0 4460 97.9840 1 2578 1 chr5D.!!$F1 2577
3 TraesCS5A01G027600 chr3A 692345338 692348217 2879 False 2086.5 2612 95.6950 1 2578 2 chr3A.!!$F1 2577
4 TraesCS5A01G027600 chr3A 91016109 91017013 904 True 1628.0 1628 99.1160 2581 3485 1 chr3A.!!$R2 904
5 TraesCS5A01G027600 chr3A 277502331 277503239 908 True 1613.0 1613 98.6810 2576 3485 1 chr3A.!!$R3 909
6 TraesCS5A01G027600 chr6D 98090515 98092123 1608 False 2567.0 2567 95.4240 1 1615 1 chr6D.!!$F2 1614
7 TraesCS5A01G027600 chr3D 496779511 496780412 901 True 1628.0 1628 99.2240 2584 3485 1 chr3D.!!$R1 901
8 TraesCS5A01G027600 chr1D 223523670 223524579 909 True 1628.0 1628 99.0110 2579 3485 1 chr1D.!!$R2 906
9 TraesCS5A01G027600 chr1D 94050649 94051557 908 False 1624.0 1624 98.9000 2577 3485 1 chr1D.!!$F1 908
10 TraesCS5A01G027600 chr1D 493219807 493220713 906 True 1620.0 1620 98.8970 2579 3485 1 chr1D.!!$R3 906
11 TraesCS5A01G027600 chr1D 407296331 407297255 924 False 730.0 730 81.3070 1616 2578 1 chr1D.!!$F2 962
12 TraesCS5A01G027600 chr2A 624462226 624463135 909 False 1622.0 1622 98.9010 2579 3485 1 chr2A.!!$F2 906
13 TraesCS5A01G027600 chr2A 19253317 19254229 912 False 1616.0 1616 98.6860 2576 3485 1 chr2A.!!$F1 909
14 TraesCS5A01G027600 chr3B 672671924 672672706 782 True 939.0 939 88.6770 848 1615 1 chr3B.!!$R2 767
15 TraesCS5A01G027600 chr3B 658557968 658558488 520 True 713.0 713 91.3630 1686 2206 1 chr3B.!!$R1 520
16 TraesCS5A01G027600 chr7A 528293845 528294703 858 True 411.5 693 87.9485 850 1615 2 chr7A.!!$R1 765
17 TraesCS5A01G027600 chr7D 561004382 561004951 569 True 560.0 560 84.6690 950 1514 1 chr7D.!!$R2 564
18 TraesCS5A01G027600 chr2B 234826355 234826896 541 False 494.0 494 83.3940 954 1491 1 chr2B.!!$F1 537
19 TraesCS5A01G027600 chr1B 547701776 547702338 562 False 370.0 370 79.2360 1616 2202 1 chr1B.!!$F1 586

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
487 488 2.104111 TGTTGAGACATGGAACCGAAGT 59.896 45.455 0.00 0.00 0.0 3.01 F
1089 1197 0.179056 ACGACAACTTGGGTGTCAGG 60.179 55.000 14.71 3.48 33.2 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2107 2.048503 GTCACAGGACCGGGTTCG 60.049 66.667 6.32 0.0 38.12 3.95 R
2957 3423 2.426023 GTGGCCACACGAGGAAGT 59.574 61.111 31.23 0.0 37.94 3.01 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
31 32 9.408648 CTAATATTTCTACTGGGATTTGTGGTT 57.591 33.333 0.00 0.00 0.00 3.67
260 261 4.046286 TGAGGTATGCTCCCATGTTTTT 57.954 40.909 0.00 0.00 32.85 1.94
487 488 2.104111 TGTTGAGACATGGAACCGAAGT 59.896 45.455 0.00 0.00 0.00 3.01
525 526 9.154847 CATCATCATTTTGTCAGACTAAGTGTA 57.845 33.333 16.13 7.21 0.00 2.90
558 559 5.070580 AGGTACTCTATTGGCAACCTCATAC 59.929 44.000 0.00 3.26 31.78 2.39
617 618 7.201145 TCCGTGCTCTTAAGTCAATCTATTAC 58.799 38.462 1.63 0.00 0.00 1.89
1026 1116 1.179152 CATGCATCAGGAAGCCAACA 58.821 50.000 0.00 0.00 0.00 3.33
1048 1153 2.359230 GCCAGAGCTTGAAGGCGT 60.359 61.111 4.30 0.00 37.41 5.68
1049 1154 2.684843 GCCAGAGCTTGAAGGCGTG 61.685 63.158 4.30 0.00 37.41 5.34
1050 1155 2.037136 CCAGAGCTTGAAGGCGTGG 61.037 63.158 0.00 0.00 35.82 4.94
1051 1156 1.004560 CAGAGCTTGAAGGCGTGGA 60.005 57.895 0.00 0.00 37.29 4.02
1052 1157 1.018226 CAGAGCTTGAAGGCGTGGAG 61.018 60.000 0.00 0.00 37.29 3.86
1089 1197 0.179056 ACGACAACTTGGGTGTCAGG 60.179 55.000 14.71 3.48 33.20 3.86
1183 1301 2.079158 ACACATTCAGACTTGCATCCG 58.921 47.619 0.00 0.00 0.00 4.18
1389 1509 6.101997 AGCAGTCTTTTTCTTCCAAAGTTTG 58.898 36.000 8.73 8.73 33.61 2.93
1410 1530 5.471556 TGGCATTGATGTCTGTCAATTTT 57.528 34.783 0.00 0.00 44.23 1.82
1759 2208 2.093658 GGATTGGCTCGAGTTTAGGACA 60.094 50.000 15.13 0.00 0.00 4.02
1830 2279 1.285078 GGCCTTCTACCAGTTTGGGAT 59.715 52.381 0.00 0.00 43.37 3.85
1831 2280 2.508300 GGCCTTCTACCAGTTTGGGATA 59.492 50.000 0.00 0.00 43.37 2.59
1895 2359 2.908351 TCCACTTTAGTTACCAGGGACC 59.092 50.000 0.00 0.00 0.00 4.46
1999 2465 5.598416 CTATGGGAGGAATATATGCGACA 57.402 43.478 0.00 0.00 0.00 4.35
2155 2621 6.761242 TCGTGATATGCCCTATATTGTTATGC 59.239 38.462 0.00 0.00 32.09 3.14
2957 3423 6.018180 CGTATATCATCATTCCGGACTCGATA 60.018 42.308 1.83 7.16 39.00 2.92
2990 3456 1.741706 GCCACACATCCATCTCAACAG 59.258 52.381 0.00 0.00 0.00 3.16
3163 3629 1.143838 CGCCACTTCATCCATCCGA 59.856 57.895 0.00 0.00 0.00 4.55
3473 3948 8.923838 ATATCTCCTTGTATATCCCTTGTGAT 57.076 34.615 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.370104 TGAAACAACCACAAATCCCAGT 58.630 40.909 0.00 0.00 0.00 4.00
31 32 5.705441 AGCTTTGTCCTAATCGATTGAAACA 59.295 36.000 20.87 16.68 0.00 2.83
558 559 6.317140 ACTTGTAATGATAGTTGATGCAGGTG 59.683 38.462 0.00 0.00 0.00 4.00
617 618 4.211164 GGACAAAAGCCTTTGATTTTTCCG 59.789 41.667 14.64 0.00 44.03 4.30
1183 1301 9.620259 ATTCTTTCCATGTTCCTATCTAACTTC 57.380 33.333 0.00 0.00 0.00 3.01
1389 1509 5.472148 TGAAAATTGACAGACATCAATGCC 58.528 37.500 1.94 0.00 46.35 4.40
1410 1530 3.006003 TCGCACACATGTAACTTACCTGA 59.994 43.478 0.00 0.00 0.00 3.86
1447 1567 7.746475 CCGAGATTAAGAAATCAACAACTTGTC 59.254 37.037 0.00 0.00 43.44 3.18
1518 1656 8.847196 ACTGGTATTTTAAAGAGACCAAAAGTC 58.153 33.333 15.00 0.00 46.71 3.01
1662 2107 2.048503 GTCACAGGACCGGGTTCG 60.049 66.667 6.32 0.00 38.12 3.95
1759 2208 2.774234 CCACCCTGATCATGACCTAGTT 59.226 50.000 0.00 0.00 0.00 2.24
1830 2279 6.312141 TCAATTGACTGATCCTGTTCCATA 57.688 37.500 3.38 0.00 0.00 2.74
1831 2280 5.183530 TCAATTGACTGATCCTGTTCCAT 57.816 39.130 3.38 0.00 0.00 3.41
1895 2359 2.485426 AGCCACACATTCAACAATCTCG 59.515 45.455 0.00 0.00 0.00 4.04
1999 2465 5.171339 AGCAACATATCCTGAAGTCAACT 57.829 39.130 0.00 0.00 0.00 3.16
2112 2578 6.918067 TCACGATCATATCCAATCTAACCT 57.082 37.500 0.00 0.00 0.00 3.50
2155 2621 7.384124 CAATGTTAGAACTACGATTCGTCAAG 58.616 38.462 16.10 11.04 41.54 3.02
2957 3423 2.426023 GTGGCCACACGAGGAAGT 59.574 61.111 31.23 0.00 37.94 3.01
2990 3456 3.188786 GTGTGGCGGAGATGCGTC 61.189 66.667 0.00 0.00 35.06 5.19
3163 3629 5.551760 GATGTGAACCATCGAATCAAAGT 57.448 39.130 0.00 0.00 40.60 2.66


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

AutoCloner maintained by Alex Coulton.