Multiple sequence alignment - TraesCS3A01G522800

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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 TraesCS3A01G522800 chr3A 100.000 4484 0 0 1 4484 738680259 738675776 0.000000e+00 8281.0
1 TraesCS3A01G522800 chr3A 99.693 2278 7 0 2048 4325 738503541 738501264 0.000000e+00 4169.0
2 TraesCS3A01G522800 chr3A 99.707 2047 5 1 1 2046 738601293 738599247 0.000000e+00 3746.0
3 TraesCS3A01G522800 chr3A 86.130 2235 243 35 2201 4400 738919480 738917278 0.000000e+00 2348.0
4 TraesCS3A01G522800 chr3A 86.899 1893 207 21 2365 4228 738245398 738243518 0.000000e+00 2084.0
5 TraesCS3A01G522800 chr3A 89.506 1477 143 6 2204 3674 738691900 738690430 0.000000e+00 1858.0
6 TraesCS3A01G522800 chr3A 90.698 1333 115 5 2216 3541 738708701 738707371 0.000000e+00 1766.0
7 TraesCS3A01G522800 chr3A 99.688 962 2 1 1 961 738504960 738503999 0.000000e+00 1759.0
8 TraesCS3A01G522800 chr3A 87.181 1529 164 20 2202 3704 738223499 738221977 0.000000e+00 1709.0
9 TraesCS3A01G522800 chr3A 86.270 925 59 22 3593 4484 738707371 738706482 0.000000e+00 942.0
10 TraesCS3A01G522800 chr3A 76.692 1566 298 40 382 1911 738307561 738306027 0.000000e+00 808.0
11 TraesCS3A01G522800 chr3A 79.388 849 152 19 405 1237 738250853 738250012 1.080000e-160 577.0
12 TraesCS3A01G522800 chr3A 79.598 696 106 21 1257 1927 738865911 738865227 2.440000e-127 466.0
13 TraesCS3A01G522800 chr3A 81.589 516 73 15 1426 1927 738320134 738319627 1.500000e-109 407.0
14 TraesCS3A01G522800 chr3A 82.772 267 43 1 1065 1331 738804513 738804250 7.500000e-58 235.0
15 TraesCS3A01G522800 chr3A 78.667 225 41 4 1619 1840 738489107 738488887 4.680000e-30 143.0
16 TraesCS3A01G522800 chr3A 88.571 70 8 0 3 72 738718772 738718703 7.990000e-13 86.1
17 TraesCS3A01G522800 chr3A 90.323 62 6 0 1 62 738490952 738490891 1.030000e-11 82.4
18 TraesCS3A01G522800 chr3A 90.323 62 6 0 1 62 738585128 738585067 1.030000e-11 82.4
19 TraesCS3A01G522800 chr3A 90.323 62 6 0 1 62 738663620 738663559 1.030000e-11 82.4
20 TraesCS3A01G522800 chrUn 99.707 2047 5 1 1 2046 344272302 344270256 0.000000e+00 3746.0
21 TraesCS3A01G522800 chrUn 86.139 1378 162 18 2192 3544 42326903 42325530 0.000000e+00 1459.0
22 TraesCS3A01G522800 chrUn 100.000 682 0 0 1 682 339064507 339065188 0.000000e+00 1260.0
23 TraesCS3A01G522800 chrUn 76.523 1001 194 26 456 1435 42328777 42327797 4.000000e-140 508.0
24 TraesCS3A01G522800 chrUn 75.631 792 156 24 662 1435 367634632 367633860 4.260000e-95 359.0
25 TraesCS3A01G522800 chrUn 76.744 516 85 20 1425 1927 42327770 42327277 5.760000e-64 255.0
26 TraesCS3A01G522800 chrUn 85.774 239 34 0 767 1005 259684597 259684359 2.070000e-63 254.0
27 TraesCS3A01G522800 chrUn 78.667 225 41 4 1619 1840 259683721 259683501 4.680000e-30 143.0
28 TraesCS3A01G522800 chrUn 78.667 225 41 4 1619 1840 397601972 397602192 4.680000e-30 143.0
29 TraesCS3A01G522800 chrUn 78.667 225 41 4 1619 1840 431190572 431190352 4.680000e-30 143.0
30 TraesCS3A01G522800 chrUn 78.667 225 41 4 1619 1840 435741135 435740915 4.680000e-30 143.0
31 TraesCS3A01G522800 chrUn 90.323 62 6 0 1 62 388555802 388555863 1.030000e-11 82.4
32 TraesCS3A01G522800 chrUn 89.286 56 6 0 950 1005 431191263 431191208 2.240000e-08 71.3
33 TraesCS3A01G522800 chr3D 88.570 1741 160 24 2200 3914 605676557 605678284 0.000000e+00 2076.0
34 TraesCS3A01G522800 chr3D 90.801 1435 115 5 2164 3591 605973519 605974943 0.000000e+00 1903.0
35 TraesCS3A01G522800 chr3D 87.893 1272 118 24 2647 3893 606002615 606003875 0.000000e+00 1463.0
36 TraesCS3A01G522800 chr3D 77.028 1171 201 43 456 1591 606775933 606774796 1.070000e-170 610.0
37 TraesCS3A01G522800 chr3D 81.427 743 127 9 379 1112 605953236 605953976 8.300000e-167 597.0
38 TraesCS3A01G522800 chr3D 78.969 737 132 12 379 1106 605971421 605972143 8.720000e-132 481.0
39 TraesCS3A01G522800 chr3D 76.147 872 169 26 456 1308 605747454 605748305 5.360000e-114 422.0
40 TraesCS3A01G522800 chr3D 77.486 533 90 21 1403 1929 606001464 606001972 4.390000e-75 292.0
41 TraesCS3A01G522800 chr3D 88.350 206 24 0 4190 4395 605636884 605637089 9.630000e-62 248.0
42 TraesCS3A01G522800 chr3D 77.836 379 69 10 1282 1652 605972265 605972636 2.100000e-53 220.0
43 TraesCS3A01G522800 chr3B 89.727 1538 115 21 2720 4220 816039928 816038397 0.000000e+00 1925.0
44 TraesCS3A01G522800 chr3B 86.502 1378 157 18 2192 3544 816172137 816170764 0.000000e+00 1487.0
45 TraesCS3A01G522800 chr3B 86.445 1114 129 13 2200 3303 816154361 816153260 0.000000e+00 1201.0
46 TraesCS3A01G522800 chr3B 76.264 712 141 19 741 1435 816173731 816173031 1.980000e-93 353.0
47 TraesCS3A01G522800 chr3B 81.199 367 61 6 1073 1435 816177421 816177059 5.680000e-74 289.0
48 TraesCS3A01G522800 chr3B 76.744 516 85 20 1425 1927 816173004 816172511 5.760000e-64 255.0
49 TraesCS3A01G522800 chr5B 80.805 745 130 8 382 1113 621480073 621479329 5.030000e-159 571.0
50 TraesCS3A01G522800 chr5B 80.426 751 122 15 382 1113 621471270 621470526 2.360000e-152 549.0


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 TraesCS3A01G522800 chr3A 738675776 738680259 4483 True 8281.000000 8281 100.000000 1 4484 1 chr3A.!!$R9 4483
1 TraesCS3A01G522800 chr3A 738599247 738601293 2046 True 3746.000000 3746 99.707000 1 2046 1 chr3A.!!$R7 2045
2 TraesCS3A01G522800 chr3A 738501264 738504960 3696 True 2964.000000 4169 99.690500 1 4325 2 chr3A.!!$R16 4324
3 TraesCS3A01G522800 chr3A 738917278 738919480 2202 True 2348.000000 2348 86.130000 2201 4400 1 chr3A.!!$R14 2199
4 TraesCS3A01G522800 chr3A 738243518 738245398 1880 True 2084.000000 2084 86.899000 2365 4228 1 chr3A.!!$R2 1863
5 TraesCS3A01G522800 chr3A 738690430 738691900 1470 True 1858.000000 1858 89.506000 2204 3674 1 chr3A.!!$R10 1470
6 TraesCS3A01G522800 chr3A 738221977 738223499 1522 True 1709.000000 1709 87.181000 2202 3704 1 chr3A.!!$R1 1502
7 TraesCS3A01G522800 chr3A 738706482 738708701 2219 True 1354.000000 1766 88.484000 2216 4484 2 chr3A.!!$R17 2268
8 TraesCS3A01G522800 chr3A 738306027 738307561 1534 True 808.000000 808 76.692000 382 1911 1 chr3A.!!$R4 1529
9 TraesCS3A01G522800 chr3A 738250012 738250853 841 True 577.000000 577 79.388000 405 1237 1 chr3A.!!$R3 832
10 TraesCS3A01G522800 chr3A 738865227 738865911 684 True 466.000000 466 79.598000 1257 1927 1 chr3A.!!$R13 670
11 TraesCS3A01G522800 chr3A 738319627 738320134 507 True 407.000000 407 81.589000 1426 1927 1 chr3A.!!$R5 501
12 TraesCS3A01G522800 chrUn 344270256 344272302 2046 True 3746.000000 3746 99.707000 1 2046 1 chrUn.!!$R1 2045
13 TraesCS3A01G522800 chrUn 339064507 339065188 681 False 1260.000000 1260 100.000000 1 682 1 chrUn.!!$F1 681
14 TraesCS3A01G522800 chrUn 42325530 42328777 3247 True 740.666667 1459 79.802000 456 3544 3 chrUn.!!$R4 3088
15 TraesCS3A01G522800 chrUn 367633860 367634632 772 True 359.000000 359 75.631000 662 1435 1 chrUn.!!$R2 773
16 TraesCS3A01G522800 chr3D 605676557 605678284 1727 False 2076.000000 2076 88.570000 2200 3914 1 chr3D.!!$F2 1714
17 TraesCS3A01G522800 chr3D 606001464 606003875 2411 False 877.500000 1463 82.689500 1403 3893 2 chr3D.!!$F6 2490
18 TraesCS3A01G522800 chr3D 605971421 605974943 3522 False 868.000000 1903 82.535333 379 3591 3 chr3D.!!$F5 3212
19 TraesCS3A01G522800 chr3D 606774796 606775933 1137 True 610.000000 610 77.028000 456 1591 1 chr3D.!!$R1 1135
20 TraesCS3A01G522800 chr3D 605953236 605953976 740 False 597.000000 597 81.427000 379 1112 1 chr3D.!!$F4 733
21 TraesCS3A01G522800 chr3D 605747454 605748305 851 False 422.000000 422 76.147000 456 1308 1 chr3D.!!$F3 852
22 TraesCS3A01G522800 chr3B 816038397 816039928 1531 True 1925.000000 1925 89.727000 2720 4220 1 chr3B.!!$R1 1500
23 TraesCS3A01G522800 chr3B 816153260 816154361 1101 True 1201.000000 1201 86.445000 2200 3303 1 chr3B.!!$R2 1103
24 TraesCS3A01G522800 chr3B 816170764 816177421 6657 True 596.000000 1487 80.177250 741 3544 4 chr3B.!!$R3 2803
25 TraesCS3A01G522800 chr5B 621479329 621480073 744 True 571.000000 571 80.805000 382 1113 1 chr5B.!!$R2 731
26 TraesCS3A01G522800 chr5B 621470526 621471270 744 True 549.000000 549 80.426000 382 1113 1 chr5B.!!$R1 731

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
736 741 6.351286 GGTGATCAAATTTGGCAATCCTACTT 60.351 38.462 17.9 0.0 0.0 2.24 F
737 742 7.099120 GTGATCAAATTTGGCAATCCTACTTT 58.901 34.615 17.9 0.0 0.0 2.66 F
738 743 8.250332 GTGATCAAATTTGGCAATCCTACTTTA 58.750 33.333 17.9 0.0 0.0 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 5194 0.443478 TGTGAAATCGTGCATGAGCG 59.557 50.000 15.04 0.9 46.23 5.03 R
2660 6114 3.070018 AGACAACATCCAAAGAGCTTCG 58.930 45.455 0.00 0.0 0.00 3.79 R
4428 7994 1.463444 GCAACGGAAACATACGAGCTT 59.537 47.619 0.00 0.0 34.08 3.74 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
736 741 6.351286 GGTGATCAAATTTGGCAATCCTACTT 60.351 38.462 17.9 0.0 0.00 2.24
737 742 7.099120 GTGATCAAATTTGGCAATCCTACTTT 58.901 34.615 17.9 0.0 0.00 2.66
738 743 8.250332 GTGATCAAATTTGGCAATCCTACTTTA 58.750 33.333 17.9 0.0 0.00 1.85
739 744 8.980596 TGATCAAATTTGGCAATCCTACTTTAT 58.019 29.630 17.9 0.0 0.00 1.40
740 745 9.822185 GATCAAATTTGGCAATCCTACTTTATT 57.178 29.630 17.9 0.0 0.00 1.40
4434 8000 0.314935 ATTTTGTGTGCCCAAGCTCG 59.685 50.000 0.0 0.0 40.80 5.03
4441 8007 1.165270 GTGCCCAAGCTCGTATGTTT 58.835 50.000 0.0 0.0 40.80 2.83
4447 8013 2.159707 CCAAGCTCGTATGTTTCCGTTG 60.160 50.000 0.0 0.0 0.00 4.10
4478 8044 0.777446 TTTGCTGAGGTTAAGGGCCT 59.223 50.000 0.0 0.0 39.42 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
736 741 5.534654 CGGAGGCCCAGATTGAATTTAATAA 59.465 40.000 0.00 0.00 0.00 1.40
737 742 5.070001 CGGAGGCCCAGATTGAATTTAATA 58.930 41.667 0.00 0.00 0.00 0.98
738 743 3.891366 CGGAGGCCCAGATTGAATTTAAT 59.109 43.478 0.00 0.00 0.00 1.40
739 744 3.287222 CGGAGGCCCAGATTGAATTTAA 58.713 45.455 0.00 0.00 0.00 1.52
740 745 2.241176 ACGGAGGCCCAGATTGAATTTA 59.759 45.455 0.00 0.00 0.00 1.40
741 746 1.005924 ACGGAGGCCCAGATTGAATTT 59.994 47.619 0.00 0.00 0.00 1.82
742 747 0.625849 ACGGAGGCCCAGATTGAATT 59.374 50.000 0.00 0.00 0.00 2.17
743 748 0.181350 GACGGAGGCCCAGATTGAAT 59.819 55.000 0.00 0.00 0.00 2.57
744 749 0.909610 AGACGGAGGCCCAGATTGAA 60.910 55.000 0.00 0.00 0.00 2.69
2046 5194 0.443478 TGTGAAATCGTGCATGAGCG 59.557 50.000 15.04 0.90 46.23 5.03
2660 6114 3.070018 AGACAACATCCAAAGAGCTTCG 58.930 45.455 0.00 0.00 0.00 3.79
4428 7994 1.463444 GCAACGGAAACATACGAGCTT 59.537 47.619 0.00 0.00 34.08 3.74
4434 8000 7.804614 TTAAATTGATGCAACGGAAACATAC 57.195 32.000 0.00 0.00 0.00 2.39
4441 8007 5.348179 CAGCAAATTAAATTGATGCAACGGA 59.652 36.000 8.46 0.00 39.51 4.69
4447 8013 6.973229 AACCTCAGCAAATTAAATTGATGC 57.027 33.333 15.12 5.21 44.24 3.91


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

AutoCloner maintained by Alex Coulton.