Multiple sequence alignment - TraesCS5B01G454100

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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 TraesCS5B01G454100 chr5B 100.000 8043 0 0 1 8043 626837041 626845083 0.000000e+00 14853.0
1 TraesCS5B01G454100 chr5B 99.416 8053 37 3 1 8043 623166065 623174117 0.000000e+00 14602.0
2 TraesCS5B01G454100 chr5B 96.401 2334 70 3 218 2551 628693680 628695999 0.000000e+00 3832.0
3 TraesCS5B01G454100 chr5B 95.851 2338 79 7 218 2551 625114127 625116450 0.000000e+00 3764.0
4 TraesCS5B01G454100 chr5B 92.763 2570 131 20 1 2551 629894681 629897214 0.000000e+00 3664.0
5 TraesCS5B01G454100 chr5B 96.317 1955 56 6 5190 7129 629897205 629899158 0.000000e+00 3197.0
6 TraesCS5B01G454100 chr5B 96.320 1685 56 5 5409 7090 625117263 625118944 0.000000e+00 2763.0
7 TraesCS5B01G454100 chr5B 96.261 1685 57 5 5409 7090 628696812 628698493 0.000000e+00 2758.0
8 TraesCS5B01G454100 chr5B 94.370 1723 91 4 5409 7129 633176722 633175004 0.000000e+00 2639.0
9 TraesCS5B01G454100 chr5B 91.735 1464 57 20 893 2328 633179460 633178033 0.000000e+00 1975.0
10 TraesCS5B01G454100 chr5B 93.864 929 50 3 7121 8043 482315249 482314322 0.000000e+00 1393.0
11 TraesCS5B01G454100 chr5B 92.857 910 61 4 7134 8043 19644852 19645757 0.000000e+00 1317.0
12 TraesCS5B01G454100 chr5B 78.317 1236 186 39 3990 5190 562302860 562301672 0.000000e+00 723.0
13 TraesCS5B01G454100 chr5B 90.638 235 2 2 5190 5404 625116441 625116675 2.200000e-75 294.0
14 TraesCS5B01G454100 chr5B 90.638 235 2 2 5190 5404 628695990 628696224 2.200000e-75 294.0
15 TraesCS5B01G454100 chr5B 91.257 183 15 1 1 183 628693501 628693682 1.730000e-61 248.0
16 TraesCS5B01G454100 chr5B 90.710 183 16 1 1 183 625113948 625114129 8.060000e-60 243.0
17 TraesCS5B01G454100 chr5B 97.561 41 1 0 7089 7129 625119059 625119099 4.030000e-08 71.3
18 TraesCS5B01G454100 chr5B 97.561 41 1 0 7089 7129 628698608 628698648 4.030000e-08 71.3
19 TraesCS5B01G454100 chr7B 99.093 2645 14 6 2548 5191 438012074 438009439 0.000000e+00 4743.0
20 TraesCS5B01G454100 chr7B 93.464 918 55 3 7129 8043 678967963 678968878 0.000000e+00 1358.0
21 TraesCS5B01G454100 chr7B 78.827 307 52 10 3989 4293 444440164 444439869 2.290000e-45 195.0
22 TraesCS5B01G454100 chr7B 79.623 265 45 7 3989 4252 474277661 474277917 1.780000e-41 182.0
23 TraesCS5B01G454100 chrUn 100.000 2193 0 0 3681 5873 349937392 349939584 0.000000e+00 4050.0
24 TraesCS5B01G454100 chrUn 99.863 2193 3 0 3681 5873 349939685 349941877 0.000000e+00 4034.0
25 TraesCS5B01G454100 chrUn 81.119 143 19 3 452 594 104050860 104050726 3.070000e-19 108.0
26 TraesCS5B01G454100 chrUn 76.098 205 40 4 453 657 76959351 76959546 1.850000e-16 99.0
27 TraesCS5B01G454100 chr5A 95.309 1620 74 2 5510 7129 625733836 625732219 0.000000e+00 2569.0
28 TraesCS5B01G454100 chr5A 94.070 1602 69 11 893 2478 625738874 625737283 0.000000e+00 2409.0
29 TraesCS5B01G454100 chr5A 85.306 245 4 9 5190 5404 625737176 625736934 2.920000e-54 224.0
30 TraesCS5B01G454100 chr5A 97.959 98 2 0 5409 5506 625734890 625734793 3.860000e-38 171.0
31 TraesCS5B01G454100 chr1B 86.541 1538 160 29 3149 4677 136962277 136960778 0.000000e+00 1650.0
32 TraesCS5B01G454100 chr1B 88.813 438 38 8 2583 3011 136962727 136962292 1.990000e-145 527.0
33 TraesCS5B01G454100 chr1B 83.977 518 72 4 4675 5189 136933338 136932829 3.370000e-133 486.0
34 TraesCS5B01G454100 chr1B 74.725 364 67 14 452 802 14651883 14652234 1.090000e-28 139.0
35 TraesCS5B01G454100 chr1D 86.364 1540 161 30 3147 4677 83939147 83937648 0.000000e+00 1635.0
36 TraesCS5B01G454100 chr1D 84.534 472 41 12 2558 3021 83939597 83939150 9.580000e-119 438.0
37 TraesCS5B01G454100 chr1D 78.713 202 35 6 659 856 18267070 18266873 2.360000e-25 128.0
38 TraesCS5B01G454100 chr5D 90.968 919 75 3 7129 8043 420995203 420994289 0.000000e+00 1230.0
39 TraesCS5B01G454100 chr5D 87.062 371 36 6 6767 7127 297092971 297092603 7.510000e-110 409.0
40 TraesCS5B01G454100 chr5D 81.683 404 49 9 470 857 499443816 499444210 6.060000e-81 313.0
41 TraesCS5B01G454100 chr5D 77.722 395 66 14 473 858 505933936 505933555 1.050000e-53 222.0
42 TraesCS5B01G454100 chr6D 90.781 922 79 3 7124 8043 398169819 398168902 0.000000e+00 1227.0
43 TraesCS5B01G454100 chr6D 77.566 1364 201 57 1000 2307 29768994 29770308 0.000000e+00 726.0
44 TraesCS5B01G454100 chr6D 80.228 966 184 6 5855 6816 468096600 468095638 0.000000e+00 719.0
45 TraesCS5B01G454100 chr6D 77.000 300 51 16 4001 4293 444669537 444669825 1.080000e-33 156.0
46 TraesCS5B01G454100 chr6A 90.731 917 76 5 7129 8043 607695867 607694958 0.000000e+00 1214.0
47 TraesCS5B01G454100 chr6A 83.723 1026 159 7 5804 6824 32898759 32897737 0.000000e+00 963.0
48 TraesCS5B01G454100 chr6A 80.145 967 183 8 5855 6816 614162790 614161828 0.000000e+00 713.0
49 TraesCS5B01G454100 chr6A 76.582 1375 210 67 1000 2307 32900824 32899495 0.000000e+00 652.0
50 TraesCS5B01G454100 chr6A 85.547 256 36 1 198 452 463161973 463162228 4.790000e-67 267.0
51 TraesCS5B01G454100 chr6A 75.309 405 72 21 470 857 2055295 2055688 1.390000e-37 169.0
52 TraesCS5B01G454100 chr3D 90.249 923 82 6 7126 8043 510913355 510914274 0.000000e+00 1199.0
53 TraesCS5B01G454100 chr3D 90.492 915 75 7 7133 8043 307933451 307932545 0.000000e+00 1197.0
54 TraesCS5B01G454100 chr2B 77.159 880 131 33 4348 5189 672321997 672321150 1.590000e-121 448.0
55 TraesCS5B01G454100 chr2B 79.205 654 87 22 4348 4984 658483761 658484382 7.510000e-110 409.0
56 TraesCS5B01G454100 chr2B 82.064 407 43 18 48 452 415034274 415033896 3.620000e-83 320.0
57 TraesCS5B01G454100 chr2B 97.500 40 1 0 4403 4442 384318982 384318943 1.450000e-07 69.4
58 TraesCS5B01G454100 chr3B 90.476 252 23 1 203 454 741337483 741337733 1.670000e-86 331.0
59 TraesCS5B01G454100 chr3B 91.558 154 13 0 48 201 596435323 596435170 6.320000e-51 213.0
60 TraesCS5B01G454100 chr3B 93.846 65 4 0 205 269 596435186 596435122 1.850000e-16 99.0
61 TraesCS5B01G454100 chr2D 81.034 406 53 9 470 861 601984952 601984557 1.310000e-77 302.0
62 TraesCS5B01G454100 chr3A 80.344 407 56 6 48 452 19187722 19187338 3.670000e-73 287.0
63 TraesCS5B01G454100 chr3A 77.427 412 60 16 470 858 732515866 732515465 1.760000e-51 215.0
64 TraesCS5B01G454100 chr3A 84.492 187 25 3 671 855 661470272 661470456 1.780000e-41 182.0
65 TraesCS5B01G454100 chr3A 89.796 49 5 0 3 51 624927864 624927816 6.740000e-06 63.9
66 TraesCS5B01G454100 chr7D 77.700 426 68 14 452 858 566575003 566574586 1.350000e-57 235.0
67 TraesCS5B01G454100 chr7D 92.308 52 4 0 452 503 166482919 166482868 3.110000e-09 75.0
68 TraesCS5B01G454100 chr4D 75.377 398 72 16 472 858 400168500 400168882 1.390000e-37 169.0
69 TraesCS5B01G454100 chr6B 84.076 157 25 0 1093 1249 714336607 714336451 1.400000e-32 152.0
70 TraesCS5B01G454100 chr4B 79.581 191 29 7 654 838 135000003 135000189 2.360000e-25 128.0
71 TraesCS5B01G454100 chr2A 91.667 48 2 2 408 455 288121173 288121218 1.870000e-06 65.8


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 TraesCS5B01G454100 chr5B 626837041 626845083 8042 False 14853.00 14853 100.0000 1 8043 1 chr5B.!!$F3 8042
1 TraesCS5B01G454100 chr5B 623166065 623174117 8052 False 14602.00 14602 99.4160 1 8043 1 chr5B.!!$F2 8042
2 TraesCS5B01G454100 chr5B 629894681 629899158 4477 False 3430.50 3664 94.5400 1 7129 2 chr5B.!!$F6 7128
3 TraesCS5B01G454100 chr5B 633175004 633179460 4456 True 2307.00 2639 93.0525 893 7129 2 chr5B.!!$R3 6236
4 TraesCS5B01G454100 chr5B 628693501 628698648 5147 False 1440.66 3832 94.4236 1 7129 5 chr5B.!!$F5 7128
5 TraesCS5B01G454100 chr5B 625113948 625119099 5151 False 1427.06 3764 94.2160 1 7129 5 chr5B.!!$F4 7128
6 TraesCS5B01G454100 chr5B 482314322 482315249 927 True 1393.00 1393 93.8640 7121 8043 1 chr5B.!!$R1 922
7 TraesCS5B01G454100 chr5B 19644852 19645757 905 False 1317.00 1317 92.8570 7134 8043 1 chr5B.!!$F1 909
8 TraesCS5B01G454100 chr5B 562301672 562302860 1188 True 723.00 723 78.3170 3990 5190 1 chr5B.!!$R2 1200
9 TraesCS5B01G454100 chr7B 438009439 438012074 2635 True 4743.00 4743 99.0930 2548 5191 1 chr7B.!!$R1 2643
10 TraesCS5B01G454100 chr7B 678967963 678968878 915 False 1358.00 1358 93.4640 7129 8043 1 chr7B.!!$F2 914
11 TraesCS5B01G454100 chrUn 349937392 349941877 4485 False 4042.00 4050 99.9315 3681 5873 2 chrUn.!!$F2 2192
12 TraesCS5B01G454100 chr5A 625732219 625738874 6655 True 1343.25 2569 93.1610 893 7129 4 chr5A.!!$R1 6236
13 TraesCS5B01G454100 chr1B 136960778 136962727 1949 True 1088.50 1650 87.6770 2583 4677 2 chr1B.!!$R2 2094
14 TraesCS5B01G454100 chr1B 136932829 136933338 509 True 486.00 486 83.9770 4675 5189 1 chr1B.!!$R1 514
15 TraesCS5B01G454100 chr1D 83937648 83939597 1949 True 1036.50 1635 85.4490 2558 4677 2 chr1D.!!$R2 2119
16 TraesCS5B01G454100 chr5D 420994289 420995203 914 True 1230.00 1230 90.9680 7129 8043 1 chr5D.!!$R2 914
17 TraesCS5B01G454100 chr6D 398168902 398169819 917 True 1227.00 1227 90.7810 7124 8043 1 chr6D.!!$R1 919
18 TraesCS5B01G454100 chr6D 29768994 29770308 1314 False 726.00 726 77.5660 1000 2307 1 chr6D.!!$F1 1307
19 TraesCS5B01G454100 chr6D 468095638 468096600 962 True 719.00 719 80.2280 5855 6816 1 chr6D.!!$R2 961
20 TraesCS5B01G454100 chr6A 607694958 607695867 909 True 1214.00 1214 90.7310 7129 8043 1 chr6A.!!$R1 914
21 TraesCS5B01G454100 chr6A 32897737 32900824 3087 True 807.50 963 80.1525 1000 6824 2 chr6A.!!$R3 5824
22 TraesCS5B01G454100 chr6A 614161828 614162790 962 True 713.00 713 80.1450 5855 6816 1 chr6A.!!$R2 961
23 TraesCS5B01G454100 chr3D 510913355 510914274 919 False 1199.00 1199 90.2490 7126 8043 1 chr3D.!!$F1 917
24 TraesCS5B01G454100 chr3D 307932545 307933451 906 True 1197.00 1197 90.4920 7133 8043 1 chr3D.!!$R1 910
25 TraesCS5B01G454100 chr2B 672321150 672321997 847 True 448.00 448 77.1590 4348 5189 1 chr2B.!!$R3 841
26 TraesCS5B01G454100 chr2B 658483761 658484382 621 False 409.00 409 79.2050 4348 4984 1 chr2B.!!$F1 636

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
311 312 0.190069 ATATACTGGTCGAGGGGGCA 59.810 55.000 0.00 0.00 0.00 5.36 F
3090 3720 3.611766 TCAGCTACTCCTTTGTTAGCC 57.388 47.619 0.00 0.00 34.56 3.93 F
3679 4313 5.009610 ACCATCAACCACATACTTCAACAAC 59.990 40.000 0.00 0.00 0.00 3.32 F
4920 7920 2.423892 CAGAGTACGTCCATACTGCAGT 59.576 50.000 25.12 25.12 35.48 4.40 F
6222 12409 2.291346 GGTTGGTACCCCATTGCTAGTT 60.291 50.000 10.07 0.00 41.49 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 1253 4.856607 CGAGGAACGCTCGAGGGC 62.857 72.222 27.56 13.29 46.06 5.19 R
4920 7920 1.227823 CACCGGTGGAACAAGCTCA 60.228 57.895 27.57 0.00 44.16 4.26 R
6222 12409 2.632996 ACCACCAGAGAGAAATTCGTGA 59.367 45.455 0.00 0.00 0.00 4.35 R
6779 12966 1.605712 GGCGGTGTGCTATATCTGTCC 60.606 57.143 0.00 0.00 45.43 4.02 R
7179 13486 2.430610 GGCAACCAAACAGGCCACA 61.431 57.895 5.01 0.00 45.70 4.17 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
311 312 0.190069 ATATACTGGTCGAGGGGGCA 59.810 55.000 0.00 0.00 0.00 5.36
3090 3720 3.611766 TCAGCTACTCCTTTGTTAGCC 57.388 47.619 0.00 0.00 34.56 3.93
3679 4313 5.009610 ACCATCAACCACATACTTCAACAAC 59.990 40.000 0.00 0.00 0.00 3.32
4920 7920 2.423892 CAGAGTACGTCCATACTGCAGT 59.576 50.000 25.12 25.12 35.48 4.40
6222 12409 2.291346 GGTTGGTACCCCATTGCTAGTT 60.291 50.000 10.07 0.00 41.49 2.24
6223 12410 3.014623 GTTGGTACCCCATTGCTAGTTC 58.985 50.000 10.07 0.00 41.49 3.01
6779 12966 0.868406 GTGGAACAAAGACCAGCGAG 59.132 55.000 0.00 0.00 44.16 5.03
6851 13038 1.000283 AGTTCTTGGACGCTGAGTGAG 60.000 52.381 0.00 0.00 0.00 3.51
7368 13678 1.471676 GGACAGGACGCCTCATAACTG 60.472 57.143 0.00 0.00 0.00 3.16
7614 13935 3.527775 CTATCTGCTGCCGGCCTCC 62.528 68.421 26.77 12.73 40.92 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
863 867 1.777199 CCACGGACTTAACGCGTTC 59.223 57.895 30.28 14.44 34.00 3.95
1226 1253 4.856607 CGAGGAACGCTCGAGGGC 62.857 72.222 27.56 13.29 46.06 5.19
3090 3720 7.111247 TGGAACCATTTATATTGGAAAGCTG 57.889 36.000 8.77 0.00 37.69 4.24
4920 7920 1.227823 CACCGGTGGAACAAGCTCA 60.228 57.895 27.57 0.00 44.16 4.26
6222 12409 2.632996 ACCACCAGAGAGAAATTCGTGA 59.367 45.455 0.00 0.00 0.00 4.35
6223 12410 3.045601 ACCACCAGAGAGAAATTCGTG 57.954 47.619 0.00 0.00 0.00 4.35
6779 12966 1.605712 GGCGGTGTGCTATATCTGTCC 60.606 57.143 0.00 0.00 45.43 4.02
7179 13486 2.430610 GGCAACCAAACAGGCCACA 61.431 57.895 5.01 0.00 45.70 4.17


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

AutoCloner maintained by Alex Coulton.