Multiple sequence alignment - TraesCS4D01G104700

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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 TraesCS4D01G104700 chr4D 100.000 4907 0 0 1 4907 82856656 82861562 0.000000e+00 9062.0
1 TraesCS4D01G104700 chr4D 95.491 1109 42 5 3530 4637 65383263 65382162 0.000000e+00 1764.0
2 TraesCS4D01G104700 chr4D 86.359 1063 37 32 1 1032 65392819 65391834 0.000000e+00 1061.0
3 TraesCS4D01G104700 chr4D 92.880 618 16 5 2481 3074 65383873 65383260 0.000000e+00 872.0
4 TraesCS4D01G104700 chr4D 92.830 265 14 3 4646 4907 65381407 65381145 3.580000e-101 379.0
5 TraesCS4D01G104700 chr5D 98.866 3351 12 5 1 3327 116662512 116659164 0.000000e+00 5954.0
6 TraesCS4D01G104700 chr5D 98.733 1578 20 0 3330 4907 116659126 116657549 0.000000e+00 2804.0
7 TraesCS4D01G104700 chr5D 83.726 934 104 23 1844 2771 350988267 350987376 0.000000e+00 839.0
8 TraesCS4D01G104700 chr5D 96.104 385 15 0 1357 1741 189237235 189237619 3.220000e-176 628.0
9 TraesCS4D01G104700 chr5D 81.984 383 38 14 701 1081 350989054 350988701 3.710000e-76 296.0
10 TraesCS4D01G104700 chr5D 95.327 107 5 0 1742 1848 189237736 189237630 2.350000e-38 171.0
11 TraesCS4D01G104700 chr4B 94.580 1513 53 6 1843 3327 377158913 377157402 0.000000e+00 2313.0
12 TraesCS4D01G104700 chr4B 92.435 423 24 4 666 1081 377159762 377159341 9.090000e-167 597.0
13 TraesCS4D01G104700 chr4B 86.888 511 44 14 1843 2342 193973808 193973310 7.180000e-153 551.0
14 TraesCS4D01G104700 chr4B 88.187 364 34 4 1988 2342 609108956 609108593 4.540000e-115 425.0
15 TraesCS4D01G104700 chr4B 94.182 275 13 3 1081 1354 377159178 377158906 2.730000e-112 416.0
16 TraesCS4D01G104700 chr4B 94.118 204 11 1 3330 3533 377157364 377157162 4.770000e-80 309.0
17 TraesCS4D01G104700 chr4B 85.780 218 26 3 3845 4059 242858551 242858336 4.940000e-55 226.0
18 TraesCS4D01G104700 chr4B 85.714 217 27 3 3845 4059 242923313 242923099 4.940000e-55 226.0
19 TraesCS4D01G104700 chr4B 95.960 99 4 0 1229 1327 193973916 193973818 1.410000e-35 161.0
20 TraesCS4D01G104700 chr7D 94.444 1512 57 5 1843 3327 446193504 446195015 0.000000e+00 2302.0
21 TraesCS4D01G104700 chr7D 93.249 1496 87 10 1845 3327 215268795 215267301 0.000000e+00 2191.0
22 TraesCS4D01G104700 chr7D 94.601 1204 60 5 3331 4533 446195054 446196253 0.000000e+00 1858.0
23 TraesCS4D01G104700 chr7D 93.869 1207 66 8 3330 4533 215267263 215266062 0.000000e+00 1812.0
24 TraesCS4D01G104700 chr7D 95.568 722 29 2 360 1081 446192362 446193080 0.000000e+00 1153.0
25 TraesCS4D01G104700 chr7D 95.034 725 32 2 357 1081 215269908 215269188 0.000000e+00 1136.0
26 TraesCS4D01G104700 chr7D 94.203 276 8 4 1081 1354 446193242 446193511 9.830000e-112 414.0
27 TraesCS4D01G104700 chr7D 92.481 266 15 3 4646 4907 215265264 215265000 4.640000e-100 375.0
28 TraesCS4D01G104700 chr7D 92.075 265 16 3 4646 4907 446197156 446197418 7.760000e-98 368.0
29 TraesCS4D01G104700 chr7D 93.229 192 7 4 1081 1271 215269025 215268839 1.350000e-70 278.0
30 TraesCS4D01G104700 chr7D 96.262 107 4 0 4531 4637 446196294 446196400 5.050000e-40 176.0
31 TraesCS4D01G104700 chr7D 95.327 107 5 0 4531 4637 215266021 215265915 2.350000e-38 171.0
32 TraesCS4D01G104700 chr7D 96.000 50 2 0 1305 1354 215268839 215268790 1.130000e-11 82.4
33 TraesCS4D01G104700 chr5A 84.164 903 105 21 1888 2771 451457456 451456573 0.000000e+00 841.0
34 TraesCS4D01G104700 chr5A 77.014 422 65 19 672 1081 451458598 451458197 3.850000e-51 213.0
35 TraesCS4D01G104700 chr5B 84.318 880 100 19 1897 2771 411801791 411800945 0.000000e+00 826.0
36 TraesCS4D01G104700 chr5B 96.021 377 15 0 1365 1741 126610019 126610395 9.030000e-172 614.0
37 TraesCS4D01G104700 chr5B 80.867 392 44 18 701 1081 411802672 411802301 3.740000e-71 279.0
38 TraesCS4D01G104700 chr5B 94.444 108 6 0 1741 1848 126610513 126610406 3.040000e-37 167.0
39 TraesCS4D01G104700 chr2D 93.077 520 31 3 4017 4533 602005378 602005895 0.000000e+00 756.0
40 TraesCS4D01G104700 chr2D 94.301 386 21 1 1357 1741 468829696 468829311 1.520000e-164 590.0
41 TraesCS4D01G104700 chr2D 87.280 511 42 13 1843 2342 624266723 624267221 3.320000e-156 562.0
42 TraesCS4D01G104700 chr2D 88.806 134 14 1 4400 4533 434931875 434931743 3.930000e-36 163.0
43 TraesCS4D01G104700 chr2D 93.458 107 7 0 4531 4637 602005936 602006042 5.080000e-35 159.0
44 TraesCS4D01G104700 chr2D 91.589 107 6 1 4531 4637 434931702 434931599 1.420000e-30 145.0
45 TraesCS4D01G104700 chr2A 88.852 601 46 12 2001 2593 526300843 526301430 0.000000e+00 719.0
46 TraesCS4D01G104700 chr2A 87.279 283 33 2 3545 3825 526301428 526301709 2.200000e-83 320.0
47 TraesCS4D01G104700 chr3D 96.084 383 13 2 1359 1741 366249204 366248824 1.500000e-174 623.0
48 TraesCS4D01G104700 chr1B 95.408 392 16 2 1352 1741 432109147 432109538 1.500000e-174 623.0
49 TraesCS4D01G104700 chr1B 87.582 153 16 3 3330 3480 112749809 112749960 1.820000e-39 174.0
50 TraesCS4D01G104700 chr1B 89.552 134 13 1 4400 4533 113821953 113822085 8.450000e-38 169.0
51 TraesCS4D01G104700 chr1B 94.444 108 6 0 1741 1848 432109656 432109549 3.040000e-37 167.0
52 TraesCS4D01G104700 chr6B 95.550 382 17 0 1360 1741 149422779 149423160 3.250000e-171 612.0
53 TraesCS4D01G104700 chr6B 86.078 510 49 8 1843 2342 297532386 297532883 3.360000e-146 529.0
54 TraesCS4D01G104700 chr6B 91.321 265 14 4 4646 4907 672939922 672940180 2.170000e-93 353.0
55 TraesCS4D01G104700 chr6B 83.232 328 45 4 3999 4324 296786841 296786522 4.800000e-75 292.0
56 TraesCS4D01G104700 chr6B 80.332 361 39 18 3966 4324 715533818 715534148 1.360000e-60 244.0
57 TraesCS4D01G104700 chr6B 80.332 361 39 18 3966 4324 715539866 715540196 1.360000e-60 244.0
58 TraesCS4D01G104700 chr6B 89.286 140 14 1 4394 4533 544666061 544666199 1.820000e-39 174.0
59 TraesCS4D01G104700 chr6B 93.519 108 7 0 1741 1848 120154758 120154865 1.410000e-35 161.0
60 TraesCS4D01G104700 chr6B 89.683 126 13 0 1229 1354 297532268 297532393 1.410000e-35 161.0
61 TraesCS4D01G104700 chr6B 93.069 101 4 1 4531 4631 155474467 155474564 1.420000e-30 145.0
62 TraesCS4D01G104700 chr7B 95.312 384 17 1 1358 1741 458563453 458563071 4.200000e-170 608.0
63 TraesCS4D01G104700 chr7B 89.883 257 26 0 4646 4902 24151049 24150793 1.020000e-86 331.0
64 TraesCS4D01G104700 chr7A 94.792 384 20 0 1358 1741 152849206 152848823 2.530000e-167 599.0
65 TraesCS4D01G104700 chr7A 100.000 107 0 0 1742 1848 152848706 152848812 1.080000e-46 198.0
66 TraesCS4D01G104700 chr1D 88.961 154 13 4 3330 3480 71283123 71283275 2.330000e-43 187.0
67 TraesCS4D01G104700 chr4A 89.933 149 6 5 4762 4907 181631314 181631172 3.020000e-42 183.0
68 TraesCS4D01G104700 chr4A 93.388 121 8 0 4646 4766 181640491 181640371 3.900000e-41 180.0
69 TraesCS4D01G104700 chr4A 97.143 105 3 0 1744 1848 201619855 201619751 1.400000e-40 178.0
70 TraesCS4D01G104700 chr3B 97.222 108 3 0 1741 1848 726444187 726444080 3.020000e-42 183.0
71 TraesCS4D01G104700 chr3B 89.286 140 14 1 4394 4533 703909177 703909315 1.820000e-39 174.0
72 TraesCS4D01G104700 chr3B 92.523 107 5 1 4531 4637 703909356 703909459 3.060000e-32 150.0
73 TraesCS4D01G104700 chr6D 87.742 155 16 2 4173 4324 448551972 448552126 1.400000e-40 178.0
74 TraesCS4D01G104700 chr2B 94.444 108 5 1 1741 1848 14342367 14342473 1.090000e-36 165.0
75 TraesCS4D01G104700 chr2B 91.089 101 6 2 4531 4631 116842367 116842464 3.080000e-27 134.0


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 TraesCS4D01G104700 chr4D 82856656 82861562 4906 False 9062.000000 9062 100.000000 1 4907 1 chr4D.!!$F1 4906
1 TraesCS4D01G104700 chr4D 65391834 65392819 985 True 1061.000000 1061 86.359000 1 1032 1 chr4D.!!$R1 1031
2 TraesCS4D01G104700 chr4D 65381145 65383873 2728 True 1005.000000 1764 93.733667 2481 4907 3 chr4D.!!$R2 2426
3 TraesCS4D01G104700 chr5D 116657549 116662512 4963 True 4379.000000 5954 98.799500 1 4907 2 chr5D.!!$R2 4906
4 TraesCS4D01G104700 chr5D 350987376 350989054 1678 True 567.500000 839 82.855000 701 2771 2 chr5D.!!$R3 2070
5 TraesCS4D01G104700 chr4B 377157162 377159762 2600 True 908.750000 2313 93.828750 666 3533 4 chr4B.!!$R5 2867
6 TraesCS4D01G104700 chr4B 193973310 193973916 606 True 356.000000 551 91.424000 1229 2342 2 chr4B.!!$R4 1113
7 TraesCS4D01G104700 chr7D 446192362 446197418 5056 False 1045.166667 2302 94.525500 360 4907 6 chr7D.!!$F1 4547
8 TraesCS4D01G104700 chr7D 215265000 215269908 4908 True 863.628571 2191 94.169857 357 4907 7 chr7D.!!$R1 4550
9 TraesCS4D01G104700 chr5A 451456573 451458598 2025 True 527.000000 841 80.589000 672 2771 2 chr5A.!!$R1 2099
10 TraesCS4D01G104700 chr5B 411800945 411802672 1727 True 552.500000 826 82.592500 701 2771 2 chr5B.!!$R2 2070
11 TraesCS4D01G104700 chr2D 602005378 602006042 664 False 457.500000 756 93.267500 4017 4637 2 chr2D.!!$F2 620
12 TraesCS4D01G104700 chr2A 526300843 526301709 866 False 519.500000 719 88.065500 2001 3825 2 chr2A.!!$F1 1824
13 TraesCS4D01G104700 chr6B 297532268 297532883 615 False 345.000000 529 87.880500 1229 2342 2 chr6B.!!$F8 1113

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
1291 1827 6.210185 CCTTTCTTGATTTCAGAAACCATCCT 59.790 38.462 0.0 0.0 0.00 3.24 F
1553 2126 0.041839 GATGATGTTGGTGATCGCGC 60.042 55.000 0.0 0.0 0.00 6.86 F
1810 2383 0.883833 CGATGTTCTTGCTTGGGCTT 59.116 50.000 0.0 0.0 39.59 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 3066 4.103153 TCCACCCCAATCTAAATAGCTCAG 59.897 45.833 0.00 0.00 0.00 3.35 R
3463 4157 4.616835 GCACTTGCCTAGTCAAAATTCAGG 60.617 45.833 0.00 0.00 33.85 3.86 R
4328 5027 6.201806 CGAACTTAAGAATCTTATGGCTGGAG 59.798 42.308 10.09 7.26 0.00 3.86 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
1291 1827 6.210185 CCTTTCTTGATTTCAGAAACCATCCT 59.790 38.462 0.00 0.00 0.00 3.24
1354 1926 3.488721 GCCATACAGTACGTCGACTTGAT 60.489 47.826 14.70 0.00 0.00 2.57
1404 1977 9.141400 GGATACGTATCTTTCCATTGATAGAAC 57.859 37.037 29.40 7.86 33.19 3.01
1479 2052 0.321653 GAGGCATGGAAGTGGACGTT 60.322 55.000 0.00 0.00 0.00 3.99
1553 2126 0.041839 GATGATGTTGGTGATCGCGC 60.042 55.000 0.00 0.00 0.00 6.86
1810 2383 0.883833 CGATGTTCTTGCTTGGGCTT 59.116 50.000 0.00 0.00 39.59 4.35
2053 2640 5.728637 AGGAAAAAGGCTTTTATGGTGAG 57.271 39.130 24.34 0.00 34.83 3.51
2208 2816 8.846943 TGCATTTCTTGTTCTTAGTTAGATCA 57.153 30.769 0.00 0.00 32.13 2.92
2454 3066 4.272261 GCCTGCATACTTTCTTCTAAGAGC 59.728 45.833 0.00 0.00 36.22 4.09
3463 4157 8.950403 AAAGTTTAGAACGATGCACTATTTTC 57.050 30.769 0.00 0.00 36.23 2.29
4328 5027 7.761038 TTCCTTTGAATTTAGAAGAAGGGAC 57.239 36.000 0.00 0.00 35.50 4.46
4360 5059 7.148239 CCATAAGATTCTTAAGTTCGTTGGCTT 60.148 37.037 10.07 0.00 0.00 4.35
4442 5141 2.298629 CGATCGGATCAGCACGCAG 61.299 63.158 17.53 0.00 0.00 5.18
4478 5180 3.357079 CGCCGCAAGCCTCACTTT 61.357 61.111 0.00 0.00 36.04 2.66
4516 5218 1.831106 TGCACCTACATCCACTTCGAT 59.169 47.619 0.00 0.00 0.00 3.59
4524 5226 1.120530 ATCCACTTCGATAGGCCGTT 58.879 50.000 0.00 0.00 0.00 4.44
4712 6204 3.510531 TGCACATGGGGTAACAAAGTA 57.489 42.857 0.00 0.00 39.74 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1221 1742 6.293845 CCAAAGAGGAAACTGAAGAACATCAG 60.294 42.308 5.66 5.66 45.68 2.90
1291 1827 1.317431 CCCATCACGTCCCTGTCGTA 61.317 60.000 0.00 0.00 39.55 3.43
1404 1977 1.086696 CCATGCTGTAAACACTCCCG 58.913 55.000 0.00 0.00 0.00 5.14
1479 2052 0.534203 GAACCCCGTCTGTTTGCTCA 60.534 55.000 0.00 0.00 0.00 4.26
1810 2383 2.989639 CAGATCGGTGGGGAAGCA 59.010 61.111 0.00 0.00 0.00 3.91
2053 2640 0.582005 GAACGCGGTATTGATCCTGC 59.418 55.000 12.47 0.00 0.00 4.85
2208 2816 6.211184 TGATTAAAAACACATCCCTCTGCATT 59.789 34.615 0.00 0.00 0.00 3.56
2454 3066 4.103153 TCCACCCCAATCTAAATAGCTCAG 59.897 45.833 0.00 0.00 0.00 3.35
3327 3986 6.068010 TGTTGGTCACTTGAAATACCTGAAT 58.932 36.000 0.00 0.00 32.99 2.57
3463 4157 4.616835 GCACTTGCCTAGTCAAAATTCAGG 60.617 45.833 0.00 0.00 33.85 3.86
4328 5027 6.201806 CGAACTTAAGAATCTTATGGCTGGAG 59.798 42.308 10.09 7.26 0.00 3.86
4442 5141 2.458610 GCGATCCGAACGGGTTTCC 61.459 63.158 13.29 0.00 37.00 3.13
4474 5176 4.999950 CAGAGGTTGATCTGTTGCTAAAGT 59.000 41.667 0.00 0.00 41.52 2.66
4478 5180 2.302733 TGCAGAGGTTGATCTGTTGCTA 59.697 45.455 5.69 0.00 46.93 3.49
4516 5218 6.935771 TGAAATAAACTTTGACTAACGGCCTA 59.064 34.615 0.00 0.00 0.00 3.93
4658 6150 3.480133 CCGGCTGGGTTCCCCTAG 61.480 72.222 2.57 0.00 45.70 3.02
4673 6165 4.560035 GTGCAATGATCATCAAAACTTCCG 59.440 41.667 9.06 0.00 0.00 4.30
4712 6204 7.807977 TCTGACTTGATCTTTGTAAAGCTTT 57.192 32.000 17.30 17.30 35.99 3.51


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

AutoCloner maintained by Alex Coulton.