Multiple sequence alignment - TraesCS3B01G529900

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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 TraesCS3B01G529900 chr3B 100.000 2522 0 0 1 2522 771241041 771243562 0.000000e+00 4658
1 TraesCS3B01G529900 chr3B 93.208 1811 100 3 1 1792 770965677 770963871 0.000000e+00 2641
2 TraesCS3B01G529900 chr3B 92.857 1624 71 10 1 1610 771177507 771179099 0.000000e+00 2314
3 TraesCS3B01G529900 chr3B 93.107 914 48 10 1609 2522 771179182 771180080 0.000000e+00 1325
4 TraesCS3B01G529900 chr3B 89.270 699 51 15 1825 2522 770963870 770963195 0.000000e+00 854
5 TraesCS3B01G529900 chr3B 75.835 389 81 9 1887 2268 214443126 214442744 4.280000e-43 185
6 TraesCS3B01G529900 chr3B 84.783 184 24 3 520 702 420436314 420436134 5.540000e-42 182
7 TraesCS3B01G529900 chr3D 91.626 1839 113 10 704 2522 577668970 577667153 0.000000e+00 2505
8 TraesCS3B01G529900 chr3D 90.176 1761 143 22 47 1799 577780535 577778797 0.000000e+00 2266
9 TraesCS3B01G529900 chr3D 89.056 1800 139 15 19 1792 578040126 578041893 0.000000e+00 2180
10 TraesCS3B01G529900 chr3D 90.428 1097 87 12 704 1799 577753004 577751925 0.000000e+00 1428
11 TraesCS3B01G529900 chr3D 91.143 700 46 10 1825 2522 578041894 578042579 0.000000e+00 935
12 TraesCS3B01G529900 chr3D 91.781 73 6 0 421 493 577669213 577669141 4.440000e-18 102
13 TraesCS3B01G529900 chr3A 87.540 1862 168 29 698 2522 713308513 713306679 0.000000e+00 2095
14 TraesCS3B01G529900 chr3A 85.801 1648 180 24 904 2519 713342779 713341154 0.000000e+00 1698
15 TraesCS3B01G529900 chr3A 89.896 673 59 5 645 1314 713418437 713417771 0.000000e+00 857
16 TraesCS3B01G529900 chr3A 81.243 837 117 12 1344 2154 713417774 713416952 7.610000e-180 640
17 TraesCS3B01G529900 chr3A 93.137 102 7 0 701 802 713343477 713343376 1.560000e-32 150
18 TraesCS3B01G529900 chr2A 77.634 465 89 15 1872 2328 726134181 726134638 4.140000e-68 268
19 TraesCS3B01G529900 chr2A 87.879 165 20 0 541 705 367649322 367649158 7.120000e-46 195
20 TraesCS3B01G529900 chr2A 90.299 134 13 0 288 421 34657937 34658070 2.580000e-40 176
21 TraesCS3B01G529900 chr2A 91.892 111 7 2 180 289 34657965 34658074 1.210000e-33 154
22 TraesCS3B01G529900 chr7B 75.322 466 103 8 1872 2328 528255076 528254614 1.970000e-51 213
23 TraesCS3B01G529900 chr7B 89.781 137 14 0 284 420 540618345 540618481 2.580000e-40 176
24 TraesCS3B01G529900 chr7B 92.233 103 8 0 180 282 540618377 540618479 2.020000e-31 147
25 TraesCS3B01G529900 chr4D 88.889 171 18 1 541 710 386984667 386984837 2.540000e-50 209
26 TraesCS3B01G529900 chr4A 77.586 348 70 6 1872 2214 34746069 34746413 1.180000e-48 204
27 TraesCS3B01G529900 chr6D 92.701 137 10 0 284 420 377566427 377566291 5.500000e-47 198
28 TraesCS3B01G529900 chr6D 92.233 103 8 0 180 282 452639625 452639727 2.020000e-31 147
29 TraesCS3B01G529900 chr1D 87.135 171 19 3 534 703 73725582 73725750 9.210000e-45 191
30 TraesCS3B01G529900 chr1B 86.982 169 20 2 542 709 24349052 24349219 3.310000e-44 189
31 TraesCS3B01G529900 chr2D 89.437 142 14 1 284 424 284574944 284574803 7.170000e-41 178
32 TraesCS3B01G529900 chr6B 89.781 137 12 2 284 419 135792839 135792974 9.270000e-40 174
33 TraesCS3B01G529900 chr7A 91.589 107 9 0 179 285 565767107 565767001 5.620000e-32 148
34 TraesCS3B01G529900 chr6A 92.233 103 8 0 180 282 196882427 196882325 2.020000e-31 147


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 TraesCS3B01G529900 chr3B 771241041 771243562 2521 False 4658.0 4658 100.0000 1 2522 1 chr3B.!!$F1 2521
1 TraesCS3B01G529900 chr3B 771177507 771180080 2573 False 1819.5 2314 92.9820 1 2522 2 chr3B.!!$F2 2521
2 TraesCS3B01G529900 chr3B 770963195 770965677 2482 True 1747.5 2641 91.2390 1 2522 2 chr3B.!!$R3 2521
3 TraesCS3B01G529900 chr3D 577778797 577780535 1738 True 2266.0 2266 90.1760 47 1799 1 chr3D.!!$R2 1752
4 TraesCS3B01G529900 chr3D 578040126 578042579 2453 False 1557.5 2180 90.0995 19 2522 2 chr3D.!!$F1 2503
5 TraesCS3B01G529900 chr3D 577751925 577753004 1079 True 1428.0 1428 90.4280 704 1799 1 chr3D.!!$R1 1095
6 TraesCS3B01G529900 chr3D 577667153 577669213 2060 True 1303.5 2505 91.7035 421 2522 2 chr3D.!!$R3 2101
7 TraesCS3B01G529900 chr3A 713306679 713308513 1834 True 2095.0 2095 87.5400 698 2522 1 chr3A.!!$R1 1824
8 TraesCS3B01G529900 chr3A 713341154 713343477 2323 True 924.0 1698 89.4690 701 2519 2 chr3A.!!$R2 1818
9 TraesCS3B01G529900 chr3A 713416952 713418437 1485 True 748.5 857 85.5695 645 2154 2 chr3A.!!$R3 1509

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
172 175 0.179078 AACGGTGTGTTAACTCGGCA 60.179 50.0 7.22 0.0 39.61 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2933 0.320683 TGGTGTGTCTTCGGCAGATG 60.321 55.0 0.0 0.0 32.6 2.9 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
26 28 6.396829 AGTTTTTCTAGCAAAGCTTGATGT 57.603 33.333 0.00 0.00 39.72 3.06
103 105 3.153369 TCTTAGTGGCCAAATCTTGCA 57.847 42.857 7.24 0.00 0.00 4.08
114 117 2.762327 CAAATCTTGCACCTAGCCCAAT 59.238 45.455 0.00 0.00 44.83 3.16
137 140 4.814294 GTGTCGGGGGCTAGCACG 62.814 72.222 18.24 17.20 0.00 5.34
172 175 0.179078 AACGGTGTGTTAACTCGGCA 60.179 50.000 7.22 0.00 39.61 5.69
296 300 8.598041 AGATATAGAAGACTTGACCAACACTTT 58.402 33.333 0.00 0.00 0.00 2.66
313 317 2.756760 ACTTTATCGGACGGCTGTAGAA 59.243 45.455 0.00 0.00 0.00 2.10
357 361 2.614481 GGCTAGAACAATTCGGGTGACA 60.614 50.000 0.00 0.00 34.02 3.58
449 453 6.400568 CCTTGCATGATTCAAAAGGTATTGT 58.599 36.000 13.89 0.00 34.04 2.71
471 484 8.774546 TTGTGGGCCAAGATAAATAATAATGA 57.225 30.769 8.40 0.00 0.00 2.57
505 518 6.920210 GCCTTATAGAAGAATTTGGTGAATGC 59.080 38.462 0.00 0.00 34.25 3.56
942 1624 7.783090 ATATATAGCTTGCATCTTTCGATGG 57.217 36.000 0.00 0.00 45.72 3.51
1030 1715 2.496470 CACACTACCCTCCTCCTTGTAC 59.504 54.545 0.00 0.00 0.00 2.90
1062 1747 2.345244 CTTCTCACTGCCACCGCT 59.655 61.111 0.00 0.00 35.36 5.52
1173 1858 1.043816 CGGAGGGAGTGCATGACTAT 58.956 55.000 0.00 0.00 33.83 2.12
1179 1864 2.158842 GGGAGTGCATGACTATGAGCTT 60.159 50.000 0.00 0.00 36.36 3.74
1186 1871 1.746470 TGACTATGAGCTTCGACCGA 58.254 50.000 0.00 0.00 0.00 4.69
1242 1927 1.025812 AATTTCGTGTTGACGGCCAA 58.974 45.000 2.24 0.00 46.11 4.52
1649 2447 6.739100 CCATTTGTTCATGATTGCAAAATTCG 59.261 34.615 18.12 10.77 34.99 3.34
1699 2498 4.578871 TGGACAGTGAATGTGTTATCTGG 58.421 43.478 0.00 0.00 44.17 3.86
1882 2687 2.861274 TGTCATGTCAGCATTGGAACA 58.139 42.857 0.00 0.00 31.99 3.18
1921 2728 4.095400 ATCGCCCCTCCCTCACCT 62.095 66.667 0.00 0.00 0.00 4.00
1922 2729 4.779733 TCGCCCCTCCCTCACCTC 62.780 72.222 0.00 0.00 0.00 3.85
1960 2769 2.695359 TGTATTGCAGTCGGAAAGTCC 58.305 47.619 0.00 0.00 0.00 3.85
1998 2808 2.498644 TGACCAACACACCAGAACAA 57.501 45.000 0.00 0.00 0.00 2.83
2123 2933 3.535561 ACCACCGATTGAATCTCATGAC 58.464 45.455 3.43 0.00 0.00 3.06
2132 2942 2.431782 TGAATCTCATGACATCTGCCGA 59.568 45.455 0.00 0.00 0.00 5.54
2162 2972 0.392863 CCACATGCCCTTCGATGACA 60.393 55.000 0.00 0.00 0.00 3.58
2175 2986 2.035066 TCGATGACACGAGATGCATCAT 59.965 45.455 27.81 12.71 39.69 2.45
2275 3088 5.804979 CACAAACCCTAAACAAACTCACAAG 59.195 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 12 4.036027 CACCCATACATCAAGCTTTGCTAG 59.964 45.833 0.00 0.00 38.25 3.42
26 28 4.804597 AGATGCTACTACTCACACCCATA 58.195 43.478 0.00 0.00 0.00 2.74
114 117 0.469331 CTAGCCCCCGACACCATCTA 60.469 60.000 0.00 0.00 0.00 1.98
137 140 0.712222 CGTTTCGTTCTTACCGCTCC 59.288 55.000 0.00 0.00 0.00 4.70
172 175 1.964223 CAGCATAGATCGGTACCCACT 59.036 52.381 6.25 5.89 0.00 4.00
296 300 2.816087 GGTATTCTACAGCCGTCCGATA 59.184 50.000 0.00 0.00 0.00 2.92
313 317 4.686091 CGTTGATGCAACATAGATCGGTAT 59.314 41.667 10.48 0.00 43.70 2.73
357 361 5.883685 TCTATGTCTTCTCATGAAGCCAT 57.116 39.130 7.33 7.33 46.50 4.40
449 453 6.723977 GGGTCATTATTATTTATCTTGGCCCA 59.276 38.462 0.00 0.00 40.45 5.36
471 484 2.250273 TCTTCTATAAGGCCCTGAGGGT 59.750 50.000 20.64 1.16 46.51 4.34
533 674 8.537728 TTAGAAACGGTGGGACTATCTTATTA 57.462 34.615 0.00 0.00 0.00 0.98
681 824 2.781681 ACTCCCACCGTTCCTAAATG 57.218 50.000 0.00 0.00 0.00 2.32
942 1624 6.909357 GCTTTGCAGATATATTTGTGTGAGAC 59.091 38.462 5.25 0.00 0.00 3.36
1030 1715 4.346418 AGTGAGAAGGATGGCTACTATTGG 59.654 45.833 0.00 0.00 0.00 3.16
1083 1768 4.149019 TTGTTGGCTGTGGGGGCA 62.149 61.111 0.00 0.00 39.99 5.36
1173 1858 2.257371 CCGTTCGGTCGAAGCTCA 59.743 61.111 6.02 0.00 34.49 4.26
1179 1864 2.567497 AAAGGAGCCGTTCGGTCGA 61.567 57.895 12.81 0.00 40.06 4.20
1186 1871 1.053424 TGTACCTCAAAGGAGCCGTT 58.947 50.000 0.00 0.00 37.67 4.44
1242 1927 1.131883 GTGCTGTAGTGGACGTCGTAT 59.868 52.381 9.92 0.00 0.00 3.06
1454 2139 2.628178 ACTTGTGTCGATCTTGGAGTCA 59.372 45.455 0.00 0.00 0.00 3.41
1626 2424 7.424227 ACGAATTTTGCAATCATGAACAAAT 57.576 28.000 17.46 8.18 32.50 2.32
1649 2447 7.323656 CACCTCGTTAATTGAAATCTCACAAAC 59.676 37.037 0.00 0.00 0.00 2.93
1699 2498 2.706339 ACCATCATGCCTTCTCTGAC 57.294 50.000 0.00 0.00 0.00 3.51
1921 2728 4.751767 ACAAAATTTTTGGCCTGACTGA 57.248 36.364 22.27 0.00 0.00 3.41
1922 2729 6.566376 GCAATACAAAATTTTTGGCCTGACTG 60.566 38.462 22.27 11.87 0.00 3.51
1998 2808 3.162666 TCTCTTCATAGGTGACGGTTGT 58.837 45.455 0.00 0.00 33.11 3.32
2123 2933 0.320683 TGGTGTGTCTTCGGCAGATG 60.321 55.000 0.00 0.00 32.60 2.90
2132 2942 0.823356 GGCATGTGGTGGTGTGTCTT 60.823 55.000 0.00 0.00 0.00 3.01
2162 2972 2.804527 CCATTTCGATGATGCATCTCGT 59.195 45.455 30.11 18.46 38.59 4.18
2175 2986 2.915869 GCCTAGCCCCCATTTCGA 59.084 61.111 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.