Multiple sequence alignment - TraesCS5B01G557200

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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 TraesCS5B01G557200 chr5B 100.000 2264 0 0 1 2264 705251017 705248754 0.000000e+00 4181.0
1 TraesCS5B01G557200 chr5B 92.275 1890 94 22 1 1846 123786950 123788831 0.000000e+00 2634.0
2 TraesCS5B01G557200 chr5B 91.782 1874 101 27 1 1834 514050647 514052507 0.000000e+00 2558.0
3 TraesCS5B01G557200 chr5B 92.709 1783 95 12 1 1752 353930759 353928981 0.000000e+00 2540.0
4 TraesCS5B01G557200 chr5B 83.983 231 36 1 2035 2264 18186081 18186311 1.050000e-53 220.0
5 TraesCS5B01G557200 chr5B 83.550 231 37 1 2035 2264 353928763 353928533 4.900000e-52 215.0
6 TraesCS5B01G557200 chr3D 94.027 2143 94 12 1 2115 581472605 581474741 0.000000e+00 3217.0
7 TraesCS5B01G557200 chr6B 90.425 2141 159 27 1 2115 77328193 77326073 0.000000e+00 2776.0
8 TraesCS5B01G557200 chr6B 89.157 2158 175 31 1 2118 715471860 715469722 0.000000e+00 2634.0
9 TraesCS5B01G557200 chr6B 89.404 151 16 0 2112 2262 715469798 715469648 8.250000e-45 191.0
10 TraesCS5B01G557200 chr4A 89.874 2143 147 32 1 2130 692377076 692374991 0.000000e+00 2691.0
11 TraesCS5B01G557200 chr4A 89.542 153 16 0 2112 2264 692374974 692374822 6.380000e-46 195.0
12 TraesCS5B01G557200 chr7B 92.544 1891 92 21 1 1849 535437174 535435291 0.000000e+00 2665.0
13 TraesCS5B01G557200 chr7B 91.809 1880 108 22 1 1846 666615818 666617685 0.000000e+00 2577.0
14 TraesCS5B01G557200 chr7B 92.680 1612 87 9 1 1584 664951493 664949885 0.000000e+00 2294.0
15 TraesCS5B01G557200 chr7B 89.579 451 31 5 1674 2115 692398609 692399052 1.960000e-155 558.0
16 TraesCS5B01G557200 chr7B 92.500 160 12 0 2105 2264 692398972 692399131 1.750000e-56 230.0
17 TraesCS5B01G557200 chr7B 84.649 228 34 1 2038 2264 666617852 666618079 2.260000e-55 226.0
18 TraesCS5B01G557200 chr3B 91.327 1891 129 16 1 1865 21644963 21646844 0.000000e+00 2551.0
19 TraesCS5B01G557200 chr3B 83.333 228 37 1 2038 2264 734225392 734225165 2.280000e-50 209.0
20 TraesCS5B01G557200 chr4B 91.841 1716 95 16 433 2115 633304982 633306685 0.000000e+00 2351.0
21 TraesCS5B01G557200 chr4B 87.321 1396 125 22 721 2107 624362518 624363870 0.000000e+00 1550.0
22 TraesCS5B01G557200 chr4B 91.250 160 14 0 2105 2264 633306605 633306764 3.790000e-53 219.0
23 TraesCS5B01G557200 chr2D 93.822 1554 85 7 720 2262 126689046 126687493 0.000000e+00 2327.0
24 TraesCS5B01G557200 chr2D 96.419 726 26 0 1 726 126713124 126712399 0.000000e+00 1197.0
25 TraesCS5B01G557200 chr2D 88.095 84 10 0 2035 2118 126687650 126687567 1.430000e-17 100.0
26 TraesCS5B01G557200 chr2D 87.671 73 9 0 2046 2118 126686170 126686098 4.010000e-13 86.1


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 TraesCS5B01G557200 chr5B 705248754 705251017 2263 True 4181.0 4181 100.000000 1 2264 1 chr5B.!!$R1 2263
1 TraesCS5B01G557200 chr5B 123786950 123788831 1881 False 2634.0 2634 92.275000 1 1846 1 chr5B.!!$F2 1845
2 TraesCS5B01G557200 chr5B 514050647 514052507 1860 False 2558.0 2558 91.782000 1 1834 1 chr5B.!!$F3 1833
3 TraesCS5B01G557200 chr5B 353928533 353930759 2226 True 1377.5 2540 88.129500 1 2264 2 chr5B.!!$R2 2263
4 TraesCS5B01G557200 chr3D 581472605 581474741 2136 False 3217.0 3217 94.027000 1 2115 1 chr3D.!!$F1 2114
5 TraesCS5B01G557200 chr6B 77326073 77328193 2120 True 2776.0 2776 90.425000 1 2115 1 chr6B.!!$R1 2114
6 TraesCS5B01G557200 chr6B 715469648 715471860 2212 True 1412.5 2634 89.280500 1 2262 2 chr6B.!!$R2 2261
7 TraesCS5B01G557200 chr4A 692374822 692377076 2254 True 1443.0 2691 89.708000 1 2264 2 chr4A.!!$R1 2263
8 TraesCS5B01G557200 chr7B 535435291 535437174 1883 True 2665.0 2665 92.544000 1 1849 1 chr7B.!!$R1 1848
9 TraesCS5B01G557200 chr7B 664949885 664951493 1608 True 2294.0 2294 92.680000 1 1584 1 chr7B.!!$R2 1583
10 TraesCS5B01G557200 chr7B 666615818 666618079 2261 False 1401.5 2577 88.229000 1 2264 2 chr7B.!!$F1 2263
11 TraesCS5B01G557200 chr7B 692398609 692399131 522 False 394.0 558 91.039500 1674 2264 2 chr7B.!!$F2 590
12 TraesCS5B01G557200 chr3B 21644963 21646844 1881 False 2551.0 2551 91.327000 1 1865 1 chr3B.!!$F1 1864
13 TraesCS5B01G557200 chr4B 624362518 624363870 1352 False 1550.0 1550 87.321000 721 2107 1 chr4B.!!$F1 1386
14 TraesCS5B01G557200 chr4B 633304982 633306764 1782 False 1285.0 2351 91.545500 433 2264 2 chr4B.!!$F2 1831
15 TraesCS5B01G557200 chr2D 126712399 126713124 725 True 1197.0 1197 96.419000 1 726 1 chr2D.!!$R1 725
16 TraesCS5B01G557200 chr2D 126686098 126689046 2948 True 837.7 2327 89.862667 720 2262 3 chr2D.!!$R2 1542

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
831 912 0.037605 GTGGTTCGGTGGTGGTAGAG 60.038 60.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2627 1.102978 GCATAGGACCAAAACGCCAT 58.897 50.0 0.0 0.0 0.0 4.4 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
256 257 4.070716 GTGCGAGAGGCCTAGTAAGTATA 58.929 47.826 4.42 0.00 42.61 1.47
313 314 7.423199 GTCGTCAGGAAATATACATGTGTCTA 58.577 38.462 9.11 0.00 0.00 2.59
400 405 1.074951 CAACCCTTCCTGGACCCAC 59.925 63.158 0.00 0.00 38.35 4.61
421 426 4.100963 CACCACAGTGGCCTGACTATAATA 59.899 45.833 20.48 0.00 42.67 0.98
425 430 3.580458 CAGTGGCCTGACTATAATAGCCT 59.420 47.826 3.32 0.00 41.50 4.58
484 494 5.514834 CCCAAGGGTAGAATCAGACAGAAAA 60.515 44.000 0.00 0.00 0.00 2.29
648 659 4.469469 AAGGAAAACATCAAAGGAGGGA 57.531 40.909 0.00 0.00 0.00 4.20
764 844 1.884579 GAGTGGACAACGTGGTAGAGA 59.115 52.381 0.00 0.00 0.00 3.10
768 848 1.549170 GGACAACGTGGTAGAGATGGT 59.451 52.381 0.00 0.00 0.00 3.55
788 868 1.062121 TGCTAATGGAGGCCCTAGAGT 60.062 52.381 0.00 0.00 0.00 3.24
831 912 0.037605 GTGGTTCGGTGGTGGTAGAG 60.038 60.000 0.00 0.00 0.00 2.43
1195 1285 6.037281 GTGGACGGAAGGAAGAAGATATTTTC 59.963 42.308 0.00 0.00 0.00 2.29
1220 1310 3.200605 TGTCCCAACTATGCACATGATCT 59.799 43.478 0.00 0.00 0.00 2.75
1226 1316 0.249405 TATGCACATGATCTCGCGCA 60.249 50.000 8.75 0.00 0.00 6.09
1240 1330 2.895372 CGCATCCCACTAACGCCC 60.895 66.667 0.00 0.00 0.00 6.13
1268 1359 4.520179 GTCCCACCGGTATGTTAGAAAAT 58.480 43.478 6.87 0.00 0.00 1.82
1389 1480 3.996921 ATGAAGTGCCAGAAGATGTCT 57.003 42.857 0.00 0.00 36.88 3.41
1446 1537 6.710744 ACAACGACTGTTTGAAGAATCCTTAT 59.289 34.615 0.00 0.00 35.72 1.73
1537 1628 0.952497 CGCAAAGAGAAGGCAGCTCA 60.952 55.000 8.92 0.00 34.85 4.26
1552 1643 1.290431 AGCTCATCAAGAGGAGAGGGA 59.710 52.381 15.18 0.00 44.86 4.20
1652 1745 4.018960 ACCCATAGAGACTTGAATGTGCTT 60.019 41.667 0.00 0.00 0.00 3.91
1829 2013 7.171653 TCATTAGTTGTCCATGTGGTGAATTA 58.828 34.615 0.00 0.00 36.34 1.40
1846 2030 7.042187 TGGTGAATTATGCAACAAAATTGTCAC 60.042 33.333 0.00 1.29 41.31 3.67
1865 2051 7.159322 TGTCACATCTAGAGAGGTAAAACTC 57.841 40.000 0.00 0.00 36.90 3.01
1886 2095 1.075374 CCCCCTGATGAAACCAAGACA 59.925 52.381 0.00 0.00 0.00 3.41
2030 2291 0.036858 GGTGTCTTGGTCTCTGCTCC 60.037 60.000 0.00 0.00 0.00 4.70
2031 2292 0.681733 GTGTCTTGGTCTCTGCTCCA 59.318 55.000 0.00 0.00 0.00 3.86
2032 2293 0.972134 TGTCTTGGTCTCTGCTCCAG 59.028 55.000 0.00 0.00 35.05 3.86
2033 2294 0.972883 GTCTTGGTCTCTGCTCCAGT 59.027 55.000 0.00 0.00 35.05 4.00
2034 2295 1.067213 GTCTTGGTCTCTGCTCCAGTC 60.067 57.143 0.00 0.00 35.05 3.51
2035 2296 0.248843 CTTGGTCTCTGCTCCAGTCC 59.751 60.000 0.00 0.00 35.05 3.85
2036 2297 0.178921 TTGGTCTCTGCTCCAGTCCT 60.179 55.000 0.00 0.00 35.05 3.85
2055 2316 2.355920 CCTAGACACTAGAGACCACGGT 60.356 54.545 0.00 0.00 0.00 4.83
2082 2343 2.036089 GGCCGTATCCAGAGAGGTAAAG 59.964 54.545 0.00 0.00 39.02 1.85
2085 2346 4.142790 CCGTATCCAGAGAGGTAAAGCTA 58.857 47.826 0.00 0.00 39.02 3.32
2086 2347 4.767928 CCGTATCCAGAGAGGTAAAGCTAT 59.232 45.833 0.00 0.00 39.02 2.97
2087 2348 5.244178 CCGTATCCAGAGAGGTAAAGCTATT 59.756 44.000 0.00 0.00 39.02 1.73
2107 2368 0.536006 GTTGCTCCTCTGCACACCTT 60.536 55.000 0.00 0.00 43.20 3.50
2110 2406 0.250467 GCTCCTCTGCACACCTTGAA 60.250 55.000 0.00 0.00 0.00 2.69
2124 2420 2.397413 CTTGAAGCCAGGGACCACGT 62.397 60.000 0.00 0.00 0.00 4.49
2191 2627 0.320374 CACCTAGACGCCAAGGTTGA 59.680 55.000 0.67 0.00 43.77 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.749076 CGGTTTCCTCTGAATGCATCAA 59.251 45.455 0.00 0.00 37.67 2.57
256 257 0.254178 AGATGAGAGCACGGCCAATT 59.746 50.000 2.24 0.00 0.00 2.32
295 296 7.936847 TGTCCCATTAGACACATGTATATTTCC 59.063 37.037 0.00 0.00 41.78 3.13
400 405 3.845781 ATTATAGTCAGGCCACTGTGG 57.154 47.619 22.46 22.46 45.14 4.17
425 430 2.140792 GGATCGGGCCTAAGCTCCA 61.141 63.158 0.84 0.00 35.31 3.86
484 494 1.689273 GTCCATATCGCCTCTCAACCT 59.311 52.381 0.00 0.00 0.00 3.50
648 659 1.882352 GCCTGACTCGTGGTTGGATTT 60.882 52.381 0.00 0.00 0.00 2.17
764 844 0.995675 AGGGCCTCCATTAGCACCAT 60.996 55.000 0.00 0.00 30.65 3.55
768 848 1.062121 ACTCTAGGGCCTCCATTAGCA 60.062 52.381 10.74 0.00 34.83 3.49
788 868 0.112995 ACGACCACCACTACTACCCA 59.887 55.000 0.00 0.00 0.00 4.51
831 912 2.885894 CCTTATCAGTCCTCCGTACTCC 59.114 54.545 0.00 0.00 0.00 3.85
1195 1285 2.183478 TGTGCATAGTTGGGACACAG 57.817 50.000 0.00 0.00 39.29 3.66
1220 1310 2.202690 CGTTAGTGGGATGCGCGA 60.203 61.111 12.10 0.00 0.00 5.87
1226 1316 0.180406 GTCATGGGCGTTAGTGGGAT 59.820 55.000 0.00 0.00 0.00 3.85
1240 1330 0.529773 CATACCGGTGGGACGTCATG 60.530 60.000 19.93 6.32 36.97 3.07
1268 1359 8.884323 AGTGAATCATAATGGAGAATAGCCTAA 58.116 33.333 0.00 0.00 0.00 2.69
1446 1537 2.952978 GTTCTTCATCCTCGGCTCTCTA 59.047 50.000 0.00 0.00 0.00 2.43
1475 1566 1.687493 CCGCTCCTTCCTCTCCCTT 60.687 63.158 0.00 0.00 0.00 3.95
1537 1628 5.311913 AGTTTTCTTTCCCTCTCCTCTTGAT 59.688 40.000 0.00 0.00 0.00 2.57
1552 1643 1.609072 GAGCCCTCGCAAGTTTTCTTT 59.391 47.619 0.00 0.00 38.17 2.52
1575 1666 2.702478 CCTCATCCTCCTCTTGTGCATA 59.298 50.000 0.00 0.00 0.00 3.14
1829 2013 7.175467 TCTCTAGATGTGACAATTTTGTTGCAT 59.825 33.333 11.05 11.05 42.43 3.96
1846 2030 4.345547 GGGGGAGTTTTACCTCTCTAGATG 59.654 50.000 0.00 0.00 32.25 2.90
1886 2095 2.159382 CAAAATGCCGTAGTTCCTGGT 58.841 47.619 0.00 0.00 0.00 4.00
2030 2291 3.942748 GTGGTCTCTAGTGTCTAGGACTG 59.057 52.174 16.67 0.00 33.15 3.51
2031 2292 3.369681 CGTGGTCTCTAGTGTCTAGGACT 60.370 52.174 16.67 0.00 33.15 3.85
2032 2293 2.937799 CGTGGTCTCTAGTGTCTAGGAC 59.062 54.545 12.51 12.51 0.00 3.85
2033 2294 2.093075 CCGTGGTCTCTAGTGTCTAGGA 60.093 54.545 4.32 0.00 0.00 2.94
2034 2295 2.290464 CCGTGGTCTCTAGTGTCTAGG 58.710 57.143 4.32 0.00 0.00 3.02
2035 2296 2.678836 CACCGTGGTCTCTAGTGTCTAG 59.321 54.545 0.00 0.00 0.00 2.43
2036 2297 2.039480 ACACCGTGGTCTCTAGTGTCTA 59.961 50.000 3.03 0.00 37.05 2.59
2055 2316 2.693591 CTCTCTGGATACGGCCTAAACA 59.306 50.000 0.00 0.00 45.18 2.83
2065 2326 7.056844 ACAATAGCTTTACCTCTCTGGATAC 57.943 40.000 0.00 0.00 39.71 2.24
2068 2329 5.734720 CAACAATAGCTTTACCTCTCTGGA 58.265 41.667 0.00 0.00 39.71 3.86
2082 2343 1.742761 TGCAGAGGAGCAACAATAGC 58.257 50.000 0.00 0.00 42.46 2.97
2107 2368 2.847234 ACGTGGTCCCTGGCTTCA 60.847 61.111 0.00 0.00 0.00 3.02
2124 2420 1.679680 CTCTGGATACGGCCTAAACGA 59.320 52.381 0.00 0.00 45.18 3.85
2191 2627 1.102978 GCATAGGACCAAAACGCCAT 58.897 50.000 0.00 0.00 0.00 4.40
2232 2669 6.013379 AGGTTGAAGAATGAGTTATGGAGTGA 60.013 38.462 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.