Multiple sequence alignment - TraesCS5B01G216300

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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 TraesCS5B01G216300 chr5B 100.000 2508 0 0 1 2508 389819987 389822494 0.000000e+00 4632.0
1 TraesCS5B01G216300 chr5B 86.301 73 10 0 1132 1204 94092999 94093071 2.070000e-11 80.5
2 TraesCS5B01G216300 chr5A 92.821 2549 118 23 16 2508 435040174 435042713 0.000000e+00 3633.0
3 TraesCS5B01G216300 chr5A 84.127 567 66 16 836 1401 686506677 686506134 6.140000e-146 527.0
4 TraesCS5B01G216300 chr5A 84.932 73 11 0 1132 1204 82306861 82306933 9.620000e-10 75.0
5 TraesCS5B01G216300 chr5D 95.319 2051 62 13 468 2506 333382698 333384726 0.000000e+00 3225.0
6 TraesCS5B01G216300 chr5D 86.083 503 35 15 1 470 333377943 333378443 2.230000e-140 508.0
7 TraesCS5B01G216300 chr5D 80.556 144 21 7 107 246 61343492 61343632 1.230000e-18 104.0
8 TraesCS5B01G216300 chr5D 80.741 135 20 6 107 239 453836837 453836967 1.590000e-17 100.0
9 TraesCS5B01G216300 chr5D 84.932 73 11 0 1132 1204 88520332 88520404 9.620000e-10 75.0
10 TraesCS5B01G216300 chr4B 80.137 146 21 7 108 248 118637934 118638076 4.410000e-18 102.0
11 TraesCS5B01G216300 chr7B 79.452 146 25 4 108 250 246073194 246073051 5.710000e-17 99.0
12 TraesCS5B01G216300 chr1B 80.435 138 20 7 112 245 139374861 139374727 5.710000e-17 99.0
13 TraesCS5B01G216300 chr1B 79.433 141 24 4 108 245 429226021 429225883 7.390000e-16 95.3
14 TraesCS5B01G216300 chr6A 80.292 137 20 7 107 239 123762716 123762849 2.050000e-16 97.1


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 TraesCS5B01G216300 chr5B 389819987 389822494 2507 False 4632 4632 100.000 1 2508 1 chr5B.!!$F2 2507
1 TraesCS5B01G216300 chr5A 435040174 435042713 2539 False 3633 3633 92.821 16 2508 1 chr5A.!!$F2 2492
2 TraesCS5B01G216300 chr5A 686506134 686506677 543 True 527 527 84.127 836 1401 1 chr5A.!!$R1 565
3 TraesCS5B01G216300 chr5D 333382698 333384726 2028 False 3225 3225 95.319 468 2506 1 chr5D.!!$F4 2038
4 TraesCS5B01G216300 chr5D 333377943 333378443 500 False 508 508 86.083 1 470 1 chr5D.!!$F3 469

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
220 221 0.817634 TCCAACGAAGGCTGTTGTGG 60.818 55.0 14.4 8.58 44.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2239 0.885879 GCGGGGTAAAACCTCCTTTG 59.114 55.0 0.0 0.0 34.38 2.77 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
46 47 7.606073 TCTGCTTATGTTACTTTGATGCTACAA 59.394 33.333 0.00 0.00 0.00 2.41
66 67 4.460382 ACAAACACCACTCCATTCATCATC 59.540 41.667 0.00 0.00 0.00 2.92
110 111 2.693797 ATGAGCAAGCACTTGTTTCG 57.306 45.000 11.77 0.00 42.31 3.46
127 128 2.577606 TCGGGTGTGGTTGAATTGAT 57.422 45.000 0.00 0.00 0.00 2.57
130 131 3.754323 TCGGGTGTGGTTGAATTGATAAC 59.246 43.478 0.00 0.00 0.00 1.89
138 139 6.545666 TGTGGTTGAATTGATAACTCAACTGT 59.454 34.615 13.37 0.00 45.33 3.55
143 144 9.515020 GTTGAATTGATAACTCAACTGTCAAAA 57.485 29.630 8.20 0.00 43.92 2.44
220 221 0.817634 TCCAACGAAGGCTGTTGTGG 60.818 55.000 14.40 8.58 44.00 4.17
283 287 4.536090 AGTGAGGTGATTTGTATTCCCTCA 59.464 41.667 0.00 0.00 44.55 3.86
289 293 4.332819 GTGATTTGTATTCCCTCAGTTCCG 59.667 45.833 0.00 0.00 0.00 4.30
299 303 2.678336 CCCTCAGTTCCGAAATAAGTGC 59.322 50.000 0.00 0.00 0.00 4.40
301 305 3.334691 CTCAGTTCCGAAATAAGTGCCA 58.665 45.455 0.00 0.00 0.00 4.92
328 360 7.512402 TGGACATACATCCCTATTATCAAGACA 59.488 37.037 0.00 0.00 38.06 3.41
332 364 9.429359 CATACATCCCTATTATCAAGACAAGTC 57.571 37.037 0.00 0.00 0.00 3.01
418 454 1.373748 GGTTAGACGAGCAACCGCA 60.374 57.895 0.00 0.00 42.27 5.69
446 483 8.466086 AATCAGAAACAAACACTCAAAGTTTC 57.534 30.769 0.00 0.00 44.99 2.78
535 573 2.959516 TGAGTGGCTGTACAATTCTCG 58.040 47.619 0.00 0.00 0.00 4.04
568 613 1.472376 GCGGATACTTGAGCAAGCTCT 60.472 52.381 21.35 5.68 43.12 4.09
890 939 4.935205 GCTTAAATCATTTGGGTGGGAAAC 59.065 41.667 0.00 0.00 0.00 2.78
900 949 2.780924 TGGGAAACTGGGGGCACT 60.781 61.111 0.00 0.00 0.00 4.40
922 971 1.663445 CCGTACGCATCGATTCTCCTC 60.663 57.143 10.49 0.00 0.00 3.71
1332 1381 3.633094 CTCGCACAGGAGGGTGTCG 62.633 68.421 0.00 0.00 40.89 4.35
1529 1578 4.522114 GCATAGAGCTTCTTCTCCCTTTT 58.478 43.478 0.00 0.00 41.15 2.27
1538 1587 5.241728 GCTTCTTCTCCCTTTTCTTTTGCTA 59.758 40.000 0.00 0.00 0.00 3.49
1568 1620 5.829062 ACCGGGGCACAATTTACTATATA 57.171 39.130 6.32 0.00 0.00 0.86
1614 1673 6.554982 AGGCAAAGACATACTATGGTGAGATA 59.445 38.462 1.11 0.00 33.60 1.98
1662 1721 4.093850 GGTATGTTACAAAGTTACTGCCCG 59.906 45.833 0.00 0.00 0.00 6.13
1688 1747 8.353423 AGTTACAAGGATGAAAACAGCATATT 57.647 30.769 0.00 0.00 32.24 1.28
1727 1786 1.233019 CATGCAGTACTAGCCATGCC 58.767 55.000 13.88 0.00 37.89 4.40
1728 1787 0.839277 ATGCAGTACTAGCCATGCCA 59.161 50.000 12.71 1.49 37.89 4.92
1729 1788 0.839277 TGCAGTACTAGCCATGCCAT 59.161 50.000 12.71 0.00 37.89 4.40
1730 1789 1.233019 GCAGTACTAGCCATGCCATG 58.767 55.000 0.00 0.00 32.49 3.66
1731 1790 1.233019 CAGTACTAGCCATGCCATGC 58.767 55.000 0.00 0.00 0.00 4.06
1826 1885 1.971357 CTGTGGGTGGTTCTCTGTAGT 59.029 52.381 0.00 0.00 0.00 2.73
1840 1899 2.364324 TCTGTAGTTGTGTGGTCCAGTC 59.636 50.000 0.00 0.00 0.00 3.51
2026 2085 2.485426 CTGGCGATGCAGAAGAGAAAAA 59.515 45.455 0.00 0.00 0.00 1.94
2169 2230 6.220726 TCACATCGAAACATCCATCTCTTA 57.779 37.500 0.00 0.00 0.00 2.10
2195 2256 0.885879 CGCAAAGGAGGTTTTACCCC 59.114 55.000 0.00 0.00 39.75 4.95
2199 2260 2.044650 GGAGGTTTTACCCCGCCC 60.045 66.667 0.00 0.00 39.75 6.13
2201 2262 1.077930 GAGGTTTTACCCCGCCCTC 60.078 63.158 0.00 0.00 39.75 4.30
2243 2304 3.256704 TCCATAACCTCCACCTCTTGTT 58.743 45.455 0.00 0.00 0.00 2.83
2244 2305 3.655777 TCCATAACCTCCACCTCTTGTTT 59.344 43.478 0.00 0.00 0.00 2.83
2245 2306 3.758554 CCATAACCTCCACCTCTTGTTTG 59.241 47.826 0.00 0.00 0.00 2.93
2247 2308 5.514136 CCATAACCTCCACCTCTTGTTTGTA 60.514 44.000 0.00 0.00 0.00 2.41
2302 2365 8.807948 ACTGTATTATGCACTACAGGAAAATT 57.192 30.769 25.11 9.91 45.87 1.82
2330 2393 4.418392 CTGCCGAGTATTAACGTGTAAGT 58.582 43.478 0.00 0.00 0.00 2.24
2358 2425 7.136772 AGTGTTAAAACATTCTCGGCTTAAAC 58.863 34.615 0.00 0.00 41.59 2.01
2393 2460 4.084287 AGTAGTGACCGGAGAATACACAA 58.916 43.478 9.46 0.00 34.47 3.33
2429 2496 1.067212 CGGCTTCCATACGAGTAAGCT 59.933 52.381 0.00 0.00 43.04 3.74
2450 2517 2.962089 GTGTGTGCACAAAAGGCTG 58.038 52.632 23.59 0.00 43.77 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.581309 AGATGATGAATGGAGTGGTGTT 57.419 40.909 0.00 0.00 0.00 3.32
100 101 1.099689 AACCACACCCGAAACAAGTG 58.900 50.000 0.00 0.00 37.53 3.16
110 111 4.764823 TGAGTTATCAATTCAACCACACCC 59.235 41.667 0.00 0.00 30.61 4.61
127 128 8.556213 ACTTGTAAGTTTTGACAGTTGAGTTA 57.444 30.769 0.00 0.00 35.21 2.24
130 131 9.651718 GAATACTTGTAAGTTTTGACAGTTGAG 57.348 33.333 2.20 0.00 40.37 3.02
138 139 7.152645 AGCGAGAGAATACTTGTAAGTTTTGA 58.847 34.615 2.20 0.00 40.37 2.69
143 144 5.185249 TGGAAGCGAGAGAATACTTGTAAGT 59.815 40.000 2.51 2.51 42.91 2.24
220 221 5.304614 TGATAGCCCACAAAGTATAGGAGAC 59.695 44.000 0.00 0.00 0.00 3.36
276 280 4.575885 CACTTATTTCGGAACTGAGGGAA 58.424 43.478 5.17 0.00 0.00 3.97
283 287 3.016736 CCATGGCACTTATTTCGGAACT 58.983 45.455 0.00 0.00 0.00 3.01
289 293 6.294176 GGATGTATGTCCATGGCACTTATTTC 60.294 42.308 6.96 9.25 38.20 2.17
299 303 7.199167 TGATAATAGGGATGTATGTCCATGG 57.801 40.000 4.97 4.97 40.17 3.66
301 305 8.543774 GTCTTGATAATAGGGATGTATGTCCAT 58.456 37.037 0.00 0.00 40.17 3.41
328 360 6.665992 TGGATACACTTGTAAGACAGACTT 57.334 37.500 0.00 0.00 46.17 3.01
332 364 4.820897 TGCTGGATACACTTGTAAGACAG 58.179 43.478 0.00 11.19 46.17 3.51
367 403 9.077885 AGATGAGGCTCACTTTGTTTTTATTTA 57.922 29.630 21.37 0.00 0.00 1.40
418 454 7.830739 ACTTTGAGTGTTTGTTTCTGATTCTT 58.169 30.769 0.00 0.00 0.00 2.52
535 573 4.468095 AGTATCCGCAATATTTTCACGC 57.532 40.909 0.00 0.00 0.00 5.34
568 613 3.776781 CCGTCACCGTATGCCCCA 61.777 66.667 0.00 0.00 0.00 4.96
913 962 6.913673 GTGTATTCTAGTTGTCGAGGAGAATC 59.086 42.308 9.30 4.93 37.83 2.52
922 971 5.230306 GCTAGCTTGTGTATTCTAGTTGTCG 59.770 44.000 7.70 0.00 33.06 4.35
1048 1097 1.080093 GGTTGAGGTCGATGTCGCA 60.080 57.895 0.00 0.00 39.60 5.10
1126 1175 3.833070 TGGGAGGAGTAGAACTTCTTGTC 59.167 47.826 0.00 0.00 33.19 3.18
1268 1317 4.120755 CCTTCCCTCCCCTGCTGC 62.121 72.222 0.00 0.00 0.00 5.25
1568 1620 6.380274 TGCCTTGCTTATGAGTAGTAGTACTT 59.620 38.462 8.40 0.00 39.78 2.24
1614 1673 1.001641 GGCCATTCTGGAGCAGTGT 60.002 57.895 0.00 0.00 40.96 3.55
1662 1721 5.689383 TGCTGTTTTCATCCTTGTAACTC 57.311 39.130 0.00 0.00 0.00 3.01
1688 1747 2.022195 GTGTCCATGTCTCGCCTAGTA 58.978 52.381 0.00 0.00 0.00 1.82
1826 1885 2.110213 GCCGACTGGACCACACAA 59.890 61.111 0.00 0.00 37.49 3.33
1840 1899 2.257207 TCCTATCCTATTGGAAGGCCG 58.743 52.381 14.89 0.00 46.80 6.13
2026 2085 2.101415 GCTGCTTTCCTTTTCCACAAGT 59.899 45.455 0.00 0.00 0.00 3.16
2178 2239 0.885879 GCGGGGTAAAACCTCCTTTG 59.114 55.000 0.00 0.00 34.38 2.77
2285 2348 5.653769 AGCATGTAATTTTCCTGTAGTGCAT 59.346 36.000 0.00 0.00 0.00 3.96
2302 2365 3.181484 ACGTTAATACTCGGCAGCATGTA 60.181 43.478 0.00 0.00 39.31 2.29
2358 2425 1.822990 TCACTACTCGGCTTAGGTTGG 59.177 52.381 0.00 0.00 0.00 3.77
2446 2513 3.044305 GGTCGTGCACAGACAGCC 61.044 66.667 29.46 17.05 40.20 4.85
2450 2517 0.170561 AGTATCGGTCGTGCACAGAC 59.829 55.000 24.34 24.34 37.86 3.51


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

AutoCloner maintained by Alex Coulton.