Multiple sequence alignment - TraesCS5B01G150500

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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 TraesCS5B01G150500 chr5B 100.000 2590 0 0 1 2590 278227707 278230296 0.000000e+00 4783
1 TraesCS5B01G150500 chr5A 92.614 2058 103 21 63 2084 328943658 328945702 0.000000e+00 2913
2 TraesCS5B01G150500 chr5A 95.481 509 20 2 2084 2590 328945760 328946267 0.000000e+00 809
3 TraesCS5B01G150500 chr5D 94.698 943 32 7 2 930 244704376 244705314 0.000000e+00 1448
4 TraesCS5B01G150500 chr5D 92.966 725 38 6 1361 2084 244705837 244706549 0.000000e+00 1044
5 TraesCS5B01G150500 chr5D 96.480 483 15 2 884 1364 244705310 244705792 0.000000e+00 797
6 TraesCS5B01G150500 chr5D 94.477 507 26 2 2086 2590 244706609 244707115 0.000000e+00 780
7 TraesCS5B01G150500 chr5D 91.736 121 10 0 2084 2204 222429050 222428930 4.430000e-38 169
8 TraesCS5B01G150500 chr3B 93.388 121 6 2 2084 2203 738374985 738374866 7.360000e-41 178
9 TraesCS5B01G150500 chr2A 93.333 120 8 0 2084 2203 549290307 549290426 7.360000e-41 178
10 TraesCS5B01G150500 chr4B 92.500 120 9 0 2084 2203 106227442 106227561 3.430000e-39 172
11 TraesCS5B01G150500 chr7D 91.736 121 10 0 2084 2204 117755246 117755366 4.430000e-38 169
12 TraesCS5B01G150500 chr1A 91.667 120 10 0 2084 2203 395177568 395177449 1.590000e-37 167
13 TraesCS5B01G150500 chr4A 89.313 131 13 1 2084 2214 48887430 48887301 2.060000e-36 163


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 TraesCS5B01G150500 chr5B 278227707 278230296 2589 False 4783.00 4783 100.00000 1 2590 1 chr5B.!!$F1 2589
1 TraesCS5B01G150500 chr5A 328943658 328946267 2609 False 1861.00 2913 94.04750 63 2590 2 chr5A.!!$F1 2527
2 TraesCS5B01G150500 chr5D 244704376 244707115 2739 False 1017.25 1448 94.65525 2 2590 4 chr5D.!!$F1 2588

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
935 1008 0.470268 ACCGGCTATCTCTCCCCTTC 60.47 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2467 2663 0.923358 TTTGGTTCTGGGTGGACTGT 59.077 50.0 0.0 0.0 0.0 3.55 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
102 103 5.490159 TGCAGATTGACTACACATGAATGA 58.510 37.500 0.00 0.00 0.00 2.57
135 136 8.330466 TCGGAATTTCTAGCACAAAATCTTTA 57.670 30.769 0.00 0.00 0.00 1.85
235 253 6.891361 TCAAACACCATCTTAACATGGATGAT 59.109 34.615 15.86 3.77 45.79 2.45
237 255 6.189859 AACACCATCTTAACATGGATGATGT 58.810 36.000 15.86 6.67 45.44 3.06
262 280 2.504175 GGCCTTGTACCATAGTCCAGAA 59.496 50.000 0.00 0.00 0.00 3.02
271 289 1.414181 CATAGTCCAGAAGCATCCGGT 59.586 52.381 0.00 0.00 0.00 5.28
286 304 1.597854 CGGTGTGTGTGCAGGATGT 60.598 57.895 0.00 0.00 39.31 3.06
299 317 3.181440 TGCAGGATGTCAAGAAAGAACCT 60.181 43.478 0.00 0.00 39.31 3.50
452 471 2.724977 CGTACCCATCGCAGTCATAT 57.275 50.000 0.00 0.00 0.00 1.78
461 480 1.964223 TCGCAGTCATATCTTCCTCCC 59.036 52.381 0.00 0.00 0.00 4.30
481 500 1.284313 CCTCCTTCCTTTCAGGCTCT 58.716 55.000 0.00 0.00 34.61 4.09
577 596 2.573869 CGAGGAGCGGCAGAAGAA 59.426 61.111 1.45 0.00 36.03 2.52
756 779 0.764890 TGGGTTCAGTCTTCAGTGGG 59.235 55.000 0.00 0.00 0.00 4.61
760 783 2.289133 GGTTCAGTCTTCAGTGGGAGAC 60.289 54.545 15.57 15.57 0.00 3.36
767 790 4.349342 AGTCTTCAGTGGGAGACAGATTTT 59.651 41.667 21.68 5.26 34.06 1.82
769 792 4.594920 TCTTCAGTGGGAGACAGATTTTCT 59.405 41.667 0.00 0.00 0.00 2.52
865 891 3.147595 TGCCACGATCCTCCTCCG 61.148 66.667 0.00 0.00 0.00 4.63
935 1008 0.470268 ACCGGCTATCTCTCCCCTTC 60.470 60.000 0.00 0.00 0.00 3.46
954 1027 4.640201 CCTTCCATTCAATTGATGTACGGT 59.360 41.667 9.40 0.00 0.00 4.83
1094 1167 3.357079 CCACACCGGCTTCTGTGC 61.357 66.667 15.58 0.00 37.12 4.57
1210 1288 4.611581 GCGTGTCAAGTCTCCTCAAAATTC 60.612 45.833 0.00 0.00 0.00 2.17
1227 1305 6.154534 TCAAAATTCTACACCTAGCTCTAGCA 59.845 38.462 4.54 0.00 45.16 3.49
1287 1365 5.525378 CCTCTAGACATCATTAACCAAGCAC 59.475 44.000 0.00 0.00 0.00 4.40
1325 1403 6.377146 TCCTGAAGTAATTAAACTGGATTGGC 59.623 38.462 8.33 0.00 0.00 4.52
1575 1709 1.370810 TGGCACAAGCGTGATGAGA 59.629 52.632 6.65 0.00 46.80 3.27
1632 1766 6.295292 GGTCCTCCTTTCAAGTAATTGCATTT 60.295 38.462 0.00 0.00 0.00 2.32
1751 1885 6.317140 TGATAGCTTCCAGCAATGTTCTAAAG 59.683 38.462 0.00 0.00 45.56 1.85
1837 1971 3.730662 GCATATGCGTCCATTTTGAACGT 60.731 43.478 12.82 0.00 38.60 3.99
1912 2046 3.674997 TGCAGAGGTCAAACCAATCTAC 58.325 45.455 0.00 0.00 41.95 2.59
1927 2061 6.180472 ACCAATCTACGTCTTCCATTCATTT 58.820 36.000 0.00 0.00 0.00 2.32
1937 2071 5.586643 GTCTTCCATTCATTTAGTGAGGACC 59.413 44.000 0.00 0.00 38.29 4.46
1945 2079 6.349243 TCATTTAGTGAGGACCGTCTTTTA 57.651 37.500 0.00 0.00 31.80 1.52
1953 2087 4.174762 GAGGACCGTCTTTTATGTGAGTC 58.825 47.826 0.00 0.00 0.00 3.36
1969 2103 7.609760 ATGTGAGTCGATGCTAAATTTTGTA 57.390 32.000 0.00 0.00 0.00 2.41
2015 2150 5.751990 CCTGCTGCTCCATTAATTCAAATTC 59.248 40.000 0.00 0.00 0.00 2.17
2036 2171 6.903883 TTCTAGACGTTTATTTCTCATGGC 57.096 37.500 0.00 0.00 0.00 4.40
2146 2340 4.946772 TGTTTGTTCACTCATTTCAGTCCA 59.053 37.500 0.00 0.00 0.00 4.02
2151 2345 8.492673 TTGTTCACTCATTTCAGTCCATATAC 57.507 34.615 0.00 0.00 0.00 1.47
2205 2399 9.442047 CTATATTTGTGAATGGAGGGAGTATTC 57.558 37.037 0.00 0.00 0.00 1.75
2215 2409 2.103941 GAGGGAGTATTCCTCAAGCCTG 59.896 54.545 4.04 0.00 45.84 4.85
2237 2431 6.455360 TGGCATTTTAGACAGATCCAATTC 57.545 37.500 0.00 0.00 0.00 2.17
2253 2447 3.947834 CCAATTCCAACTCCACCATACTC 59.052 47.826 0.00 0.00 0.00 2.59
2372 2566 4.699925 TTAGTGCCCTGTAAACAGAACT 57.300 40.909 11.69 12.97 46.59 3.01
2484 2680 0.986019 ACACAGTCCACCCAGAACCA 60.986 55.000 0.00 0.00 0.00 3.67
2507 2703 6.254804 CCAAACCAAAACTTGTACAAGCTTAC 59.745 38.462 30.97 0.00 41.99 2.34
2527 2723 2.224621 ACCCATGACTTCAGAACAGTGG 60.225 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.010420 GCTAGAAATTCCGAGCCTTTGT 58.990 45.455 6.29 0.00 0.00 2.83
262 280 2.669569 GCACACACACCGGATGCT 60.670 61.111 9.46 0.00 33.44 3.79
271 289 1.140652 TCTTGACATCCTGCACACACA 59.859 47.619 0.00 0.00 0.00 3.72
299 317 5.766670 CCTTCGTCGGCCATATAGGTATATA 59.233 44.000 2.24 0.00 40.61 0.86
406 425 1.001641 ATGGCTCAGGCTTGACACC 60.002 57.895 0.00 0.00 38.73 4.16
440 459 2.564947 GGGAGGAAGATATGACTGCGAT 59.435 50.000 0.00 0.00 0.00 4.58
452 471 1.162951 AGGAAGGAGGGGGAGGAAGA 61.163 60.000 0.00 0.00 0.00 2.87
481 500 3.379445 GACGCTTCCCGGGAGTCA 61.379 66.667 27.97 13.89 42.52 3.41
767 790 2.093235 CCAAAGGCCCAACAAAAACAGA 60.093 45.455 0.00 0.00 0.00 3.41
769 792 1.065126 CCCAAAGGCCCAACAAAAACA 60.065 47.619 0.00 0.00 0.00 2.83
771 794 0.548510 CCCCAAAGGCCCAACAAAAA 59.451 50.000 0.00 0.00 0.00 1.94
935 1008 5.559427 TCAACCGTACATCAATTGAATGG 57.441 39.130 13.09 13.16 0.00 3.16
954 1027 2.083774 GCATCCACAAAGTCCGATCAA 58.916 47.619 0.00 0.00 0.00 2.57
1094 1167 0.394565 GAATGGAGGATGGAGGGACG 59.605 60.000 0.00 0.00 0.00 4.79
1210 1288 6.642707 ACTTAATGCTAGAGCTAGGTGTAG 57.357 41.667 19.04 19.04 42.66 2.74
1227 1305 5.356751 TCACAGCAACAACTGACAACTTAAT 59.643 36.000 0.00 0.00 40.25 1.40
1287 1365 3.496160 CAGGAGGGGATGCTGGGG 61.496 72.222 0.00 0.00 43.30 4.96
1481 1615 3.655276 TTTTCTGACTCCAGTACCGTC 57.345 47.619 0.00 0.00 41.16 4.79
1600 1734 1.938585 TGAAAGGAGGACCGATGAGT 58.061 50.000 0.00 0.00 41.83 3.41
1632 1766 2.193127 ACGATACAATGGAAGGGTGGA 58.807 47.619 0.00 0.00 0.00 4.02
1751 1885 6.252599 TGGATATGATATGGGCATAACTCC 57.747 41.667 0.00 0.00 32.10 3.85
1835 1969 4.867047 AGCAGATACTGAGTTTGAATGACG 59.133 41.667 0.00 0.00 32.44 4.35
1837 1971 7.559486 ACATAGCAGATACTGAGTTTGAATGA 58.441 34.615 0.00 0.00 32.44 2.57
1912 2046 5.292101 GTCCTCACTAAATGAATGGAAGACG 59.708 44.000 0.00 0.00 34.34 4.18
1927 2061 4.768448 TCACATAAAAGACGGTCCTCACTA 59.232 41.667 4.14 0.00 0.00 2.74
1937 2071 3.859961 AGCATCGACTCACATAAAAGACG 59.140 43.478 0.00 0.00 33.12 4.18
1945 2079 6.500684 ACAAAATTTAGCATCGACTCACAT 57.499 33.333 0.00 0.00 0.00 3.21
1993 2127 6.534475 AGAATTTGAATTAATGGAGCAGCA 57.466 33.333 0.00 0.00 0.00 4.41
2015 2150 6.851222 ATGCCATGAGAAATAAACGTCTAG 57.149 37.500 0.00 0.00 0.00 2.43
2058 2193 3.976793 ACATGACACAGCAAACAAGAG 57.023 42.857 0.00 0.00 0.00 2.85
2098 2291 9.731819 CACAGTAAAACGTGTCTATATACATCT 57.268 33.333 0.00 0.00 0.00 2.90
2120 2313 5.883661 ACTGAAATGAGTGAACAAACACAG 58.116 37.500 0.00 0.00 42.45 3.66
2129 2322 7.851228 ACTGTATATGGACTGAAATGAGTGAA 58.149 34.615 0.00 0.00 0.00 3.18
2205 2399 2.424956 GTCTAAAATGCCAGGCTTGAGG 59.575 50.000 14.15 0.00 0.00 3.86
2207 2401 3.084039 CTGTCTAAAATGCCAGGCTTGA 58.916 45.455 14.15 0.00 0.00 3.02
2215 2409 5.360714 TGGAATTGGATCTGTCTAAAATGCC 59.639 40.000 0.00 0.00 0.00 4.40
2237 2431 4.021102 ACTTTGAGTATGGTGGAGTTGG 57.979 45.455 0.00 0.00 0.00 3.77
2253 2447 6.700960 TCAATTTGTCCATGTTTGCTACTTTG 59.299 34.615 0.00 0.00 0.00 2.77
2372 2566 6.618196 AGCCCTATGTAAAAGGTAGAACCATA 59.382 38.462 0.00 0.00 41.95 2.74
2391 2585 5.707298 GCAAATTATGAGATTAGCAGCCCTA 59.293 40.000 0.00 0.00 0.00 3.53
2467 2663 0.923358 TTTGGTTCTGGGTGGACTGT 59.077 50.000 0.00 0.00 0.00 3.55
2484 2680 6.334989 GGTAAGCTTGTACAAGTTTTGGTTT 58.665 36.000 33.38 17.04 41.17 3.27
2507 2703 2.430465 CCACTGTTCTGAAGTCATGGG 58.570 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.