Multiple sequence alignment - TraesCS5B01G022600

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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 TraesCS5B01G022600 chr5B 100.000 2255 0 0 1 2255 21105951 21108205 0 4165
1 TraesCS5B01G022600 chr7A 96.692 1421 42 2 1 1416 60150108 60148688 0 2359
2 TraesCS5B01G022600 chr7A 95.621 845 32 2 1416 2255 60148655 60147811 0 1351
3 TraesCS5B01G022600 chr1D 96.692 1421 41 3 1 1416 141314956 141313537 0 2359
4 TraesCS5B01G022600 chr1D 95.976 845 29 2 1416 2255 141313504 141312660 0 1367
5 TraesCS5B01G022600 chr1B 96.622 1421 43 2 1 1416 672477340 672478760 0 2353
6 TraesCS5B01G022600 chr1B 96.552 1421 44 2 1 1416 668806982 668805562 0 2348
7 TraesCS5B01G022600 chr1B 96.481 1421 45 2 1 1416 638702487 638701067 0 2342
8 TraesCS5B01G022600 chr1B 95.508 846 31 4 1416 2255 638701034 638700190 0 1345
9 TraesCS5B01G022600 chr7B 96.554 1422 43 3 1 1416 644465622 644467043 0 2350
10 TraesCS5B01G022600 chr7B 95.976 845 29 2 1416 2255 644467076 644467920 0 1367
11 TraesCS5B01G022600 chr3A 96.552 1421 44 2 1 1416 633109433 633110853 0 2348
12 TraesCS5B01G022600 chr3A 95.621 845 32 2 1416 2255 633110886 633111730 0 1351
13 TraesCS5B01G022600 chr4B 96.411 1421 45 3 1 1416 209079338 209077919 0 2337
14 TraesCS5B01G022600 chr6B 96.270 1421 48 2 1 1416 306997811 306996391 0 2326
15 TraesCS5B01G022600 chr2B 95.858 845 30 2 1416 2255 799247603 799248447 0 1362
16 TraesCS5B01G022600 chr2B 95.606 842 34 2 1416 2255 391113204 391112364 0 1347
17 TraesCS5B01G022600 chrUn 95.621 845 32 2 1416 2255 225927885 225928729 0 1351
18 TraesCS5B01G022600 chr4D 95.503 845 33 2 1416 2255 123716061 123716905 0 1345


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 TraesCS5B01G022600 chr5B 21105951 21108205 2254 False 4165.0 4165 100.0000 1 2255 1 chr5B.!!$F1 2254
1 TraesCS5B01G022600 chr7A 60147811 60150108 2297 True 1855.0 2359 96.1565 1 2255 2 chr7A.!!$R1 2254
2 TraesCS5B01G022600 chr1D 141312660 141314956 2296 True 1863.0 2359 96.3340 1 2255 2 chr1D.!!$R1 2254
3 TraesCS5B01G022600 chr1B 672477340 672478760 1420 False 2353.0 2353 96.6220 1 1416 1 chr1B.!!$F1 1415
4 TraesCS5B01G022600 chr1B 668805562 668806982 1420 True 2348.0 2348 96.5520 1 1416 1 chr1B.!!$R1 1415
5 TraesCS5B01G022600 chr1B 638700190 638702487 2297 True 1843.5 2342 95.9945 1 2255 2 chr1B.!!$R2 2254
6 TraesCS5B01G022600 chr7B 644465622 644467920 2298 False 1858.5 2350 96.2650 1 2255 2 chr7B.!!$F1 2254
7 TraesCS5B01G022600 chr3A 633109433 633111730 2297 False 1849.5 2348 96.0865 1 2255 2 chr3A.!!$F1 2254
8 TraesCS5B01G022600 chr4B 209077919 209079338 1419 True 2337.0 2337 96.4110 1 1416 1 chr4B.!!$R1 1415
9 TraesCS5B01G022600 chr6B 306996391 306997811 1420 True 2326.0 2326 96.2700 1 1416 1 chr6B.!!$R1 1415
10 TraesCS5B01G022600 chr2B 799247603 799248447 844 False 1362.0 1362 95.8580 1416 2255 1 chr2B.!!$F1 839
11 TraesCS5B01G022600 chr2B 391112364 391113204 840 True 1347.0 1347 95.6060 1416 2255 1 chr2B.!!$R1 839
12 TraesCS5B01G022600 chrUn 225927885 225928729 844 False 1351.0 1351 95.6210 1416 2255 1 chrUn.!!$F1 839
13 TraesCS5B01G022600 chr4D 123716061 123716905 844 False 1345.0 1345 95.5030 1416 2255 1 chr4D.!!$F1 839

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
281 282 0.396835 GAGGACGTAAGCCCCCTAGT 60.397 60.0 0.0 0.0 43.28 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2188 1.069978 TGCGATGTGTCTGGAAACTCA 59.93 47.619 0.0 0.0 0.0 3.41 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
28 29 6.547880 AGTTAGAACTTCTCTGTCTCAACTCA 59.452 38.462 0.00 0.00 35.21 3.41
80 81 7.019388 AGAGATAGGGGTTTGCTATTCTCATA 58.981 38.462 0.00 0.00 0.00 2.15
142 143 4.335416 CTTGTTTCAGCCCTTCCTTCATA 58.665 43.478 0.00 0.00 0.00 2.15
206 207 1.950748 ATCTGACCTCCGGGCTACCT 61.951 60.000 0.00 0.00 35.63 3.08
281 282 0.396835 GAGGACGTAAGCCCCCTAGT 60.397 60.000 0.00 0.00 43.28 2.57
401 402 0.616395 TACCAGATCCGGTGAGCCAA 60.616 55.000 11.10 0.00 40.39 4.52
549 550 6.185511 TCGGATTCAGGTAGAAAGTAAGAGA 58.814 40.000 0.00 0.00 40.22 3.10
603 604 8.597167 ACTTAAAATTAGTAGTCCCGGTAGTTT 58.403 33.333 0.00 0.00 0.00 2.66
664 666 3.753294 AGTCCTATCATTAGTTGGCCG 57.247 47.619 0.00 0.00 0.00 6.13
725 727 6.369890 TCAGATCATTCAACTAAAGCTGTCAC 59.630 38.462 0.00 0.00 0.00 3.67
790 792 6.322201 TGTGACTGAGCAGATATGTCTATTGA 59.678 38.462 4.21 0.00 32.09 2.57
903 910 0.523072 ATGATTGCCGCTTGTGTGAC 59.477 50.000 0.00 0.00 0.00 3.67
929 936 1.452470 GTTGTGGGTCCCGTGTGTT 60.452 57.895 2.65 0.00 0.00 3.32
935 942 1.080705 GGTCCCGTGTGTTCTCGAG 60.081 63.158 5.93 5.93 33.21 4.04
1004 1011 4.189231 GTGCTGGTTATCGAGTTTATGGT 58.811 43.478 0.00 0.00 0.00 3.55
1038 1045 3.383185 TCCAAAAAGTCAAAGATGGCGTT 59.617 39.130 0.00 0.00 35.88 4.84
1231 1238 2.407340 ACCTTACCATTTTTGGGCCA 57.593 45.000 0.00 0.00 0.00 5.36
1233 1240 1.067213 CCTTACCATTTTTGGGCCACG 60.067 52.381 5.23 0.00 0.00 4.94
1334 1341 2.025887 TCTTCTTCTGGCTCAAATCCCC 60.026 50.000 0.00 0.00 0.00 4.81
1352 1359 2.310538 CCCTTTTCATATCCAGGGCAC 58.689 52.381 0.00 0.00 39.80 5.01
1363 1370 0.180406 CCAGGGCACGCTTTAGGTAT 59.820 55.000 0.00 0.00 0.00 2.73
1400 1407 8.682936 AAATCATTAAAGATATGCTCGACCTT 57.317 30.769 0.00 0.00 0.00 3.50
1401 1408 7.897575 ATCATTAAAGATATGCTCGACCTTC 57.102 36.000 0.00 0.00 0.00 3.46
1493 1537 1.460255 CCCAACCAGCTTTCTCCCA 59.540 57.895 0.00 0.00 0.00 4.37
1578 1622 1.460699 GGAACCAGCAAAGGGAGGT 59.539 57.895 0.00 0.00 35.47 3.85
1598 1642 5.582689 GGTTGAAAAGCCATAGTGCTAAT 57.417 39.130 0.00 0.00 41.80 1.73
1602 1646 9.714556 GGTTGAAAAGCCATAGTGCTAATGCAT 62.715 40.741 0.00 0.00 44.54 3.96
1627 1671 6.041523 TGCCCTGTAGTTTTGAAGCTAAAAAT 59.958 34.615 9.68 5.46 31.92 1.82
1793 1838 6.327279 GCTTGGAAAAGCCTTAAGTTTAGA 57.673 37.500 0.97 0.00 39.81 2.10
1994 2039 4.534103 AGTAGGGGCCTTGATCTATCAATC 59.466 45.833 0.84 2.19 44.92 2.67
2070 2118 2.416972 GGTCGAAGTTTAGACCGCTCAT 60.417 50.000 13.44 0.00 46.08 2.90
2140 2188 2.704065 ACCCGAATCCATTTACGATCCT 59.296 45.455 0.00 0.00 0.00 3.24
2212 2260 3.516615 CCTCAGACGGATCAAAGAAGAC 58.483 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 9.605951 AATGGGGTAAATAAATATGAGCAATCT 57.394 29.630 0.00 0.00 0.00 2.40
113 114 1.138859 AGGGCTGAAACAAGGCAAAAC 59.861 47.619 0.02 0.00 44.29 2.43
142 143 9.440761 AGATAGATTAGTACTTGGAAGGTTCAT 57.559 33.333 0.00 0.00 0.00 2.57
206 207 9.997482 GACTCAACTACTTTTTACAATTGACAA 57.003 29.630 13.59 2.74 0.00 3.18
281 282 9.726438 CAATTAGTTTAGAAGGAAGAGGAAGAA 57.274 33.333 0.00 0.00 0.00 2.52
340 341 3.135994 TCGCTTTCCTTCAACCACTTAC 58.864 45.455 0.00 0.00 0.00 2.34
342 343 2.341846 TCGCTTTCCTTCAACCACTT 57.658 45.000 0.00 0.00 0.00 3.16
401 402 6.757237 TGTATGTCCATTTTTGCTTGATGTT 58.243 32.000 0.00 0.00 0.00 2.71
549 550 7.552050 AAGCTCTCCTATGAATATGCTACTT 57.448 36.000 0.00 0.00 0.00 2.24
581 582 7.008021 TCAAACTACCGGGACTACTAATTTT 57.992 36.000 6.32 0.00 0.00 1.82
664 666 8.214721 AGCTTTCTACTTAAATTGCTATGACC 57.785 34.615 0.00 0.00 0.00 4.02
790 792 3.116079 CAAATCTGTTTTTGCTGGGCT 57.884 42.857 0.00 0.00 30.51 5.19
817 819 9.768435 TTCTGAATGAGAAAGCCTTTGGCAAAG 62.768 40.741 28.79 28.79 42.79 2.77
903 910 1.269448 CGGGACCCACAACAATGAAAG 59.731 52.381 12.15 0.00 0.00 2.62
929 936 8.750298 AGAATCCTAAAACAATCTTACTCGAGA 58.250 33.333 21.68 0.00 0.00 4.04
967 974 0.889186 AGCACCGCGGAGTCAAAAAT 60.889 50.000 35.90 1.64 0.00 1.82
970 977 2.664851 CAGCACCGCGGAGTCAAA 60.665 61.111 35.90 0.00 0.00 2.69
1004 1011 3.851897 TTTTGGATGGTCGGCGGCA 62.852 57.895 15.59 0.00 0.00 5.69
1038 1045 8.213679 AGAAGAGAGCATAATAAGTAAATGCCA 58.786 33.333 3.08 0.00 45.66 4.92
1117 1124 8.374184 AGGCCATTACAAAAACAAGGTATAAT 57.626 30.769 5.01 0.00 0.00 1.28
1155 1162 5.189928 TGCAAAATCCTTATCTTTCGGCTA 58.810 37.500 0.00 0.00 0.00 3.93
1175 1182 2.663826 AGGAACGCAAAAGTTTTGCA 57.336 40.000 38.44 0.00 45.14 4.08
1231 1238 3.761752 CAGGAAATGGAAATGGTAACCGT 59.238 43.478 0.00 0.00 0.00 4.83
1233 1240 5.337250 GGTTCAGGAAATGGAAATGGTAACC 60.337 44.000 0.00 0.00 0.00 2.85
1334 1341 1.334869 GCGTGCCCTGGATATGAAAAG 59.665 52.381 0.00 0.00 0.00 2.27
1352 1359 6.417191 TCAAACTAAAGCATACCTAAAGCG 57.583 37.500 0.00 0.00 0.00 4.68
1400 1407 5.307976 CCCTATCTCACCATGGACATAAAGA 59.692 44.000 21.47 11.25 0.00 2.52
1401 1408 5.555017 CCCTATCTCACCATGGACATAAAG 58.445 45.833 21.47 8.68 0.00 1.85
1464 1508 1.826385 CTGGTTGGGGAACTGCTAAG 58.174 55.000 0.00 0.00 0.00 2.18
1493 1537 3.843027 TGAATCTCAGGAAGGCTTTCTCT 59.157 43.478 4.67 0.00 33.68 3.10
1578 1622 4.997565 GCATTAGCACTATGGCTTTTCAA 58.002 39.130 0.00 0.00 42.71 2.69
1598 1642 2.284754 TCAAAACTACAGGGCATGCA 57.715 45.000 21.36 0.00 0.00 3.96
1602 1646 2.656947 AGCTTCAAAACTACAGGGCA 57.343 45.000 0.00 0.00 0.00 5.36
1673 1717 3.489398 CGCTCATAAAGGAAGAGTAGCGT 60.489 47.826 0.00 0.00 44.68 5.07
1793 1838 2.370189 CAGTTCAGTGAAGGAAGGGAGT 59.630 50.000 5.62 0.00 0.00 3.85
1877 1922 1.773653 GGGGCTCTCTCCAATCATTCT 59.226 52.381 0.00 0.00 0.00 2.40
1922 1967 3.946558 GGAAGTAGTACCATCACTCTCGT 59.053 47.826 0.00 0.00 0.00 4.18
1935 1980 6.210185 ACGAAAGGCTCTTTAAGGAAGTAGTA 59.790 38.462 0.00 0.00 36.70 1.82
2016 2062 5.010708 TCTTCATTTAAAAAGGGGGAGCT 57.989 39.130 0.00 0.00 0.00 4.09
2070 2118 9.931698 TGATCTTTTCTATGGGTAGAACTACTA 57.068 33.333 11.04 2.94 44.47 1.82
2140 2188 1.069978 TGCGATGTGTCTGGAAACTCA 59.930 47.619 0.00 0.00 0.00 3.41
2212 2260 2.396274 AACCAAGGAGAGGTTCCCCAG 61.396 57.143 0.00 0.00 45.98 4.45
2226 2274 5.527951 TGATGTCGAATTCCAAAAACCAAG 58.472 37.500 0.00 0.00 0.00 3.61
2227 2275 5.508825 CCTGATGTCGAATTCCAAAAACCAA 60.509 40.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.