Multiple sequence alignment - TraesCS3A01G188300

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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 TraesCS3A01G188300 chr3A 100.000 2319 0 0 1 2319 227644744 227647062 0 4283
1 TraesCS3A01G188300 chr7A 97.370 2319 61 0 1 2319 4959838 4962156 0 3945
2 TraesCS3A01G188300 chr5A 97.284 2320 57 2 1 2319 300072979 300075293 0 3930
3 TraesCS3A01G188300 chr5A 97.025 2319 61 3 1 2319 16602919 16600609 0 3893
4 TraesCS3A01G188300 chrUn 97.241 2320 58 2 1 2319 189392539 189394853 0 3925
5 TraesCS3A01G188300 chr2A 97.198 2320 59 2 1 2319 618279956 618277642 0 3919
6 TraesCS3A01G188300 chr6A 97.197 2319 59 3 1 2319 289128632 289130944 0 3917
7 TraesCS3A01G188300 chr7B 97.112 2320 61 2 1 2319 743086199 743088513 0 3908
8 TraesCS3A01G188300 chr7D 97.069 2320 62 2 1 2319 626698490 626696176 0 3903
9 TraesCS3A01G188300 chr1D 97.025 2319 63 2 1 2319 185769457 185771769 0 3895


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 TraesCS3A01G188300 chr3A 227644744 227647062 2318 False 4283 4283 100.000 1 2319 1 chr3A.!!$F1 2318
1 TraesCS3A01G188300 chr7A 4959838 4962156 2318 False 3945 3945 97.370 1 2319 1 chr7A.!!$F1 2318
2 TraesCS3A01G188300 chr5A 300072979 300075293 2314 False 3930 3930 97.284 1 2319 1 chr5A.!!$F1 2318
3 TraesCS3A01G188300 chr5A 16600609 16602919 2310 True 3893 3893 97.025 1 2319 1 chr5A.!!$R1 2318
4 TraesCS3A01G188300 chrUn 189392539 189394853 2314 False 3925 3925 97.241 1 2319 1 chrUn.!!$F1 2318
5 TraesCS3A01G188300 chr2A 618277642 618279956 2314 True 3919 3919 97.198 1 2319 1 chr2A.!!$R1 2318
6 TraesCS3A01G188300 chr6A 289128632 289130944 2312 False 3917 3917 97.197 1 2319 1 chr6A.!!$F1 2318
7 TraesCS3A01G188300 chr7B 743086199 743088513 2314 False 3908 3908 97.112 1 2319 1 chr7B.!!$F1 2318
8 TraesCS3A01G188300 chr7D 626696176 626698490 2314 True 3903 3903 97.069 1 2319 1 chr7D.!!$R1 2318
9 TraesCS3A01G188300 chr1D 185769457 185771769 2312 False 3895 3895 97.025 1 2319 1 chr1D.!!$F1 2318

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
941 944 0.40675 TTCACAGTCCCCCTACGAGA 59.593 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 1940 0.683973 ACCACAAGCTCTGACCTGAG 59.316 55.0 0.0 0.28 37.16 3.35 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
64 65 7.054124 TGAGCAAAAAGATAAGGTCGGAATAT 58.946 34.615 0.00 0.00 0.00 1.28
158 159 2.297315 CACTCGCATATCTAGAGCCCAA 59.703 50.000 0.00 0.00 35.56 4.12
207 208 4.712337 CAGACTCTACTGGTGGTATTTCCT 59.288 45.833 0.00 0.00 34.41 3.36
248 249 6.124340 TGTGCATTCATATCAGTCAGGAAAT 58.876 36.000 0.00 0.00 0.00 2.17
368 369 7.649306 CCGATCATTGACAAAAGAAGAAAAAGT 59.351 33.333 0.00 0.00 0.00 2.66
384 385 2.626088 AAGTAGCCGTACGACAACTC 57.374 50.000 18.76 2.12 33.97 3.01
406 407 4.096382 TCAAGGAATCTTTAGATTTGGCGC 59.904 41.667 0.00 0.00 44.14 6.53
425 426 2.037772 CGCCTATAGACTCAAAGGGCAT 59.962 50.000 0.00 0.00 38.16 4.40
433 434 2.237392 GACTCAAAGGGCATAGACAGGT 59.763 50.000 0.00 0.00 0.00 4.00
598 600 3.117701 TGTGATCCAAACCCAAACTCTCA 60.118 43.478 0.00 0.00 0.00 3.27
941 944 0.406750 TTCACAGTCCCCCTACGAGA 59.593 55.000 0.00 0.00 0.00 4.04
943 946 1.203087 TCACAGTCCCCCTACGAGAAA 60.203 52.381 0.00 0.00 0.00 2.52
948 951 1.683365 CCCCCTACGAGAAACCCGA 60.683 63.158 0.00 0.00 0.00 5.14
1013 1016 8.765219 GCGTAGATTCAATATGTTGATTGTACT 58.235 33.333 21.20 13.00 43.49 2.73
1050 1053 3.689161 CCTTATCACGAAAGCCACATTCA 59.311 43.478 0.00 0.00 0.00 2.57
1187 1194 2.593925 TCCTGCAGAAGACTCAGAGA 57.406 50.000 17.39 0.00 0.00 3.10
1243 1250 5.965922 TGTGATCTATTCTCGTGTCACATT 58.034 37.500 3.42 0.00 40.47 2.71
1282 1289 5.189934 CCCTCCATTTTCTTCACTACTACCT 59.810 44.000 0.00 0.00 0.00 3.08
1415 1422 4.099419 TGAAAGTGAATAGGAGCATAGCGA 59.901 41.667 0.00 0.00 0.00 4.93
1515 1522 0.034574 TTAATGCATGTCACCCGCCT 60.035 50.000 0.00 0.00 0.00 5.52
1532 1539 2.086869 GCCTGCTCTCAATACAGCAAA 58.913 47.619 0.00 0.00 44.98 3.68
1555 1562 3.818210 TGACTCTCTCTCACAAGACAGAC 59.182 47.826 0.00 0.00 0.00 3.51
1571 1578 6.037786 AGACAGACAAAGATTACCGATTCA 57.962 37.500 0.00 0.00 0.00 2.57
1572 1579 6.644347 AGACAGACAAAGATTACCGATTCAT 58.356 36.000 0.00 0.00 0.00 2.57
1573 1580 6.758886 AGACAGACAAAGATTACCGATTCATC 59.241 38.462 0.00 0.00 0.00 2.92
1574 1581 5.817816 ACAGACAAAGATTACCGATTCATCC 59.182 40.000 0.00 0.00 0.00 3.51
1575 1582 5.817296 CAGACAAAGATTACCGATTCATCCA 59.183 40.000 0.00 0.00 0.00 3.41
1653 1665 3.318839 CCTTGACAAAACCATTCTCAGCA 59.681 43.478 0.00 0.00 0.00 4.41
1656 1668 5.336150 TGACAAAACCATTCTCAGCAAAA 57.664 34.783 0.00 0.00 0.00 2.44
1683 1695 3.445450 GCCGAGCTATCTATCCAGATCAA 59.555 47.826 0.00 0.00 40.81 2.57
1699 1711 1.214367 TCAAGGTTGAACGAAGCGAC 58.786 50.000 0.00 0.00 37.13 5.19
1806 1818 1.564348 GAATGGGGAGTTAGGGCTTCA 59.436 52.381 0.00 0.00 0.00 3.02
1829 1841 3.685139 TTCCTCTGTAGCCAGTTTCAG 57.315 47.619 0.00 0.00 39.82 3.02
1928 1940 5.009610 ACATGGGTGAATCAAGTACAACAAC 59.990 40.000 0.00 0.00 0.00 3.32
1997 2009 5.836898 TCCACTCAACTAGGAAAGAAGTACA 59.163 40.000 0.00 0.00 0.00 2.90
2024 2036 4.214758 TGCTGACTGACTGTTTGAATGATG 59.785 41.667 0.00 0.00 0.00 3.07
2060 2072 8.501070 AGTAGCTAATCAAGTTAGAGTAGGGTA 58.499 37.037 0.00 0.00 41.99 3.69
2079 2091 1.672356 GCCGAGAAGCTTCTTGCCA 60.672 57.895 30.99 0.00 44.23 4.92
2307 2319 2.365237 GTAAGAGGGGACGGGCCT 60.365 66.667 0.84 0.00 36.66 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.885449 ATGAATCAAACCCCTTGTCAAAA 57.115 34.783 0.00 0.00 36.34 2.44
15 16 4.739793 AGAATGAATCAAACCCCTTGTCA 58.260 39.130 0.00 0.00 36.34 3.58
64 65 3.139077 GGAAGCAAAGAAAGAACTCCGA 58.861 45.455 0.00 0.00 0.00 4.55
158 159 1.546476 GGTGTCGTTCAGGAGAGATGT 59.454 52.381 0.00 0.00 0.00 3.06
207 208 2.484770 GCACATATTTACCCTCGCCTCA 60.485 50.000 0.00 0.00 0.00 3.86
248 249 4.991056 CGGAAAGAAGAAGAGTCATTGTCA 59.009 41.667 0.00 0.00 0.00 3.58
338 339 5.939883 TCTTCTTTTGTCAATGATCGGTGAT 59.060 36.000 1.85 0.00 0.00 3.06
368 369 1.200716 CCTTGAGTTGTCGTACGGCTA 59.799 52.381 21.92 11.16 0.00 3.93
384 385 4.354587 GCGCCAAATCTAAAGATTCCTTG 58.645 43.478 5.71 1.64 43.41 3.61
406 407 5.540337 TGTCTATGCCCTTTGAGTCTATAGG 59.460 44.000 0.00 0.00 0.00 2.57
425 426 4.699925 AAAAGTACCAGCAACCTGTCTA 57.300 40.909 0.00 0.00 37.38 2.59
710 712 4.211374 GCAACACTTCTTCACGTATTCACT 59.789 41.667 0.00 0.00 0.00 3.41
724 726 3.393800 TCACTGAGCTAAGCAACACTTC 58.606 45.455 0.00 0.00 39.97 3.01
941 944 4.407365 ACTCCTTCATTGATTTCGGGTTT 58.593 39.130 0.00 0.00 0.00 3.27
943 946 3.721087 ACTCCTTCATTGATTTCGGGT 57.279 42.857 0.00 0.00 0.00 5.28
1050 1053 4.813296 GTGTGACTTCCTCAAACGAAAT 57.187 40.909 0.00 0.00 26.84 2.17
1187 1194 4.080469 CAGCCATGCCATTAGATAGATCCT 60.080 45.833 0.00 0.00 0.00 3.24
1243 1250 2.711009 TGGAGGGAGAAGAAAGAAAGCA 59.289 45.455 0.00 0.00 0.00 3.91
1282 1289 8.846943 TGCTTCTTTGATTTATGTGTAGAAGA 57.153 30.769 11.83 0.00 39.45 2.87
1362 1369 2.279186 AGTTTGCCGGTTTTGCGC 60.279 55.556 1.90 0.00 0.00 6.09
1415 1422 1.541147 CGTGTTTGGCTTGGATGATGT 59.459 47.619 0.00 0.00 0.00 3.06
1532 1539 4.661222 TCTGTCTTGTGAGAGAGAGTCAT 58.339 43.478 0.00 0.00 44.68 3.06
1555 1562 6.262944 TGGATTGGATGAATCGGTAATCTTTG 59.737 38.462 0.00 0.00 41.45 2.77
1571 1578 6.842280 TCTGATCAAATTGGATTGGATTGGAT 59.158 34.615 0.00 0.00 33.11 3.41
1572 1579 6.196434 TCTGATCAAATTGGATTGGATTGGA 58.804 36.000 0.00 0.00 33.11 3.53
1573 1580 6.474140 TCTGATCAAATTGGATTGGATTGG 57.526 37.500 0.00 0.00 33.11 3.16
1574 1581 7.491372 CACTTCTGATCAAATTGGATTGGATTG 59.509 37.037 0.00 0.00 33.11 2.67
1575 1582 7.398047 TCACTTCTGATCAAATTGGATTGGATT 59.602 33.333 0.00 0.00 33.11 3.01
1653 1665 5.163301 TGGATAGATAGCTCGGCTTCTTTTT 60.163 40.000 3.71 0.00 40.44 1.94
1656 1668 3.501349 TGGATAGATAGCTCGGCTTCTT 58.499 45.455 3.71 0.00 40.44 2.52
1683 1695 0.600255 CCAGTCGCTTCGTTCAACCT 60.600 55.000 0.00 0.00 0.00 3.50
1764 1776 6.405278 TCTTTCTATCTTACATCGCCATCA 57.595 37.500 0.00 0.00 0.00 3.07
1829 1841 3.296322 TGTCGGCAAATGATTTGGAAC 57.704 42.857 18.52 3.14 40.94 3.62
1906 1918 5.385198 AGTTGTTGTACTTGATTCACCCAT 58.615 37.500 0.00 0.00 0.00 4.00
1928 1940 0.683973 ACCACAAGCTCTGACCTGAG 59.316 55.000 0.00 0.28 37.16 3.35
1997 2009 3.544684 TCAAACAGTCAGTCAGCAATGT 58.455 40.909 0.00 0.00 0.00 2.71
2049 2061 2.486907 GCTTCTCGGCTACCCTACTCTA 60.487 54.545 0.00 0.00 0.00 2.43
2060 2072 1.376553 GGCAAGAAGCTTCTCGGCT 60.377 57.895 33.73 18.75 45.30 5.52
2079 2091 2.043604 GCTTTGCTTTTGGGGGCACT 62.044 55.000 0.00 0.00 38.23 4.40
2279 2291 4.365368 GTCCCCTCTTACCCCTAACTAAA 58.635 47.826 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.