Multiple sequence alignment - TraesCS4B01G147500

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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 TraesCS4B01G147500 chr4B 100.000 2232 0 0 1 2232 209301332 209303563 0 4122
1 TraesCS4B01G147500 chr7B 98.031 2235 40 3 1 2232 716877113 716874880 0 3880
2 TraesCS4B01G147500 chr7B 97.942 2235 42 3 1 2232 742991113 742993346 0 3869
3 TraesCS4B01G147500 chr7B 97.320 2239 52 3 1 2232 716836902 716834665 0 3795
4 TraesCS4B01G147500 chr7A 97.986 2234 42 3 1 2232 60280981 60283213 0 3873
5 TraesCS4B01G147500 chrUn 97.942 2235 42 3 1 2232 186206753 186204520 0 3869
6 TraesCS4B01G147500 chr1A 97.851 2234 45 3 1 2232 498689559 498687327 0 3856
7 TraesCS4B01G147500 chr5A 97.498 2238 49 3 1 2232 238821140 238818904 0 3816
8 TraesCS4B01G147500 chr7D 98.087 2195 35 3 1 2189 382051747 382053940 0 3814
9 TraesCS4B01G147500 chr3A 97.186 2239 55 4 1 2232 725798416 725800653 0 3779


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 TraesCS4B01G147500 chr4B 209301332 209303563 2231 False 4122 4122 100.000 1 2232 1 chr4B.!!$F1 2231
1 TraesCS4B01G147500 chr7B 716874880 716877113 2233 True 3880 3880 98.031 1 2232 1 chr7B.!!$R2 2231
2 TraesCS4B01G147500 chr7B 742991113 742993346 2233 False 3869 3869 97.942 1 2232 1 chr7B.!!$F1 2231
3 TraesCS4B01G147500 chr7B 716834665 716836902 2237 True 3795 3795 97.320 1 2232 1 chr7B.!!$R1 2231
4 TraesCS4B01G147500 chr7A 60280981 60283213 2232 False 3873 3873 97.986 1 2232 1 chr7A.!!$F1 2231
5 TraesCS4B01G147500 chrUn 186204520 186206753 2233 True 3869 3869 97.942 1 2232 1 chrUn.!!$R1 2231
6 TraesCS4B01G147500 chr1A 498687327 498689559 2232 True 3856 3856 97.851 1 2232 1 chr1A.!!$R1 2231
7 TraesCS4B01G147500 chr5A 238818904 238821140 2236 True 3816 3816 97.498 1 2232 1 chr5A.!!$R1 2231
8 TraesCS4B01G147500 chr7D 382051747 382053940 2193 False 3814 3814 98.087 1 2189 1 chr7D.!!$F1 2188
9 TraesCS4B01G147500 chr3A 725798416 725800653 2237 False 3779 3779 97.186 1 2232 1 chr3A.!!$F1 2231

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
861 872 0.461548 TGGAGCCTATCGAAGCACTG 59.538 55.0 8.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1866 1.974343 CCGATGGGGAAACGGCAAA 60.974 57.895 0.0 0.0 40.19 3.68 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
145 146 0.617820 ATACTGAGGTGCTCCCCGTT 60.618 55.000 0.00 0.00 0.00 4.44
225 226 3.256704 ACAGAGGTGACTAATTCCCCAA 58.743 45.455 0.00 0.00 44.43 4.12
310 311 0.736325 AAGAACGGCGAAGTCCATCG 60.736 55.000 16.62 0.00 45.41 3.84
572 573 5.871465 TCGATTTCGATTTCATGAAACCA 57.129 34.783 22.71 7.19 44.22 3.67
588 589 9.076781 TCATGAAACCATTGATTCAAAGAACTA 57.923 29.630 2.68 0.00 38.88 2.24
661 667 0.801067 CGTAGTACCCGAAGCACTGC 60.801 60.000 0.00 0.00 0.00 4.40
832 843 3.914426 AACGGAGCCTGACTTATTCAT 57.086 42.857 0.00 0.00 32.17 2.57
861 872 0.461548 TGGAGCCTATCGAAGCACTG 59.538 55.000 8.00 0.00 0.00 3.66
909 920 4.338795 TCATTCTCTACAGGGGTCTCTT 57.661 45.455 0.00 0.00 0.00 2.85
1059 1070 5.195001 TCGAAAAGATGGGTTCCTTTTTG 57.805 39.130 0.00 0.00 41.17 2.44
1419 1430 1.734655 TCCATATCCCTCTCCCTTGC 58.265 55.000 0.00 0.00 0.00 4.01
1549 1560 8.138712 CGAGATAGGCTTTACTAGACATTTTCT 58.861 37.037 0.00 0.00 38.51 2.52
1625 1636 8.561738 TTAAGACAATTATCCTCACTCAAACC 57.438 34.615 0.00 0.00 0.00 3.27
1733 1747 2.042831 GGCGTGCTTCCTTGCAGAT 61.043 57.895 0.00 0.00 44.20 2.90
1852 1866 0.398522 TCCAGATACCGGTGCATCCT 60.399 55.000 19.93 3.72 0.00 3.24
1951 1965 1.676248 AGGTAAACAGGCACCCCATA 58.324 50.000 0.00 0.00 35.25 2.74
2063 2077 1.076332 GAGATCCCCGTTGTTTGACG 58.924 55.000 0.00 0.00 42.43 4.35
2174 2188 4.547671 AGACCCTATTGAGCTGCTTAGTA 58.452 43.478 2.53 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 2.526993 CGCGTCGTTCCAACAACCA 61.527 57.895 0.00 0.0 0.00 3.67
179 180 6.782000 TCCCTTCATCTTTTTGAAAGGAATCA 59.218 34.615 2.76 0.0 41.22 2.57
225 226 0.966179 GTTTTCCGCCCCAAATGAGT 59.034 50.000 0.00 0.0 0.00 3.41
310 311 6.187682 TCTTATTTCTTCATTGGAGGGTTCC 58.812 40.000 0.00 0.0 44.31 3.62
382 383 4.601857 TCCCCCACACTTCTTTATTTCTCT 59.398 41.667 0.00 0.0 0.00 3.10
572 573 6.183360 GGCTAAGCGTAGTTCTTTGAATCAAT 60.183 38.462 8.50 0.0 0.00 2.57
661 667 1.043116 TCCCGGCTACTGGATCACTG 61.043 60.000 0.00 0.0 0.00 3.66
832 843 0.937441 ATAGGCTCCACTCTCTCCCA 59.063 55.000 0.00 0.0 0.00 4.37
861 872 4.438148 GAGCCAAGGATCTTACTCTCAAC 58.562 47.826 0.00 0.0 0.00 3.18
1059 1070 3.428870 TGATTCTTTCTTTGTCGAGACGC 59.571 43.478 0.00 0.0 0.00 5.19
1161 1172 2.152016 GCTCACCAACTTCACTTACCC 58.848 52.381 0.00 0.0 0.00 3.69
1164 1175 1.414919 ACGGCTCACCAACTTCACTTA 59.585 47.619 0.00 0.0 34.57 2.24
1203 1214 1.668101 GAGTCCTCTCCGAACCGCAT 61.668 60.000 0.00 0.0 34.87 4.73
1316 1327 7.392766 TGGTTCATATAGAATCCATGTCCTT 57.607 36.000 0.00 0.0 36.48 3.36
1419 1430 5.050499 GTGCCATTTGATGAGTAAGATCGAG 60.050 44.000 0.00 0.0 0.00 4.04
1539 1550 5.305585 TCGCCTTTGTAAGAGAAAATGTCT 58.694 37.500 0.00 0.0 40.25 3.41
1549 1560 4.454504 GGAATTGTCTTCGCCTTTGTAAGA 59.545 41.667 0.00 0.0 0.00 2.10
1655 1669 4.141158 AGGAAGGACAAAGGAGACAAACAT 60.141 41.667 0.00 0.0 0.00 2.71
1852 1866 1.974343 CCGATGGGGAAACGGCAAA 60.974 57.895 0.00 0.0 40.19 3.68
2063 2077 8.950208 ATTCAATAGAAAGCCTACTTGAGTAC 57.050 34.615 0.00 0.0 37.29 2.73
2138 2152 2.836262 AGGGTCTCGAGTACGACTATG 58.164 52.381 13.13 0.0 43.81 2.23
2174 2188 3.160269 CACCAGCCAAAGAAAGGAGAAT 58.840 45.455 0.00 0.0 0.00 2.40


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

AutoCloner maintained by Alex Coulton.