Multiple sequence alignment - TraesCS4B01G147400

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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 TraesCS4B01G147400 chr4B 100.000 2712 0 0 1 2712 209303130 209300419 0 5009
1 TraesCS4B01G147400 chr5A 98.162 2720 41 4 1 2712 19245370 19248088 0 4737
2 TraesCS4B01G147400 chr7D 98.124 2718 44 3 1 2712 382053550 382050834 0 4730
3 TraesCS4B01G147400 chr7D 97.976 2718 48 3 1 2712 203503470 203500754 0 4708
4 TraesCS4B01G147400 chr7D 97.975 2716 48 3 3 2712 381927470 381924756 0 4704
5 TraesCS4B01G147400 chr7B 98.122 2715 47 3 1 2712 716875313 716878026 0 4728
6 TraesCS4B01G147400 chr7B 97.901 2715 53 3 1 2712 742992913 742990200 0 4695
7 TraesCS4B01G147400 chr7A 97.973 2714 52 3 1 2712 60282780 60280068 0 4704
8 TraesCS4B01G147400 chr1A 97.973 2714 52 3 1 2712 498687760 498690472 0 4704
9 TraesCS4B01G147400 chr6B 96.536 1501 52 0 1212 2712 297475326 297473826 0 2484
10 TraesCS4B01G147400 chr2A 95.458 1255 44 4 581 1823 779636288 779637541 0 1989


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 TraesCS4B01G147400 chr4B 209300419 209303130 2711 True 5009 5009 100.000 1 2712 1 chr4B.!!$R1 2711
1 TraesCS4B01G147400 chr5A 19245370 19248088 2718 False 4737 4737 98.162 1 2712 1 chr5A.!!$F1 2711
2 TraesCS4B01G147400 chr7D 382050834 382053550 2716 True 4730 4730 98.124 1 2712 1 chr7D.!!$R3 2711
3 TraesCS4B01G147400 chr7D 203500754 203503470 2716 True 4708 4708 97.976 1 2712 1 chr7D.!!$R1 2711
4 TraesCS4B01G147400 chr7D 381924756 381927470 2714 True 4704 4704 97.975 3 2712 1 chr7D.!!$R2 2709
5 TraesCS4B01G147400 chr7B 716875313 716878026 2713 False 4728 4728 98.122 1 2712 1 chr7B.!!$F1 2711
6 TraesCS4B01G147400 chr7B 742990200 742992913 2713 True 4695 4695 97.901 1 2712 1 chr7B.!!$R1 2711
7 TraesCS4B01G147400 chr7A 60280068 60282780 2712 True 4704 4704 97.973 1 2712 1 chr7A.!!$R1 2711
8 TraesCS4B01G147400 chr1A 498687760 498690472 2712 False 4704 4704 97.973 1 2712 1 chr1A.!!$F1 2711
9 TraesCS4B01G147400 chr6B 297473826 297475326 1500 True 2484 2484 96.536 1212 2712 1 chr6B.!!$R1 1500
10 TraesCS4B01G147400 chr2A 779636288 779637541 1253 False 1989 1989 95.458 581 1823 1 chr2A.!!$F1 1242

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
966 974 0.937441 ATAGGCTCCACTCTCTCCCA 59.063 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2053 0.326808 AGGAATACCCCCGTTAGCCA 60.327 55.0 0.0 0.0 36.73 4.75 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
139 140 4.502604 CGTTAGGAAGGACAAAGGAGACAA 60.503 45.833 0.00 0.0 0.00 3.18
143 144 4.141158 AGGAAGGACAAAGGAGACAAACAT 60.141 41.667 0.00 0.0 0.00 2.71
249 254 4.454504 GGAATTGTCTTCGCCTTTGTAAGA 59.545 41.667 0.00 0.0 0.00 2.10
259 264 5.305585 TCGCCTTTGTAAGAGAAAATGTCT 58.694 37.500 0.00 0.0 40.25 3.41
379 384 5.050499 GTGCCATTTGATGAGTAAGATCGAG 60.050 44.000 0.00 0.0 0.00 4.04
482 487 7.392766 TGGTTCATATAGAATCCATGTCCTT 57.607 36.000 0.00 0.0 36.48 3.36
634 639 1.414919 ACGGCTCACCAACTTCACTTA 59.585 47.619 0.00 0.0 34.57 2.24
637 642 2.152016 GCTCACCAACTTCACTTACCC 58.848 52.381 0.00 0.0 0.00 3.69
739 747 3.428870 TGATTCTTTCTTTGTCGAGACGC 59.571 43.478 0.00 0.0 0.00 5.19
937 945 4.438148 GAGCCAAGGATCTTACTCTCAAC 58.562 47.826 0.00 0.0 0.00 3.18
966 974 0.937441 ATAGGCTCCACTCTCTCCCA 59.063 55.000 0.00 0.0 0.00 4.37
1035 1043 0.608035 GACGATTGAAGCCCCCAACA 60.608 55.000 0.00 0.0 0.00 3.33
1137 1160 1.043116 TCCCGGCTACTGGATCACTG 61.043 60.000 0.00 0.0 0.00 3.66
1226 1254 6.183360 GGCTAAGCGTAGTTCTTTGAATCAAT 60.183 38.462 8.50 0.0 0.00 2.57
1416 1444 4.601857 TCCCCCACACTTCTTTATTTCTCT 59.398 41.667 0.00 0.0 0.00 3.10
1488 1516 6.187682 TCTTATTTCTTCATTGGAGGGTTCC 58.812 40.000 0.00 0.0 44.31 3.62
1573 1601 0.966179 GTTTTCCGCCCCAAATGAGT 59.034 50.000 0.00 0.0 0.00 3.41
1619 1647 6.782000 TCCCTTCATCTTTTTGAAAGGAATCA 59.218 34.615 2.76 0.0 41.22 2.57
1653 1681 2.526993 CGCGTCGTTCCAACAACCA 61.527 57.895 0.00 0.0 0.00 3.67
1817 1845 2.317040 TCAGACTCGACCCTGTCTTTT 58.683 47.619 2.51 0.0 41.06 2.27
2067 2095 4.574421 TGCGTATGAGAACATTGTAATGGG 59.426 41.667 9.22 0.0 40.70 4.00
2070 2098 5.997746 CGTATGAGAACATTGTAATGGGGAT 59.002 40.000 9.22 0.0 40.70 3.85
2092 2120 5.304686 TGGTCATAGCCGAAATAGGATTT 57.695 39.130 0.00 0.0 0.00 2.17
2094 2122 4.083271 GGTCATAGCCGAAATAGGATTTGC 60.083 45.833 0.00 0.0 30.49 3.68
2371 2399 5.750067 GCTGCAGAAAAAGAAGATTTGTTGA 59.250 36.000 20.43 0.0 0.00 3.18
2373 2401 7.042254 GCTGCAGAAAAAGAAGATTTGTTGAAT 60.042 33.333 20.43 0.0 0.00 2.57
2505 2533 9.849752 ATAGATATCAGGTGCCCACATATATAT 57.150 33.333 5.32 0.0 0.00 0.86
2530 2558 5.186797 AGTCAAAAGAGAGATTGAGTCCGAT 59.813 40.000 0.00 0.0 34.90 4.18
2564 2592 1.573108 TCTTGGGGCTCGAGAGATTT 58.427 50.000 18.75 0.0 40.84 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.042831 GGCGTGCTTCCTTGCAGAT 61.043 57.895 0.00 0.00 44.20 2.90
173 178 8.561738 TTAAGACAATTATCCTCACTCAAACC 57.438 34.615 0.00 0.00 0.00 3.27
249 254 8.138712 CGAGATAGGCTTTACTAGACATTTTCT 58.861 37.037 0.00 0.00 38.51 2.52
379 384 1.734655 TCCATATCCCTCTCCCTTGC 58.265 55.000 0.00 0.00 0.00 4.01
739 747 5.195001 TCGAAAAGATGGGTTCCTTTTTG 57.805 39.130 0.00 0.00 41.17 2.44
889 897 4.338795 TCATTCTCTACAGGGGTCTCTT 57.661 45.455 0.00 0.00 0.00 2.85
937 945 0.461548 TGGAGCCTATCGAAGCACTG 59.538 55.000 8.00 0.00 0.00 3.66
966 974 3.914426 AACGGAGCCTGACTTATTCAT 57.086 42.857 0.00 0.00 32.17 2.57
1137 1160 0.801067 CGTAGTACCCGAAGCACTGC 60.801 60.000 0.00 0.00 0.00 4.40
1210 1238 9.076781 TCATGAAACCATTGATTCAAAGAACTA 57.923 29.630 2.68 0.00 38.88 2.24
1226 1254 5.871465 TCGATTTCGATTTCATGAAACCA 57.129 34.783 22.71 7.19 44.22 3.67
1488 1516 0.736325 AAGAACGGCGAAGTCCATCG 60.736 55.000 16.62 0.00 45.41 3.84
1573 1601 3.256704 ACAGAGGTGACTAATTCCCCAA 58.743 45.455 0.00 0.00 44.43 4.12
1653 1681 0.617820 ATACTGAGGTGCTCCCCGTT 60.618 55.000 0.00 0.00 0.00 4.44
1817 1845 2.092267 ACAGATGGGAATGCATGCTACA 60.092 45.455 20.33 10.63 0.00 2.74
1941 1969 2.447443 CAGTGGGAGTAGTGACTAGCA 58.553 52.381 0.00 0.00 35.45 3.49
2025 2053 0.326808 AGGAATACCCCCGTTAGCCA 60.327 55.000 0.00 0.00 36.73 4.75
2067 2095 3.260884 TCCTATTTCGGCTATGACCATCC 59.739 47.826 0.00 0.00 0.00 3.51
2070 2098 4.974645 AATCCTATTTCGGCTATGACCA 57.025 40.909 0.00 0.00 0.00 4.02
2371 2399 2.856231 TGCTTCCTATGGGGGTACAATT 59.144 45.455 0.00 0.00 35.33 2.32
2373 2401 1.974028 TGCTTCCTATGGGGGTACAA 58.026 50.000 0.00 0.00 35.33 2.41
2505 2533 5.710567 TCGGACTCAATCTCTCTTTTGACTA 59.289 40.000 0.00 0.00 0.00 2.59
2564 2592 3.949430 ACTTGTGGGGCCCTATCTATTA 58.051 45.455 25.93 0.00 0.00 0.98
2658 2686 4.768130 TGGAAAACAACTTTCACGTTCA 57.232 36.364 0.00 0.00 44.61 3.18


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

AutoCloner maintained by Alex Coulton.