Multiple sequence alignment - TraesCS7A01G162800

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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 TraesCS7A01G162800 chr7A 100.000 2452 0 0 1 2452 119006860 119009311 0.000000e+00 4529.0
1 TraesCS7A01G162800 chr7A 77.246 167 34 3 1236 1402 512247841 512248003 7.220000e-16 95.3
2 TraesCS7A01G162800 chr5A 98.565 1673 23 1 1 1672 99552614 99554286 0.000000e+00 2955.0
3 TraesCS7A01G162800 chr5A 98.593 782 11 0 1671 2452 99554621 99555402 0.000000e+00 1384.0
4 TraesCS7A01G162800 chr5A 87.383 214 24 3 2232 2442 478819285 478819498 2.440000e-60 243.0
5 TraesCS7A01G162800 chr5D 86.935 199 19 5 2249 2442 377987805 377988001 1.480000e-52 217.0


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 TraesCS7A01G162800 chr7A 119006860 119009311 2451 False 4529.0 4529 100.000 1 2452 1 chr7A.!!$F1 2451
1 TraesCS7A01G162800 chr5A 99552614 99555402 2788 False 2169.5 2955 98.579 1 2452 2 chr5A.!!$F2 2451

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
727 728 1.199615 GGAGGAAGAGAACTCCCTGG 58.8 60.0 0.0 0.0 46.01 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2217 0.251916 CCATGTGCCTTCGAGGGTTA 59.748 55.0 15.82 1.9 35.37 2.85 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
468 469 5.231568 CGGTATTCGGTACTTTCAGTCAATC 59.768 44.000 0.0 0.0 33.64 2.67
727 728 1.199615 GGAGGAAGAGAACTCCCTGG 58.800 60.000 0.0 0.0 46.01 4.45
965 966 9.301897 GGATTTTAGCATAGGGAGAAATACATT 57.698 33.333 0.0 0.0 0.00 2.71
1042 1043 6.617371 AGATAGAAATGGAGGACATAACCTGT 59.383 38.462 0.0 0.0 39.40 4.00
1104 1105 2.196742 TACAGGATGGCTTGGAGGAT 57.803 50.000 0.0 0.0 43.62 3.24
1126 1127 9.440761 AGGATAGTCAAGGTATTCTCAAATACT 57.559 33.333 7.9 0.0 44.45 2.12
1173 1174 5.010617 TCACATCTATATTTAGGCTCGCACA 59.989 40.000 0.0 0.0 0.00 4.57
1320 1321 1.136329 AAGGGGAGGAAGCAAGCTCA 61.136 55.000 0.0 0.0 0.00 4.26
1432 1433 6.493116 CATTGGTAGAAAAGATGAGACATGC 58.507 40.000 0.0 0.0 0.00 4.06
1463 1464 7.309770 AGTAGGAAATTAGCTATGGGAGAAG 57.690 40.000 0.0 0.0 0.00 2.85
1531 1532 1.402968 CCCATGAGATGCCAAACTTCG 59.597 52.381 0.0 0.0 0.00 3.79
1562 1564 2.076100 TGTGCCTCTAGTTTTGCATCG 58.924 47.619 0.0 0.0 35.96 3.84
1849 2187 8.908903 TCCTACAGCAAAATTAAAAAGAAGTCA 58.091 29.630 0.0 0.0 0.00 3.41
1876 2214 4.900635 TTGCAACTTCAGAGAAAAGACC 57.099 40.909 0.0 0.0 0.00 3.85
1877 2215 3.884895 TGCAACTTCAGAGAAAAGACCA 58.115 40.909 0.0 0.0 0.00 4.02
1879 2217 4.889409 TGCAACTTCAGAGAAAAGACCAAT 59.111 37.500 0.0 0.0 0.00 3.16
1880 2218 6.061441 TGCAACTTCAGAGAAAAGACCAATA 58.939 36.000 0.0 0.0 0.00 1.90
1881 2219 6.545666 TGCAACTTCAGAGAAAAGACCAATAA 59.454 34.615 0.0 0.0 0.00 1.40
1987 2325 2.496899 ATGGTGTAAGCTGGTCCTTG 57.503 50.000 0.0 0.0 33.76 3.61
2048 2386 7.992754 AGAAAGCTTGTATTCTCATTTGTCT 57.007 32.000 0.0 0.0 30.16 3.41
2353 2691 5.598417 ACCTTTCCTGATTTAGTGTTTTGCT 59.402 36.000 0.0 0.0 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 2.024176 TCAGGCTTCACCCTAGACAA 57.976 50.000 0.00 0.0 40.58 3.18
671 672 7.205297 CCATATTTTCTGCTCCAAATAACAGG 58.795 38.462 0.00 0.0 30.51 4.00
674 675 6.572519 TGCCATATTTTCTGCTCCAAATAAC 58.427 36.000 0.00 0.0 30.51 1.89
727 728 4.684703 CGGACCTCGATTGTTCATAATACC 59.315 45.833 0.00 0.0 42.43 2.73
768 769 8.846423 TTTATAAGACCTCTCATCTTCCTCTT 57.154 34.615 0.00 0.0 37.57 2.85
983 984 7.661437 TGCAGTTCATTGACTAGACAATAAAGT 59.339 33.333 17.98 11.6 38.25 2.66
1007 1008 5.008415 CCTCCATTTCTATCTTCACATGTGC 59.992 44.000 21.38 0.0 0.00 4.57
1042 1043 5.447624 TCAACATCTTCGTAGTCTGAACA 57.552 39.130 2.52 0.0 0.00 3.18
1130 1131 8.703743 AGATGTGAATATGAGCTCTAAAACTCT 58.296 33.333 16.19 3.7 33.92 3.24
1173 1174 9.860898 CTTTAAATTATTTTGTTGCCTCTAGCT 57.139 29.630 0.00 0.0 44.23 3.32
1213 1214 5.883673 GGTGCAGTCTAACAATTTATACCCA 59.116 40.000 0.00 0.0 0.00 4.51
1279 1280 7.338710 CCTTGTTCTCCTCATATTTTCACCTA 58.661 38.462 0.00 0.0 0.00 3.08
1320 1321 6.071447 TGCCTCAATTGTTTGTAATATGCAGT 60.071 34.615 5.13 0.0 34.32 4.40
1432 1433 7.158021 CCATAGCTAATTTCCTACTTCCTCAG 58.842 42.308 0.00 0.0 0.00 3.35
1463 1464 4.252073 ACTCTGCAATGATGACTCTTGTC 58.748 43.478 0.00 0.0 43.20 3.18
1810 2148 3.327757 TGCTGTAGGATTCAAAGTCACCT 59.672 43.478 0.00 0.0 35.11 4.00
1876 2214 2.107950 TGTGCCTTCGAGGGTTATTG 57.892 50.000 15.82 0.0 35.37 1.90
1877 2215 2.643551 CATGTGCCTTCGAGGGTTATT 58.356 47.619 15.82 0.0 35.37 1.40
1879 2217 0.251916 CCATGTGCCTTCGAGGGTTA 59.748 55.000 15.82 1.9 35.37 2.85
1880 2218 1.002134 CCATGTGCCTTCGAGGGTT 60.002 57.895 15.82 0.0 35.37 4.11
1881 2219 0.907704 TACCATGTGCCTTCGAGGGT 60.908 55.000 15.82 0.0 35.37 4.34
1987 2325 3.775654 CTGAGTCCTCCCCCGTGC 61.776 72.222 0.00 0.0 0.00 5.34
2048 2386 6.644592 CGTTTTCATTATGCCTTCTTTTCCAA 59.355 34.615 0.00 0.0 0.00 3.53
2246 2584 6.431234 AGGGAGTAGCATAAAAACTTCAACTG 59.569 38.462 0.00 0.0 0.00 3.16
2353 2691 9.677567 GCAAACAGACAAATTTGACTCTATTTA 57.322 29.630 24.64 0.0 37.91 1.40


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

AutoCloner maintained by Alex Coulton.