Multiple sequence alignment - TraesCS7B01G458800

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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 TraesCS7B01G458800 chr7B 100.000 2513 0 0 1 2513 716976343 716978855 0.000000e+00 4641
1 TraesCS7B01G458800 chr7B 98.397 1809 22 4 1 1803 716700875 716699068 0.000000e+00 3173
2 TraesCS7B01G458800 chr7B 92.255 1020 71 6 1498 2513 716984475 716985490 0.000000e+00 1439
3 TraesCS7B01G458800 chr7B 92.330 678 49 3 1839 2513 716699070 716698393 0.000000e+00 961
4 TraesCS7B01G458800 chr7B 90.598 117 11 0 624 740 479983293 479983177 3.350000e-34 156
5 TraesCS7B01G458800 chr7B 89.256 121 13 0 624 744 701329821 701329701 4.330000e-33 152
6 TraesCS7B01G458800 chr7B 88.710 124 13 1 624 746 342995126 342995249 1.560000e-32 150
7 TraesCS7B01G458800 chr7A 92.645 1550 75 13 987 2513 715245929 715244396 0.000000e+00 2194
8 TraesCS7B01G458800 chr7A 92.453 1113 47 16 916 2007 715662801 715661705 0.000000e+00 1555
9 TraesCS7B01G458800 chr7A 91.267 1042 54 16 987 2007 715577731 715576706 0.000000e+00 1386
10 TraesCS7B01G458800 chr7A 91.089 909 44 16 987 1874 715333785 715332893 0.000000e+00 1195
11 TraesCS7B01G458800 chr7A 90.802 848 39 17 987 1813 715436363 715435534 0.000000e+00 1098
12 TraesCS7B01G458800 chr7A 93.475 705 40 4 1811 2513 715425505 715424805 0.000000e+00 1042
13 TraesCS7B01G458800 chr7A 95.223 628 20 3 1 625 715663641 715663021 0.000000e+00 985
14 TraesCS7B01G458800 chr7A 90.777 206 5 5 739 934 715663022 715662821 1.920000e-66 263
15 TraesCS7B01G458800 chr7D 91.129 124 10 1 624 746 352086220 352086343 1.550000e-37 167
16 TraesCS7B01G458800 chr2B 90.323 124 11 1 624 746 756641674 756641797 7.190000e-36 161
17 TraesCS7B01G458800 chr5B 88.550 131 15 0 623 753 517216987 517217117 2.590000e-35 159
18 TraesCS7B01G458800 chr6B 90.598 117 11 0 624 740 218659348 218659464 3.350000e-34 156
19 TraesCS7B01G458800 chr3B 88.710 124 13 1 624 746 546710499 546710622 1.560000e-32 150


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 TraesCS7B01G458800 chr7B 716976343 716978855 2512 False 4641.000000 4641 100.000000 1 2513 1 chr7B.!!$F2 2512
1 TraesCS7B01G458800 chr7B 716698393 716700875 2482 True 2067.000000 3173 95.363500 1 2513 2 chr7B.!!$R3 2512
2 TraesCS7B01G458800 chr7B 716984475 716985490 1015 False 1439.000000 1439 92.255000 1498 2513 1 chr7B.!!$F3 1015
3 TraesCS7B01G458800 chr7A 715244396 715245929 1533 True 2194.000000 2194 92.645000 987 2513 1 chr7A.!!$R1 1526
4 TraesCS7B01G458800 chr7A 715576706 715577731 1025 True 1386.000000 1386 91.267000 987 2007 1 chr7A.!!$R5 1020
5 TraesCS7B01G458800 chr7A 715332893 715333785 892 True 1195.000000 1195 91.089000 987 1874 1 chr7A.!!$R2 887
6 TraesCS7B01G458800 chr7A 715435534 715436363 829 True 1098.000000 1098 90.802000 987 1813 1 chr7A.!!$R4 826
7 TraesCS7B01G458800 chr7A 715424805 715425505 700 True 1042.000000 1042 93.475000 1811 2513 1 chr7A.!!$R3 702
8 TraesCS7B01G458800 chr7A 715661705 715663641 1936 True 934.333333 1555 92.817667 1 2007 3 chr7A.!!$R6 2006

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
1465 1513 2.203728 ACGGGGAGTGGCTGTACA 60.204 61.111 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2535 1.831652 AACAACCCTAGCTGCGCTCT 61.832 55.0 9.73 8.56 40.44 4.09 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
1465 1513 2.203728 ACGGGGAGTGGCTGTACA 60.204 61.111 0.00 0.00 0.00 2.90
1568 1637 6.923508 CACACAGTGTTTGTTCTCTCTATGTA 59.076 38.462 2.45 0.00 38.16 2.29
1621 1696 3.119352 TGGGGTGATTCCTCATGGT 57.881 52.632 0.00 0.00 42.62 3.55
1769 1854 5.934935 TTTTCTTTAAAATCGAGCCTCGT 57.065 34.783 14.64 0.00 34.04 4.18
1770 1855 5.934935 TTTCTTTAAAATCGAGCCTCGTT 57.065 34.783 14.64 2.41 41.35 3.85
1919 2004 2.290514 TGAAGGCACAGCTGAGCTTATT 60.291 45.455 30.75 23.04 36.40 1.40
1936 2021 5.297278 AGCTTATTGTCGTTACACAAACCAA 59.703 36.000 4.95 0.00 39.69 3.67
1969 2054 1.563879 TCCCCGATGATGGACAACATT 59.436 47.619 0.00 0.00 40.72 2.71
2034 2119 5.641777 TCAAATATCATTGAACTCTCGCG 57.358 39.130 0.00 0.00 36.42 5.87
2050 2136 0.379669 CGCGATAGTAGACCACCGTT 59.620 55.000 0.00 0.00 39.35 4.44
2058 2144 4.405116 AGTAGACCACCGTTAACAAACA 57.595 40.909 6.39 0.00 0.00 2.83
2190 2276 2.683211 AGGGACCATTCAAGCAAAGT 57.317 45.000 0.00 0.00 0.00 2.66
2213 2299 0.825425 TGCCGACAATGCCAAAGGAA 60.825 50.000 0.00 0.00 0.00 3.36
2215 2301 0.109781 CCGACAATGCCAAAGGAACG 60.110 55.000 0.00 0.00 0.00 3.95
2240 2326 7.274033 CGATGCTGACAAACAACATGAATTATT 59.726 33.333 0.00 0.00 35.74 1.40
2241 2327 7.640616 TGCTGACAAACAACATGAATTATTG 57.359 32.000 0.00 0.00 0.00 1.90
2257 2343 7.154656 TGAATTATTGATCCCATGTCTACGAG 58.845 38.462 0.00 0.00 0.00 4.18
2332 2419 3.328931 ACTGAGAAGGATTTGAGCAGGAA 59.671 43.478 0.00 0.00 0.00 3.36
2355 2442 8.787852 GGAAGATTCTTATTTGAGACAACACTT 58.212 33.333 0.00 0.00 0.00 3.16
2447 2535 1.475169 CCACTCTGCCTCTGTCACCA 61.475 60.000 0.00 0.00 0.00 4.17
2484 2572 9.067986 AGGGTTGTTATGTCTCTTTCTTTTAAG 57.932 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1465 1513 4.796231 GATGCCGTCGCTGTCCGT 62.796 66.667 0.00 0.00 38.35 4.69
1568 1637 4.526970 AGAGAAAACAATATCGCCACCAT 58.473 39.130 0.00 0.00 0.00 3.55
1621 1696 9.288576 CACTATGGAGCATTTTAATTAGATGGA 57.711 33.333 10.91 0.00 0.00 3.41
1760 1845 7.009631 CCATTGATCTAATATAAACGAGGCTCG 59.990 40.741 33.42 33.42 46.93 5.03
1808 1893 8.380099 TCTGAGGATTTAGTTACCTTGCTTTAA 58.620 33.333 0.00 0.00 33.89 1.52
1875 1960 8.225603 TCAGCCAGATTTTTGAAGGATATAAC 57.774 34.615 0.00 0.00 0.00 1.89
1919 2004 3.374678 GGACTTTGGTTTGTGTAACGACA 59.625 43.478 0.00 0.00 42.39 4.35
1936 2021 2.696526 TCGGGGATAGCTATGGACTT 57.303 50.000 11.94 0.00 0.00 3.01
2034 2119 6.158598 TGTTTGTTAACGGTGGTCTACTATC 58.841 40.000 0.26 0.00 37.06 2.08
2050 2136 4.378978 CGCGATTTGGAATCCTGTTTGTTA 60.379 41.667 0.00 0.00 0.00 2.41
2058 2144 0.679640 TTGGCGCGATTTGGAATCCT 60.680 50.000 12.10 0.00 0.00 3.24
2213 2299 2.877786 TCATGTTGTTTGTCAGCATCGT 59.122 40.909 0.00 0.00 44.08 3.73
2215 2301 8.377681 CAATAATTCATGTTGTTTGTCAGCATC 58.622 33.333 0.00 0.00 44.08 3.91
2240 2326 2.693591 GTTCCTCGTAGACATGGGATCA 59.306 50.000 0.00 0.00 0.00 2.92
2241 2327 2.693591 TGTTCCTCGTAGACATGGGATC 59.306 50.000 0.00 0.00 0.00 3.36
2257 2343 7.654022 TTTGGAAATATGTCCCTATTGTTCC 57.346 36.000 9.59 0.00 36.80 3.62
2332 2419 8.160106 AGGAAGTGTTGTCTCAAATAAGAATCT 58.840 33.333 0.00 0.00 0.00 2.40
2447 2535 1.831652 AACAACCCTAGCTGCGCTCT 61.832 55.000 9.73 8.56 40.44 4.09


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

AutoCloner maintained by Alex Coulton.