Multiple sequence alignment - TraesCS2A01G110300

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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 TraesCS2A01G110300 chr2A 100.000 2531 0 0 1 2531 62223392 62220862 0.000000e+00 4674.0
1 TraesCS2A01G110300 chrUn 95.787 1614 49 11 809 2412 162315566 162317170 0.000000e+00 2586.0
2 TraesCS2A01G110300 chr6B 97.489 876 12 4 871 1739 720804872 720805744 0.000000e+00 1487.0
3 TraesCS2A01G110300 chr6B 93.211 707 35 8 1824 2529 720805740 720806434 0.000000e+00 1027.0
4 TraesCS2A01G110300 chr6B 100.000 36 0 0 809 844 720804834 720804869 1.620000e-07 67.6
5 TraesCS2A01G110300 chr6B 88.462 52 2 1 1736 1783 219096415 219096364 2.720000e-05 60.2
6 TraesCS2A01G110300 chr4A 99.136 810 5 1 1 810 589614429 589615236 0.000000e+00 1456.0
7 TraesCS2A01G110300 chr4A 98.188 828 9 2 871 1693 743680942 743680116 0.000000e+00 1441.0
8 TraesCS2A01G110300 chr4A 94.602 389 18 3 2113 2500 743679381 743678995 1.300000e-167 599.0
9 TraesCS2A01G110300 chr4A 86.224 196 13 4 1710 1898 743679901 743679713 1.540000e-47 200.0
10 TraesCS2A01G110300 chr4A 100.000 36 0 0 809 844 743680980 743680945 1.620000e-07 67.6
11 TraesCS2A01G110300 chr7A 98.520 811 11 1 1 811 515168627 515169436 0.000000e+00 1430.0
12 TraesCS2A01G110300 chr7A 95.259 696 31 2 117 811 634079225 634079919 0.000000e+00 1101.0
13 TraesCS2A01G110300 chr5D 96.806 814 23 1 1 811 458466533 458465720 0.000000e+00 1356.0
14 TraesCS2A01G110300 chr6A 96.182 812 29 2 1 811 34726247 34725437 0.000000e+00 1327.0
15 TraesCS2A01G110300 chr7D 95.539 807 25 2 1 806 465893438 465892642 0.000000e+00 1280.0
16 TraesCS2A01G110300 chr1D 94.685 809 25 5 1 808 374563153 374563944 0.000000e+00 1240.0
17 TraesCS2A01G110300 chr1D 94.444 36 1 1 1767 1802 81645707 81645673 1.000000e-03 54.7
18 TraesCS2A01G110300 chr5A 94.132 818 35 5 1 808 552884780 552883966 0.000000e+00 1232.0
19 TraesCS2A01G110300 chr2B 94.118 799 20 8 1 799 76848413 76847642 0.000000e+00 1190.0
20 TraesCS2A01G110300 chr5B 97.561 205 5 0 607 811 161590774 161590978 4.010000e-93 351.0


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 TraesCS2A01G110300 chr2A 62220862 62223392 2530 True 4674.000000 4674 100.0000 1 2531 1 chr2A.!!$R1 2530
1 TraesCS2A01G110300 chrUn 162315566 162317170 1604 False 2586.000000 2586 95.7870 809 2412 1 chrUn.!!$F1 1603
2 TraesCS2A01G110300 chr6B 720804834 720806434 1600 False 860.533333 1487 96.9000 809 2529 3 chr6B.!!$F1 1720
3 TraesCS2A01G110300 chr4A 589614429 589615236 807 False 1456.000000 1456 99.1360 1 810 1 chr4A.!!$F1 809
4 TraesCS2A01G110300 chr4A 743678995 743680980 1985 True 576.900000 1441 94.7535 809 2500 4 chr4A.!!$R1 1691
5 TraesCS2A01G110300 chr7A 515168627 515169436 809 False 1430.000000 1430 98.5200 1 811 1 chr7A.!!$F1 810
6 TraesCS2A01G110300 chr7A 634079225 634079919 694 False 1101.000000 1101 95.2590 117 811 1 chr7A.!!$F2 694
7 TraesCS2A01G110300 chr5D 458465720 458466533 813 True 1356.000000 1356 96.8060 1 811 1 chr5D.!!$R1 810
8 TraesCS2A01G110300 chr6A 34725437 34726247 810 True 1327.000000 1327 96.1820 1 811 1 chr6A.!!$R1 810
9 TraesCS2A01G110300 chr7D 465892642 465893438 796 True 1280.000000 1280 95.5390 1 806 1 chr7D.!!$R1 805
10 TraesCS2A01G110300 chr1D 374563153 374563944 791 False 1240.000000 1240 94.6850 1 808 1 chr1D.!!$F1 807
11 TraesCS2A01G110300 chr5A 552883966 552884780 814 True 1232.000000 1232 94.1320 1 808 1 chr5A.!!$R1 807
12 TraesCS2A01G110300 chr2B 76847642 76848413 771 True 1190.000000 1190 94.1180 1 799 1 chr2B.!!$R1 798

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
942 977 1.202463 CCTTCGTCCCTAGCACATCAG 60.202 57.143 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
2196 2557 0.613777 AACTGGTGGGAACTCGGATC 59.386 55.0 0.0 0.0 0.0 3.36 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
536 556 2.684843 GCGCAGGGCTCTGTTTCAG 61.685 63.158 16.66 3.25 42.78 3.02
548 568 7.890655 AGGGCTCTGTTTCAGTTAAATTATTCT 59.109 33.333 0.00 0.00 32.61 2.40
942 977 1.202463 CCTTCGTCCCTAGCACATCAG 60.202 57.143 0.00 0.00 0.00 2.90
1325 1360 4.459089 GCTGACCCTGGCCGAGTC 62.459 72.222 11.60 11.60 0.00 3.36
1582 1617 2.237643 ACGATACCACCACCAGCATAAA 59.762 45.455 0.00 0.00 0.00 1.40
1679 1716 3.411351 CCGTGCGTGCAGTGTACC 61.411 66.667 5.73 0.00 0.00 3.34
1690 1727 5.593968 CGTGCAGTGTACCCATTTATACTA 58.406 41.667 5.73 0.00 0.00 1.82
1691 1728 6.220930 CGTGCAGTGTACCCATTTATACTAT 58.779 40.000 5.73 0.00 0.00 2.12
1754 1998 6.997239 ATTAAATACTCCCTCCGTTTTGAC 57.003 37.500 0.00 0.00 0.00 3.18
1769 2013 4.953814 CGTTTTGACGACTCAACTTTGTAC 59.046 41.667 0.00 0.00 36.06 2.90
1773 2017 7.459394 TTTGACGACTCAACTTTGTACTAAG 57.541 36.000 14.42 14.42 36.06 2.18
1820 2064 4.624015 TGACTCGTCTATTTTGAAACGGT 58.376 39.130 0.00 0.00 35.89 4.83
1821 2065 5.051816 TGACTCGTCTATTTTGAAACGGTT 58.948 37.500 0.00 0.00 35.89 4.44
1823 2067 5.051816 ACTCGTCTATTTTGAAACGGTTGA 58.948 37.500 0.00 0.00 35.89 3.18
1878 2122 7.827236 TCCATACATGTTCCTCGATTAGTTTTT 59.173 33.333 2.30 0.00 0.00 1.94
1919 2163 2.680312 AATGTCGCTACTGTGAGCAT 57.320 45.000 9.01 0.00 42.99 3.79
1920 2164 1.931906 ATGTCGCTACTGTGAGCATG 58.068 50.000 9.01 0.00 42.99 4.06
1921 2165 0.603065 TGTCGCTACTGTGAGCATGT 59.397 50.000 0.00 0.00 42.99 3.21
1922 2166 1.816224 TGTCGCTACTGTGAGCATGTA 59.184 47.619 0.00 0.00 42.99 2.29
2054 2299 2.571757 CTGCCTCGCTAACACCGA 59.428 61.111 0.00 0.00 0.00 4.69
2196 2557 0.933097 CGCAATCTGATTCTCCACCG 59.067 55.000 0.00 0.00 0.00 4.94
2308 2670 1.003839 AGCCGCCAAATGTTCTCGA 60.004 52.632 0.00 0.00 0.00 4.04
2413 2776 2.903855 ATGCATGCTGCCCTACGC 60.904 61.111 20.33 0.00 44.23 4.42
2529 2892 6.432162 ACTTATTACTATGTTAGGCCGATCGA 59.568 38.462 18.66 0.00 0.00 3.59
2530 2893 4.761235 TTACTATGTTAGGCCGATCGAG 57.239 45.455 18.66 8.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
536 556 7.633664 GGCTCACGACGTTTAGAATAATTTAAC 59.366 37.037 10.53 0.00 0.00 2.01
942 977 1.108776 TGGTAGTAGTGCGGGATGAC 58.891 55.000 0.00 0.00 0.00 3.06
1026 1061 1.144936 GAAGAGGACCATGGAGGCG 59.855 63.158 21.47 0.00 43.14 5.52
1582 1617 4.738252 CACACTCATTGTATGTACGCGTAT 59.262 41.667 23.56 11.24 35.67 3.06
1715 1953 9.740710 GAGTATTTAATTTGAGGGCTATGGTAT 57.259 33.333 0.00 0.00 0.00 2.73
1721 1959 6.183361 GGAGGGAGTATTTAATTTGAGGGCTA 60.183 42.308 0.00 0.00 0.00 3.93
1792 2036 8.270799 CGTTTCAAAATAGACGAGTCAACTTTA 58.729 33.333 5.99 0.00 37.69 1.85
1801 2045 5.585500 TCAACCGTTTCAAAATAGACGAG 57.415 39.130 0.00 0.00 37.69 4.18
1814 2058 6.235664 ACCATAGAACATACTTCAACCGTTT 58.764 36.000 0.00 0.00 0.00 3.60
1821 2065 9.952030 TGTTTGATAACCATAGAACATACTTCA 57.048 29.630 0.00 0.00 33.15 3.02
1823 2067 9.959721 AGTGTTTGATAACCATAGAACATACTT 57.040 29.630 0.00 0.00 33.15 2.24
2118 2479 3.404438 GGGGCGGGTGGTATGACA 61.404 66.667 0.00 0.00 0.00 3.58
2196 2557 0.613777 AACTGGTGGGAACTCGGATC 59.386 55.000 0.00 0.00 0.00 3.36
2268 2630 5.551233 CTGATTCAGTCAAGGGACACTTTA 58.449 41.667 5.46 0.00 46.80 1.85
2413 2776 1.134367 TGGATAGAAGCCGTCGTCAAG 59.866 52.381 0.00 0.00 0.00 3.02
2506 2869 6.822667 TCGATCGGCCTAACATAGTAATAA 57.177 37.500 16.41 0.00 0.00 1.40
2507 2870 6.432607 CTCGATCGGCCTAACATAGTAATA 57.567 41.667 16.41 0.00 0.00 0.98
2508 2871 5.312120 CTCGATCGGCCTAACATAGTAAT 57.688 43.478 16.41 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.