Multiple sequence alignment - TraesCS4A01G471800

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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 TraesCS4A01G471800 chr4A 100.000 2339 0 0 1 2339 732266353 732268691 0.000000e+00 4320
1 TraesCS4A01G471800 chr4A 89.422 1645 168 4 1 1639 2973255 2974899 0.000000e+00 2069
2 TraesCS4A01G471800 chr4A 89.314 1647 166 5 1 1638 448544947 448546592 0.000000e+00 2058
3 TraesCS4A01G471800 chr4B 97.378 1640 41 1 1 1638 670054665 670053026 0.000000e+00 2789
4 TraesCS4A01G471800 chr4B 88.396 1646 181 8 1 1638 98851991 98853634 0.000000e+00 1973
5 TraesCS4A01G471800 chr1B 95.253 1643 70 6 1 1638 159404280 159405919 0.000000e+00 2595
6 TraesCS4A01G471800 chr6B 94.762 1642 80 4 1 1638 411081967 411080328 0.000000e+00 2551
7 TraesCS4A01G471800 chr6B 91.495 1646 128 11 1 1638 301713 300072 0.000000e+00 2254
8 TraesCS4A01G471800 chr7B 92.600 1527 108 4 1 1522 630566387 630567913 0.000000e+00 2189
9 TraesCS4A01G471800 chr7B 93.494 707 32 8 1634 2339 516267990 516268683 0.000000e+00 1038
10 TraesCS4A01G471800 chr2B 89.065 1637 173 5 1 1632 452232823 452234458 0.000000e+00 2026
11 TraesCS4A01G471800 chrUn 91.845 699 39 4 1639 2335 98346113 98345431 0.000000e+00 959
12 TraesCS4A01G471800 chr5D 93.704 270 11 1 2070 2339 365175673 365175410 1.300000e-107 399
13 TraesCS4A01G471800 chr5D 92.996 257 17 1 1869 2124 365175930 365175674 7.890000e-100 374


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 TraesCS4A01G471800 chr4A 732266353 732268691 2338 False 4320.0 4320 100.000 1 2339 1 chr4A.!!$F3 2338
1 TraesCS4A01G471800 chr4A 2973255 2974899 1644 False 2069.0 2069 89.422 1 1639 1 chr4A.!!$F1 1638
2 TraesCS4A01G471800 chr4A 448544947 448546592 1645 False 2058.0 2058 89.314 1 1638 1 chr4A.!!$F2 1637
3 TraesCS4A01G471800 chr4B 670053026 670054665 1639 True 2789.0 2789 97.378 1 1638 1 chr4B.!!$R1 1637
4 TraesCS4A01G471800 chr4B 98851991 98853634 1643 False 1973.0 1973 88.396 1 1638 1 chr4B.!!$F1 1637
5 TraesCS4A01G471800 chr1B 159404280 159405919 1639 False 2595.0 2595 95.253 1 1638 1 chr1B.!!$F1 1637
6 TraesCS4A01G471800 chr6B 411080328 411081967 1639 True 2551.0 2551 94.762 1 1638 1 chr6B.!!$R2 1637
7 TraesCS4A01G471800 chr6B 300072 301713 1641 True 2254.0 2254 91.495 1 1638 1 chr6B.!!$R1 1637
8 TraesCS4A01G471800 chr7B 630566387 630567913 1526 False 2189.0 2189 92.600 1 1522 1 chr7B.!!$F2 1521
9 TraesCS4A01G471800 chr7B 516267990 516268683 693 False 1038.0 1038 93.494 1634 2339 1 chr7B.!!$F1 705
10 TraesCS4A01G471800 chr2B 452232823 452234458 1635 False 2026.0 2026 89.065 1 1632 1 chr2B.!!$F1 1631
11 TraesCS4A01G471800 chrUn 98345431 98346113 682 True 959.0 959 91.845 1639 2335 1 chrUn.!!$R1 696
12 TraesCS4A01G471800 chr5D 365175410 365175930 520 True 386.5 399 93.350 1869 2339 2 chr5D.!!$R1 470

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
965 974 2.297597 CCCGGCATTTGTTTTTCACCTA 59.702 45.455 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1814 0.32016 GTCTCCGCGGTTGGTTAGTT 60.32 55.0 27.15 0.0 0.0 2.24 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
255 257 3.300388 AGATCTCGAGATAAAGGTGGCA 58.700 45.455 27.36 0.0 34.37 4.92
385 388 7.372260 ACTTGAGAAATAGATCTGTGGCTAT 57.628 36.000 5.18 0.0 0.00 2.97
413 416 5.488919 TGAATCCAGGTTTAATGACTCTCCT 59.511 40.000 0.00 0.0 0.00 3.69
847 856 6.767423 CCTCAAAATCAAAATTTTCCTGTGGT 59.233 34.615 0.00 0.0 41.96 4.16
965 974 2.297597 CCCGGCATTTGTTTTTCACCTA 59.702 45.455 0.00 0.0 0.00 3.08
1367 1381 1.005340 CTCGCCTGCATTCAGAGTTC 58.995 55.000 0.00 0.0 42.95 3.01
1462 1486 8.994500 TGTAGTATTTCAGGTTGTGGGATTATA 58.006 33.333 0.00 0.0 0.00 0.98
1501 1525 1.740585 CCCATGGCGTTCGTTTTGATA 59.259 47.619 6.09 0.0 0.00 2.15
1608 1633 4.277174 TGTATTTCCGTTCACTTGCAATGT 59.723 37.500 0.00 0.0 0.00 2.71
1634 1661 0.109919 GTCATGCCCGGTTCGAAAAC 60.110 55.000 0.00 0.0 34.46 2.43
1641 1668 1.132643 CCCGGTTCGAAAACAAACACA 59.867 47.619 0.00 0.0 37.10 3.72
1685 1712 2.589157 GGTGTCCCCGACCATGACA 61.589 63.158 0.00 0.0 36.71 3.58
1787 1814 2.994995 ATCGCCACTGGTCGGTGA 60.995 61.111 11.18 0.0 46.59 4.02
1788 1815 2.579657 ATCGCCACTGGTCGGTGAA 61.580 57.895 11.18 0.0 45.72 3.18
1821 1848 1.304217 AGACCGTCACCATCGTCCT 60.304 57.895 0.40 0.0 0.00 3.85
1864 1891 0.533978 CCGTCATCACCAACCACACA 60.534 55.000 0.00 0.0 0.00 3.72
1926 1955 7.489574 TTTTTGCTTTGTGAAACTTTGACTT 57.510 28.000 0.00 0.0 38.04 3.01
1957 1986 1.448540 CAGTGGAGGACGCCATGAC 60.449 63.158 0.00 0.0 40.68 3.06
2038 2067 6.303054 TGTTTATCAGGTCAAAATGGAGTCA 58.697 36.000 0.00 0.0 0.00 3.41
2064 2093 4.274214 GGTAGGCACTCGTTAACTTTTGTT 59.726 41.667 3.71 0.0 42.78 2.83
2223 2307 7.870954 CCTGATAAACTAGGTACAAATATCGCA 59.129 37.037 0.00 0.0 0.00 5.10
2255 2354 0.842467 AGGGGGAGGAGGAGTTGTTG 60.842 60.000 0.00 0.0 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 257 7.391620 TGTTTACGAAGATCTTTAACTCCCAT 58.608 34.615 9.87 0.0 0.00 4.00
385 388 5.640147 AGTCATTAAACCTGGATTCAACCA 58.360 37.500 0.00 0.0 38.33 3.67
796 805 2.203625 GGCCTTCCAAACCCAGCA 60.204 61.111 0.00 0.0 0.00 4.41
818 827 4.458989 GGAAAATTTTGATTTTGAGGGGGC 59.541 41.667 8.47 0.0 34.24 5.80
847 856 4.280425 CAGAACAGCATCCTGAGATAGCTA 59.720 45.833 0.00 0.0 41.77 3.32
965 974 0.400594 GACCACTTTAGCCACAGGGT 59.599 55.000 0.00 0.0 37.19 4.34
1323 1336 6.485830 TTGTAAGATCATTCTCCCTCGATT 57.514 37.500 0.00 0.0 0.00 3.34
1433 1450 5.781306 TCCCACAACCTGAAATACTACAGTA 59.219 40.000 0.00 0.0 32.93 2.74
1462 1486 1.021968 GGCGAAAACCTGACAACACT 58.978 50.000 0.00 0.0 0.00 3.55
1537 1561 0.723981 GGAAAGATGTGCAGCGAGTC 59.276 55.000 0.00 0.0 0.00 3.36
1549 1573 3.399305 ACAACAGGAGAAAGGGGAAAGAT 59.601 43.478 0.00 0.0 0.00 2.40
1634 1661 7.851822 AATAGCTTTTGTACGAATGTGTTTG 57.148 32.000 9.75 0.0 0.00 2.93
1641 1668 9.559958 CATGAAGAAAATAGCTTTTGTACGAAT 57.440 29.630 0.00 0.0 34.73 3.34
1787 1814 0.320160 GTCTCCGCGGTTGGTTAGTT 60.320 55.000 27.15 0.0 0.00 2.24
1788 1815 1.291272 GTCTCCGCGGTTGGTTAGT 59.709 57.895 27.15 0.0 0.00 2.24
1864 1891 1.248101 GGGCTTGGTAACGGCAACAT 61.248 55.000 0.00 0.0 39.26 2.71
1918 1946 6.692681 CACTGGACACATAAAACAAGTCAAAG 59.307 38.462 0.00 0.0 0.00 2.77
1926 1955 3.392947 TCCTCCACTGGACACATAAAACA 59.607 43.478 0.00 0.0 0.00 2.83
1957 1986 3.263489 AGTGGTGCTCATCTCATTCAG 57.737 47.619 0.00 0.0 0.00 3.02
2038 2067 3.975168 AGTTAACGAGTGCCTACCAAT 57.025 42.857 0.00 0.0 0.00 3.16
2219 2303 3.343617 CCCCTTCTCAAAGTTATTGCGA 58.656 45.455 0.00 0.0 0.00 5.10
2223 2307 4.183916 TCCTCCCCCTTCTCAAAGTTATT 58.816 43.478 0.00 0.0 0.00 1.40


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

AutoCloner maintained by Alex Coulton.