Multiple sequence alignment - TraesCS1B01G436900

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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 TraesCS1B01G436900 chr1B 100.000 2489 0 0 1 2489 659947838 659945350 0.000000e+00 4597.0
1 TraesCS1B01G436900 chr2B 98.436 2494 32 4 1 2489 438604567 438607058 0.000000e+00 4383.0
2 TraesCS1B01G436900 chr2B 93.118 1918 44 16 1 1831 210670759 210672675 0.000000e+00 2730.0
3 TraesCS1B01G436900 chr2B 92.279 1904 67 22 1 1831 24026171 24024275 0.000000e+00 2628.0
4 TraesCS1B01G436900 chr2B 96.211 475 15 2 1823 2296 210672790 210673262 0.000000e+00 774.0
5 TraesCS1B01G436900 chr2B 93.952 463 27 1 2027 2489 24024111 24023650 0.000000e+00 699.0
6 TraesCS1B01G436900 chr2B 82.927 82 7 5 1873 1950 210672795 210672873 1.600000e-07 67.6
7 TraesCS1B01G436900 chr6D 89.737 1861 95 40 14 1825 454277191 454279004 0.000000e+00 2290.0
8 TraesCS1B01G436900 chr1D 89.460 1888 92 41 1 1825 359696667 359698510 0.000000e+00 2285.0
9 TraesCS1B01G436900 chr1D 87.904 959 56 19 3 910 390409897 390410846 0.000000e+00 1074.0
10 TraesCS1B01G436900 chr1D 89.210 658 57 10 1841 2489 359698731 359699383 0.000000e+00 809.0
11 TraesCS1B01G436900 chr3D 89.462 1879 91 44 14 1825 519327608 519329446 0.000000e+00 2274.0
12 TraesCS1B01G436900 chr5D 89.570 1697 97 25 1 1624 387823805 387822116 0.000000e+00 2080.0
13 TraesCS1B01G436900 chr5D 91.732 895 51 7 802 1674 370737391 370738284 0.000000e+00 1221.0
14 TraesCS1B01G436900 chr5D 90.306 588 33 13 1833 2419 370738522 370739086 0.000000e+00 749.0
15 TraesCS1B01G436900 chr5D 81.649 376 48 10 1 360 390991328 390991698 2.420000e-75 292.0
16 TraesCS1B01G436900 chr5D 87.023 131 6 4 1652 1771 54724837 54724967 1.200000e-28 137.0
17 TraesCS1B01G436900 chr4D 91.732 895 51 7 802 1674 306428177 306429070 0.000000e+00 1221.0
18 TraesCS1B01G436900 chr4D 88.282 879 66 23 1 864 306427441 306428297 0.000000e+00 1018.0
19 TraesCS1B01G436900 chr4D 90.427 585 45 8 1841 2419 306429330 306429909 0.000000e+00 760.0
20 TraesCS1B01G436900 chr2D 91.883 887 49 9 802 1666 651701767 651702652 0.000000e+00 1218.0
21 TraesCS1B01G436900 chr2D 87.076 944 80 13 1 910 103064118 103063183 0.000000e+00 1029.0
22 TraesCS1B01G436900 chr2D 88.027 877 72 17 1 864 60175111 60175967 0.000000e+00 1007.0
23 TraesCS1B01G436900 chr2D 88.235 867 67 22 14 864 651701040 651701887 0.000000e+00 1003.0
24 TraesCS1B01G436900 chr2D 90.598 585 45 7 1841 2419 60176981 60177561 0.000000e+00 767.0
25 TraesCS1B01G436900 chr2D 90.598 585 45 7 1841 2419 651702920 651703500 0.000000e+00 767.0
26 TraesCS1B01G436900 chr7A 85.806 620 57 20 2 609 13855355 13854755 1.620000e-176 628.0
27 TraesCS1B01G436900 chr7A 82.422 256 35 6 2179 2431 563627352 563627600 5.390000e-52 215.0
28 TraesCS1B01G436900 chr5B 83.303 551 73 12 1919 2461 536183099 536182560 8.000000e-135 490.0
29 TraesCS1B01G436900 chr3B 87.023 131 6 4 1654 1773 699312274 699312404 1.200000e-28 137.0
30 TraesCS1B01G436900 chr5A 89.583 96 2 5 1684 1774 575285427 575285519 5.630000e-22 115.0


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 TraesCS1B01G436900 chr1B 659945350 659947838 2488 True 4597.000000 4597 100.000000 1 2489 1 chr1B.!!$R1 2488
1 TraesCS1B01G436900 chr2B 438604567 438607058 2491 False 4383.000000 4383 98.436000 1 2489 1 chr2B.!!$F1 2488
2 TraesCS1B01G436900 chr2B 24023650 24026171 2521 True 1663.500000 2628 93.115500 1 2489 2 chr2B.!!$R1 2488
3 TraesCS1B01G436900 chr2B 210670759 210673262 2503 False 1190.533333 2730 90.752000 1 2296 3 chr2B.!!$F2 2295
4 TraesCS1B01G436900 chr6D 454277191 454279004 1813 False 2290.000000 2290 89.737000 14 1825 1 chr6D.!!$F1 1811
5 TraesCS1B01G436900 chr1D 359696667 359699383 2716 False 1547.000000 2285 89.335000 1 2489 2 chr1D.!!$F2 2488
6 TraesCS1B01G436900 chr1D 390409897 390410846 949 False 1074.000000 1074 87.904000 3 910 1 chr1D.!!$F1 907
7 TraesCS1B01G436900 chr3D 519327608 519329446 1838 False 2274.000000 2274 89.462000 14 1825 1 chr3D.!!$F1 1811
8 TraesCS1B01G436900 chr5D 387822116 387823805 1689 True 2080.000000 2080 89.570000 1 1624 1 chr5D.!!$R1 1623
9 TraesCS1B01G436900 chr5D 370737391 370739086 1695 False 985.000000 1221 91.019000 802 2419 2 chr5D.!!$F3 1617
10 TraesCS1B01G436900 chr4D 306427441 306429909 2468 False 999.666667 1221 90.147000 1 2419 3 chr4D.!!$F1 2418
11 TraesCS1B01G436900 chr2D 103063183 103064118 935 True 1029.000000 1029 87.076000 1 910 1 chr2D.!!$R1 909
12 TraesCS1B01G436900 chr2D 651701040 651703500 2460 False 996.000000 1218 90.238667 14 2419 3 chr2D.!!$F2 2405
13 TraesCS1B01G436900 chr2D 60175111 60177561 2450 False 887.000000 1007 89.312500 1 2419 2 chr2D.!!$F1 2418
14 TraesCS1B01G436900 chr7A 13854755 13855355 600 True 628.000000 628 85.806000 2 609 1 chr7A.!!$R1 607
15 TraesCS1B01G436900 chr5B 536182560 536183099 539 True 490.000000 490 83.303000 1919 2461 1 chr5B.!!$R1 542

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
80 82 0.82999 ACAAAACCCCCTGCAGTTTG 59.17 50.0 19.58 19.58 36.36 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2827 1.895798 CAGTGCACTAGGAAGAGGTGA 59.104 52.381 21.2 0.0 33.32 4.02 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
75 77 1.267574 TTTGCACAAAACCCCCTGCA 61.268 50.000 0.00 0.00 37.86 4.41
80 82 0.829990 ACAAAACCCCCTGCAGTTTG 59.170 50.000 19.58 19.58 36.36 2.93
372 465 1.004436 TGGGGAAGGGGGTATGTTTC 58.996 55.000 0.00 0.00 0.00 2.78
1175 1381 2.149383 TGGCTGACAAGGAGCAGGT 61.149 57.895 0.00 0.00 38.27 4.00
1188 1394 6.375455 ACAAGGAGCAGGTAATTACTGAATTG 59.625 38.462 15.05 12.37 38.20 2.32
1254 1461 9.304731 CTTGAGAAGAAGAAGATGTCTGATAAG 57.695 37.037 0.00 0.00 36.40 1.73
1480 1708 5.602145 AGGGTGAAGGAGATCTTAGATGAAG 59.398 44.000 0.00 0.00 35.50 3.02
1900 2631 9.175060 CATAGATAAAACACTCACTCTCATACG 57.825 37.037 0.00 0.00 0.00 3.06
2024 2804 5.163713 GCAGTTGGGTGTTTAAGAGATCATC 60.164 44.000 0.00 0.00 0.00 2.92
2025 2805 6.176183 CAGTTGGGTGTTTAAGAGATCATCT 58.824 40.000 0.00 0.00 41.27 2.90
2047 2827 7.409408 TCTATCTGGGTAGAGAATCCTACTT 57.591 40.000 0.00 0.00 39.11 2.24
2255 3035 1.736586 CTAGCTCCACTGGGTAGCG 59.263 63.158 0.00 0.00 40.26 4.26
2277 3057 3.888930 GCTTCTGCATCTACTACCTCTCT 59.111 47.826 0.00 0.00 39.41 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 1.241315 CGGGTTGAATCGGGCAAACT 61.241 55.000 0.00 0.00 33.55 2.66
80 82 3.508840 CTGCGGGTTGAATCGGGC 61.509 66.667 0.00 0.00 0.00 6.13
372 465 4.668576 TCTGCTGAAATTTTGCTACTCG 57.331 40.909 15.00 0.00 0.00 4.18
720 853 5.700832 TCACTAACAAGATGCTGTTAACTGG 59.299 40.000 13.60 4.97 40.38 4.00
1175 1381 5.929058 TGCATTGCCCAATTCAGTAATTA 57.071 34.783 6.12 0.00 33.45 1.40
1254 1461 4.406003 ACCTGATGAATGGTAGTGGTAGAC 59.594 45.833 0.00 0.00 34.36 2.59
1480 1708 8.045176 AGCTCCAACTTAATGATTTACTCAAC 57.955 34.615 0.00 0.00 37.44 3.18
2024 2804 7.175990 GTGAAGTAGGATTCTCTACCCAGATAG 59.824 44.444 8.04 0.00 40.19 2.08
2025 2805 7.005296 GTGAAGTAGGATTCTCTACCCAGATA 58.995 42.308 8.04 0.00 40.19 1.98
2047 2827 1.895798 CAGTGCACTAGGAAGAGGTGA 59.104 52.381 21.20 0.00 33.32 4.02
2253 3033 1.067821 AGGTAGTAGATGCAGAAGCGC 59.932 52.381 0.00 0.00 46.23 5.92
2255 3035 3.888930 AGAGAGGTAGTAGATGCAGAAGC 59.111 47.826 0.00 0.00 42.57 3.86
2277 3057 1.079490 CCTAGGAGGGCATGGATCCTA 59.921 57.143 14.23 0.00 41.72 2.94


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

AutoCloner maintained by Alex Coulton.