Multiple sequence alignment - TraesCS5A01G111800

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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 TraesCS5A01G111800 chr5A 100.000 3004 0 0 1 3004 216670659 216667656 0.000000e+00 5548.0
1 TraesCS5A01G111800 chr5A 96.615 768 25 1 1803 2570 308142286 308143052 0.000000e+00 1273.0
2 TraesCS5A01G111800 chr5A 96.348 356 13 0 2649 3004 84398535 84398890 1.200000e-163 586.0
3 TraesCS5A01G111800 chr7A 97.205 3005 72 6 1 3004 576352864 576349871 0.000000e+00 5073.0
4 TraesCS5A01G111800 chr7A 97.451 2315 50 3 691 3004 576320127 576317821 0.000000e+00 3940.0
5 TraesCS5A01G111800 chr7A 97.368 76 1 1 2569 2643 96200676 96200751 8.740000e-26 128.0
6 TraesCS5A01G111800 chr7B 95.829 1822 58 12 1 1805 408930034 408931854 0.000000e+00 2928.0
7 TraesCS5A01G111800 chr7B 95.448 1428 53 6 1 1418 408936346 408937771 0.000000e+00 2266.0
8 TraesCS5A01G111800 chr3B 94.484 1813 68 13 1 1805 778242829 778244617 0.000000e+00 2765.0
9 TraesCS5A01G111800 chr3B 95.466 1544 52 11 1 1527 490331742 490333284 0.000000e+00 2447.0
10 TraesCS5A01G111800 chr3B 96.329 1008 32 2 803 1805 68462583 68461576 0.000000e+00 1652.0
11 TraesCS5A01G111800 chrUn 97.544 1588 30 3 691 2278 387670229 387671807 0.000000e+00 2708.0
12 TraesCS5A01G111800 chrUn 97.272 1063 23 1 1618 2680 445370133 445371189 0.000000e+00 1797.0
13 TraesCS5A01G111800 chrUn 95.828 839 31 3 969 1805 319093744 319094580 0.000000e+00 1352.0
14 TraesCS5A01G111800 chrUn 94.370 817 36 3 1 812 379540548 379541359 0.000000e+00 1245.0
15 TraesCS5A01G111800 chrUn 94.247 817 37 3 1 812 214931817 214931006 0.000000e+00 1240.0
16 TraesCS5A01G111800 chr2D 94.847 1727 61 11 1 1715 352982256 352980546 0.000000e+00 2671.0
17 TraesCS5A01G111800 chr2D 97.472 356 9 0 2649 3004 352980358 352980003 2.560000e-170 608.0
18 TraesCS5A01G111800 chr4B 93.263 1811 74 20 1 1803 203528806 203527036 0.000000e+00 2625.0
19 TraesCS5A01G111800 chr2A 96.426 1175 33 5 1 1166 197673121 197671947 0.000000e+00 1929.0
20 TraesCS5A01G111800 chr2A 96.610 354 12 0 2651 3004 114851831 114852184 3.340000e-164 588.0
21 TraesCS5A01G111800 chr2A 98.469 196 3 0 2092 2287 197671558 197671363 2.220000e-91 346.0
22 TraesCS5A01G111800 chr6A 96.484 768 26 1 1803 2570 121648991 121648225 0.000000e+00 1267.0
23 TraesCS5A01G111800 chr3A 96.484 768 26 1 1803 2570 399611035 399610269 0.000000e+00 1267.0
24 TraesCS5A01G111800 chr3A 96.354 768 27 1 1803 2570 403984523 403983757 0.000000e+00 1262.0
25 TraesCS5A01G111800 chr5D 95.312 768 25 1 1803 2570 80898856 80898100 0.000000e+00 1208.0
26 TraesCS5A01G111800 chr5D 96.910 356 10 1 2649 3004 80897903 80897549 1.990000e-166 595.0
27 TraesCS5A01G111800 chr7D 96.910 356 11 0 2649 3004 165956093 165955738 5.540000e-167 597.0
28 TraesCS5A01G111800 chr6B 96.910 356 11 0 2649 3004 695218731 695218376 5.540000e-167 597.0
29 TraesCS5A01G111800 chr1A 96.610 354 12 0 2651 3004 65256032 65256385 3.340000e-164 588.0
30 TraesCS5A01G111800 chr1A 97.917 48 1 0 2598 2645 65241132 65241085 1.920000e-12 84.2
31 TraesCS5A01G111800 chr6D 97.659 299 7 0 2269 2567 419595723 419595425 5.740000e-142 514.0
32 TraesCS5A01G111800 chr5B 90.643 171 5 2 789 948 564596409 564596579 1.810000e-52 217.0
33 TraesCS5A01G111800 chr2B 96.104 77 3 0 2569 2645 260620212 260620136 3.140000e-25 126.0
34 TraesCS5A01G111800 chr4A 100.000 45 0 0 2598 2642 11173435 11173479 1.920000e-12 84.2


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 TraesCS5A01G111800 chr5A 216667656 216670659 3003 True 5548.0 5548 100.0000 1 3004 1 chr5A.!!$R1 3003
1 TraesCS5A01G111800 chr5A 308142286 308143052 766 False 1273.0 1273 96.6150 1803 2570 1 chr5A.!!$F2 767
2 TraesCS5A01G111800 chr7A 576349871 576352864 2993 True 5073.0 5073 97.2050 1 3004 1 chr7A.!!$R2 3003
3 TraesCS5A01G111800 chr7A 576317821 576320127 2306 True 3940.0 3940 97.4510 691 3004 1 chr7A.!!$R1 2313
4 TraesCS5A01G111800 chr7B 408930034 408931854 1820 False 2928.0 2928 95.8290 1 1805 1 chr7B.!!$F1 1804
5 TraesCS5A01G111800 chr7B 408936346 408937771 1425 False 2266.0 2266 95.4480 1 1418 1 chr7B.!!$F2 1417
6 TraesCS5A01G111800 chr3B 778242829 778244617 1788 False 2765.0 2765 94.4840 1 1805 1 chr3B.!!$F2 1804
7 TraesCS5A01G111800 chr3B 490331742 490333284 1542 False 2447.0 2447 95.4660 1 1527 1 chr3B.!!$F1 1526
8 TraesCS5A01G111800 chr3B 68461576 68462583 1007 True 1652.0 1652 96.3290 803 1805 1 chr3B.!!$R1 1002
9 TraesCS5A01G111800 chrUn 387670229 387671807 1578 False 2708.0 2708 97.5440 691 2278 1 chrUn.!!$F3 1587
10 TraesCS5A01G111800 chrUn 445370133 445371189 1056 False 1797.0 1797 97.2720 1618 2680 1 chrUn.!!$F4 1062
11 TraesCS5A01G111800 chrUn 319093744 319094580 836 False 1352.0 1352 95.8280 969 1805 1 chrUn.!!$F1 836
12 TraesCS5A01G111800 chrUn 379540548 379541359 811 False 1245.0 1245 94.3700 1 812 1 chrUn.!!$F2 811
13 TraesCS5A01G111800 chrUn 214931006 214931817 811 True 1240.0 1240 94.2470 1 812 1 chrUn.!!$R1 811
14 TraesCS5A01G111800 chr2D 352980003 352982256 2253 True 1639.5 2671 96.1595 1 3004 2 chr2D.!!$R1 3003
15 TraesCS5A01G111800 chr4B 203527036 203528806 1770 True 2625.0 2625 93.2630 1 1803 1 chr4B.!!$R1 1802
16 TraesCS5A01G111800 chr2A 197671363 197673121 1758 True 1137.5 1929 97.4475 1 2287 2 chr2A.!!$R1 2286
17 TraesCS5A01G111800 chr6A 121648225 121648991 766 True 1267.0 1267 96.4840 1803 2570 1 chr6A.!!$R1 767
18 TraesCS5A01G111800 chr3A 399610269 399611035 766 True 1267.0 1267 96.4840 1803 2570 1 chr3A.!!$R1 767
19 TraesCS5A01G111800 chr3A 403983757 403984523 766 True 1262.0 1262 96.3540 1803 2570 1 chr3A.!!$R2 767
20 TraesCS5A01G111800 chr5D 80897549 80898856 1307 True 901.5 1208 96.1110 1803 3004 2 chr5D.!!$R1 1201

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
141 147 0.607762 TCTCGCTCAGCTGTGACTCT 60.608 55.0 19.61 0.0 0.0 3.24 F
1324 1461 0.615331 TGACCTCATGTTGCTCCCTC 59.385 55.0 0.00 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2091 1.112916 TGGACTGAAGAGTGTGCGGA 61.113 55.0 0.0 0.0 30.16 5.54 R
2721 2991 7.232118 ACTCCTTGTTGGAATTTATTGGAAG 57.768 36.0 0.0 0.0 45.63 3.46 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
141 147 0.607762 TCTCGCTCAGCTGTGACTCT 60.608 55.000 19.61 0.00 0.00 3.24
202 208 2.892425 GAAGCTACGCCGCAGCAT 60.892 61.111 12.50 0.00 41.66 3.79
214 220 3.095163 CAGCATGCTCCCTCCCCT 61.095 66.667 19.68 0.00 0.00 4.79
331 339 2.188207 GCTCTTCCCTCTTCCGGC 59.812 66.667 0.00 0.00 0.00 6.13
416 453 7.348815 TGTCCTGATGATTTTTACTGATGGAT 58.651 34.615 0.00 0.00 0.00 3.41
548 585 0.798159 TGCTCATTGTTGCGCAGTAG 59.202 50.000 11.31 4.35 38.60 2.57
593 630 0.760567 TGCAGGTCTAGCCCATCGAT 60.761 55.000 0.00 0.00 38.26 3.59
787 824 9.247861 AGGCAGAGTTCTTATTTATGACAAAAT 57.752 29.630 0.00 0.00 33.69 1.82
992 1029 1.671901 CTTGGTGGGCGTGGTTTTGT 61.672 55.000 0.00 0.00 0.00 2.83
1324 1461 0.615331 TGACCTCATGTTGCTCCCTC 59.385 55.000 0.00 0.00 0.00 4.30
1380 1521 6.238184 GCTTGTGCTTCTTTTGCAGTAATTTT 60.238 34.615 0.00 0.00 41.41 1.82
1381 1522 7.608308 TTGTGCTTCTTTTGCAGTAATTTTT 57.392 28.000 0.00 0.00 41.41 1.94
1543 1684 9.482627 CTGAACTTCAGTACATTACTTCTCTTT 57.517 33.333 10.27 0.00 39.58 2.52
1834 1986 5.187772 TCAGTCCACATACATAGTCTGCTTT 59.812 40.000 0.00 0.00 0.00 3.51
1939 2091 0.828677 GGCCTGTACCACGGATTAGT 59.171 55.000 0.00 0.00 0.00 2.24
2596 2748 1.825474 TCAGTACTGCTCCAGCTTACC 59.175 52.381 18.45 0.00 42.66 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 208 2.041265 GAAGGAGGGGAGGGAGCA 59.959 66.667 0.00 0.00 0.00 4.26
214 220 0.549169 AATCCGGTCCCCAAGAAGGA 60.549 55.000 0.00 0.00 41.22 3.36
416 453 3.945981 TGAGTCGCCTATGTGTACAAA 57.054 42.857 0.00 0.00 0.00 2.83
548 585 7.392673 AGAGCCACAATATAATCCATGATTCAC 59.607 37.037 0.00 0.00 33.95 3.18
593 630 2.750637 GAGGAGGAGCCGTCGTCA 60.751 66.667 10.61 0.00 43.43 4.35
787 824 7.962995 ATAAGAACTCTGTCTAGACATCCAA 57.037 36.000 25.35 11.23 41.01 3.53
992 1029 9.567776 TCAAAATTAGAGAAGACATGGTTGTTA 57.432 29.630 0.00 0.00 35.79 2.41
1324 1461 7.067372 CAGATCTCTATAGGAAGGTATCTGCTG 59.933 44.444 0.00 0.00 33.45 4.41
1543 1684 4.600692 TTCGAGGACATCTTCAAGTCAA 57.399 40.909 0.00 0.00 36.50 3.18
1834 1986 4.039245 CCACCAACTTCTCTTCACTCACTA 59.961 45.833 0.00 0.00 0.00 2.74
1939 2091 1.112916 TGGACTGAAGAGTGTGCGGA 61.113 55.000 0.00 0.00 30.16 5.54
2596 2748 7.707104 AGACTGAACATGTTCTAAAGTTTTGG 58.293 34.615 32.57 14.96 40.14 3.28
2721 2991 7.232118 ACTCCTTGTTGGAATTTATTGGAAG 57.768 36.000 0.00 0.00 45.63 3.46
2757 3027 8.598202 TGTCCTTGTGTATACCTTGTCTAATA 57.402 34.615 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.