Multiple sequence alignment - TraesCS4A01G146200

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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 TraesCS4A01G146200 chr4A 100.000 2460 0 0 1 2460 254604545 254607004 0.000000e+00 4543
1 TraesCS4A01G146200 chr4A 96.192 1707 59 3 754 2460 232104052 232102352 0.000000e+00 2787
2 TraesCS4A01G146200 chr4A 96.574 759 26 0 1 759 232121903 232121145 0.000000e+00 1258
3 TraesCS4A01G146200 chr4A 96.218 238 9 0 1993 2230 257861240 257861003 8.250000e-105 390
4 TraesCS4A01G146200 chr4A 95.763 236 8 1 2225 2460 257851974 257851741 1.790000e-101 379
5 TraesCS4A01G146200 chr4A 87.778 90 7 4 1553 1638 536090324 536090235 4.330000e-18 102
6 TraesCS4A01G146200 chr1B 91.566 1980 129 16 1 1965 318980309 318978353 0.000000e+00 2697
7 TraesCS4A01G146200 chr1B 91.304 1012 77 8 1 1010 320713813 320714815 0.000000e+00 1371
8 TraesCS4A01G146200 chr1B 92.593 945 52 10 1035 1965 320735989 320736929 0.000000e+00 1341
9 TraesCS4A01G146200 chr1B 92.555 497 32 3 1965 2460 318978178 318977686 0.000000e+00 708
10 TraesCS4A01G146200 chr1B 92.200 500 32 3 1965 2460 320737103 320737599 0.000000e+00 701
11 TraesCS4A01G146200 chr1B 92.405 79 3 1 2209 2284 672545600 672545522 2.590000e-20 110
12 TraesCS4A01G146200 chr1D 95.294 1530 55 11 1 1517 104024734 104026259 0.000000e+00 2410
13 TraesCS4A01G146200 chr1D 93.952 496 30 0 1965 2460 104031485 104031980 0.000000e+00 750
14 TraesCS4A01G146200 chr1D 96.476 454 15 1 1512 1965 104030859 104031311 0.000000e+00 749
15 TraesCS4A01G146200 chr5A 89.435 1893 172 23 1 1878 400065380 400067259 0.000000e+00 2362
16 TraesCS4A01G146200 chr5A 84.462 251 31 6 1965 2208 400067584 400067833 8.790000e-60 241
17 TraesCS4A01G146200 chr5A 92.045 88 6 1 1878 1965 400067326 400067412 3.320000e-24 122
18 TraesCS4A01G146200 chrUn 94.737 228 12 0 1738 1965 480131499 480131726 3.010000e-94 355
19 TraesCS4A01G146200 chrUn 92.405 79 3 1 2209 2284 171012611 171012533 2.590000e-20 110
20 TraesCS4A01G146200 chr2B 83.523 352 40 12 1530 1877 218085945 218086282 1.840000e-81 313
21 TraesCS4A01G146200 chr2B 83.523 352 40 12 1530 1877 218088089 218088426 1.840000e-81 313
22 TraesCS4A01G146200 chr2B 91.753 97 8 0 2280 2376 218086833 218086929 4.270000e-28 135
23 TraesCS4A01G146200 chr2B 91.753 97 8 0 2280 2376 218088977 218089073 4.270000e-28 135
24 TraesCS4A01G146200 chr2B 92.045 88 7 0 1878 1965 218086333 218086420 9.240000e-25 124
25 TraesCS4A01G146200 chr2B 92.045 88 7 0 1878 1965 218088477 218088564 9.240000e-25 124
26 TraesCS4A01G146200 chr2B 92.045 88 7 0 1878 1965 218090617 218090704 9.240000e-25 124
27 TraesCS4A01G146200 chr2B 92.405 79 3 1 2209 2284 391149127 391149049 2.590000e-20 110
28 TraesCS4A01G146200 chr6D 90.816 98 8 1 2280 2376 224147489 224147586 1.990000e-26 130
29 TraesCS4A01G146200 chr6D 89.796 98 9 1 2280 2376 224150530 224150627 9.240000e-25 124
30 TraesCS4A01G146200 chr7B 92.405 79 3 1 2209 2284 54044853 54044931 2.590000e-20 110


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 TraesCS4A01G146200 chr4A 254604545 254607004 2459 False 4543.000000 4543 100.000000 1 2460 1 chr4A.!!$F1 2459
1 TraesCS4A01G146200 chr4A 232102352 232104052 1700 True 2787.000000 2787 96.192000 754 2460 1 chr4A.!!$R1 1706
2 TraesCS4A01G146200 chr4A 232121145 232121903 758 True 1258.000000 1258 96.574000 1 759 1 chr4A.!!$R2 758
3 TraesCS4A01G146200 chr1B 318977686 318980309 2623 True 1702.500000 2697 92.060500 1 2460 2 chr1B.!!$R2 2459
4 TraesCS4A01G146200 chr1B 320713813 320714815 1002 False 1371.000000 1371 91.304000 1 1010 1 chr1B.!!$F1 1009
5 TraesCS4A01G146200 chr1B 320735989 320737599 1610 False 1021.000000 1341 92.396500 1035 2460 2 chr1B.!!$F2 1425
6 TraesCS4A01G146200 chr1D 104024734 104026259 1525 False 2410.000000 2410 95.294000 1 1517 1 chr1D.!!$F1 1516
7 TraesCS4A01G146200 chr1D 104030859 104031980 1121 False 749.500000 750 95.214000 1512 2460 2 chr1D.!!$F2 948
8 TraesCS4A01G146200 chr5A 400065380 400067833 2453 False 908.333333 2362 88.647333 1 2208 3 chr5A.!!$F1 2207

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
307 316 2.348872 CGTGATTGCCTCGTCATATTGC 60.349 50.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1862 3.308438 TCAGCGGTAAGTCAAGTAACC 57.692 47.619 0.0 0.0 0.0 2.85 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
125 131 7.202016 TCAATGGATGAAGTTACTGTGAAAC 57.798 36.000 0.00 0.0 34.30 2.78
158 164 9.764363 CCATAATGATTGAGCTTACTAAGTACA 57.236 33.333 0.00 0.0 0.00 2.90
202 209 8.136165 GGTGATTTACGTGAGATATAGTTGAGT 58.864 37.037 0.00 0.0 0.00 3.41
247 254 2.564771 CTTGTCCTGTGAAGCAGTTGA 58.435 47.619 0.00 0.0 43.55 3.18
307 316 2.348872 CGTGATTGCCTCGTCATATTGC 60.349 50.000 0.00 0.0 0.00 3.56
326 335 3.738982 TGCCTGACTTCAATTTCTTCGA 58.261 40.909 0.00 0.0 0.00 3.71
348 357 6.701400 TCGATGGTGTATTCATGATGTAGTTG 59.299 38.462 0.00 0.0 0.00 3.16
413 422 7.214460 TGGTTGGAGATGTTTATATGGGTTA 57.786 36.000 0.00 0.0 0.00 2.85
448 458 4.141914 ACCGTTGGAGTTCTAATCAGATCC 60.142 45.833 0.00 0.0 32.55 3.36
458 468 7.275920 AGTTCTAATCAGATCCGTAATTTGCT 58.724 34.615 0.00 0.0 0.00 3.91
831 842 8.650490 TGAGTCTTTTAGCATATGTGGATATGA 58.350 33.333 4.29 0.0 42.96 2.15
939 951 8.827177 TGACTACTGATTTCGAAGTAATTTGT 57.173 30.769 0.00 0.0 0.00 2.83
1840 1879 4.559153 TGTAAGGTTACTTGACTTACCGC 58.441 43.478 10.27 0.0 43.55 5.68
1908 2014 7.037514 ACCCCTAAAGAGTATAAGCAGAAAAGT 60.038 37.037 0.00 0.0 0.00 2.66
1981 2262 9.938280 GGGTATGCATACAAAGTATAGACATAA 57.062 33.333 32.19 0.0 34.98 1.90
2071 2359 4.032960 TGTGGATAACCTTGTGCTGATT 57.967 40.909 0.00 0.0 37.04 2.57
2072 2360 5.172687 TGTGGATAACCTTGTGCTGATTA 57.827 39.130 0.00 0.0 37.04 1.75
2078 2366 7.067372 TGGATAACCTTGTGCTGATTATTTCAG 59.933 37.037 0.00 0.0 44.56 3.02
2171 2459 6.392354 CCAGACATTAGCATGAATTGTGTTT 58.608 36.000 0.00 0.0 34.11 2.83
2181 2469 5.979517 GCATGAATTGTGTTTCCCTATAAGC 59.020 40.000 0.00 0.0 0.00 3.09
2231 2519 0.543410 TCTTTCGGGTAGAGGCACCA 60.543 55.000 0.00 0.0 40.65 4.17
2391 2682 5.950758 AGCTCGTCGACTATAGATTTGAT 57.049 39.130 14.70 0.0 0.00 2.57
2438 2730 6.154363 ACTTCAATGTTCCAGTTTTTCTTCCA 59.846 34.615 0.00 0.0 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.186198 ACTTATCGACAAGGGGAGAAAATG 58.814 41.667 8.55 0.0 0.00 2.32
23 24 5.429130 GACTTATCGACAAGGGGAGAAAAT 58.571 41.667 8.55 0.0 0.00 1.82
247 254 1.319614 ACACCAAACAAAGCCACGCT 61.320 50.000 0.00 0.0 42.56 5.07
307 316 4.697352 ACCATCGAAGAAATTGAAGTCAGG 59.303 41.667 0.00 0.0 43.58 3.86
326 335 7.067372 CCAACAACTACATCATGAATACACCAT 59.933 37.037 0.00 0.0 0.00 3.55
348 357 2.674796 AAGAGTAGACGCCATCCAAC 57.325 50.000 0.00 0.0 0.00 3.77
413 422 1.172180 CCAACGGTGTCAGCCACAAT 61.172 55.000 0.00 0.0 46.44 2.71
428 438 5.012328 ACGGATCTGATTAGAACTCCAAC 57.988 43.478 9.00 0.0 33.49 3.77
448 458 5.094812 ACACACATATGCAAGCAAATTACG 58.905 37.500 1.58 0.0 0.00 3.18
458 468 9.264719 CTCAGATATCTAAACACACATATGCAA 57.735 33.333 4.54 0.0 0.00 4.08
884 896 9.705290 ATCAAAATTATTTTCGCACTAGGTTTT 57.295 25.926 0.00 0.0 0.00 2.43
960 972 6.013293 AGCTTCCCACATTTAGACTTAGAAGT 60.013 38.462 0.00 0.0 43.16 3.01
1161 1174 9.988815 AGAGTTCTACATATTACCTATGCTTTG 57.011 33.333 0.00 0.0 40.88 2.77
1162 1175 9.988815 CAGAGTTCTACATATTACCTATGCTTT 57.011 33.333 0.00 0.0 40.88 3.51
1477 1513 5.801947 GCACTATCAAAACCATGTCATGTTC 59.198 40.000 11.84 0.0 0.00 3.18
1533 1571 9.038072 TCTACCAACAACAACACCTATTAGATA 57.962 33.333 0.00 0.0 0.00 1.98
1547 1585 7.165485 AGCATACTTAACATCTACCAACAACA 58.835 34.615 0.00 0.0 0.00 3.33
1673 1712 6.734104 ACTTCTTGACAAGTATGAGATTGC 57.266 37.500 14.75 0.0 34.70 3.56
1676 1715 6.410540 GGGAACTTCTTGACAAGTATGAGAT 58.589 40.000 14.75 4.6 35.45 2.75
1823 1862 3.308438 TCAGCGGTAAGTCAAGTAACC 57.692 47.619 0.00 0.0 0.00 2.85
1840 1879 9.449719 AACCTCCATAATAGTACAAAAGTTCAG 57.550 33.333 0.00 0.0 0.00 3.02
1981 2262 5.352569 CCGAGAAAGATAAACAATGCTCAGT 59.647 40.000 0.00 0.0 0.00 3.41
2071 2359 8.497554 GCATTTGACAATTTGAAAGCTGAAATA 58.502 29.630 2.79 0.0 0.00 1.40
2072 2360 7.012515 TGCATTTGACAATTTGAAAGCTGAAAT 59.987 29.630 2.79 0.0 0.00 2.17
2171 2459 9.914834 AGTATATTTTTGTTGTGCTTATAGGGA 57.085 29.630 0.00 0.0 0.00 4.20
2231 2519 7.496346 TCCTCTGGACAAAGATTACATTAGT 57.504 36.000 0.00 0.0 0.00 2.24
2291 2582 8.712285 AATTGCAGATTGTTCCATCATTTTAG 57.288 30.769 0.00 0.0 0.00 1.85
2378 2669 8.717717 TGAGAATGTGGGAATCAAATCTATAGT 58.282 33.333 0.00 0.0 0.00 2.12
2391 2682 6.817765 GTGAAACTAATGAGAATGTGGGAA 57.182 37.500 0.00 0.0 0.00 3.97
2438 2730 1.841663 GCGTGGCGACTTCACAACAT 61.842 55.000 0.00 0.0 35.03 2.71


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

AutoCloner maintained by Alex Coulton.