Multiple sequence alignment - TraesCS4A01G494200

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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 TraesCS4A01G494200 chr4A 100.000 2606 0 0 1 2606 742272664 742270059 0.000000e+00 4813.0
1 TraesCS4A01G494200 chr4A 97.056 2310 61 6 301 2606 739830640 739832946 0.000000e+00 3882.0
2 TraesCS4A01G494200 chr4A 94.536 2306 90 17 306 2606 740063939 740061665 0.000000e+00 3528.0
3 TraesCS4A01G494200 chr4A 92.754 2291 109 19 306 2593 733929752 733927516 0.000000e+00 3258.0
4 TraesCS4A01G494200 chr4A 90.601 1032 93 2 997 2028 739806203 739807230 0.000000e+00 1365.0
5 TraesCS4A01G494200 chr4A 94.346 283 12 3 29 311 739830217 739830495 5.150000e-117 431.0
6 TraesCS4A01G494200 chr4A 94.466 253 13 1 30 282 740064341 740064090 3.150000e-104 388.0
7 TraesCS4A01G494200 chr4A 84.585 253 10 8 30 282 733930129 733929906 9.390000e-55 224.0
8 TraesCS4A01G494200 chr7D 89.409 1218 106 17 957 2162 3731313 3730107 0.000000e+00 1513.0
9 TraesCS4A01G494200 chr7D 91.168 1019 83 4 997 2013 3697390 3698403 0.000000e+00 1376.0
10 TraesCS4A01G494200 chr7D 88.188 618 50 11 1780 2386 3582468 3583073 0.000000e+00 715.0
11 TraesCS4A01G494200 chr7D 90.860 186 16 1 2384 2568 3583121 3583306 5.570000e-62 248.0
12 TraesCS4A01G494200 chr7D 93.182 44 3 0 2563 2606 3583325 3583368 6.020000e-07 65.8
13 TraesCS4A01G494200 chr7A 89.318 1217 108 17 957 2162 2554257 2553052 0.000000e+00 1507.0
14 TraesCS4A01G494200 chr7A 90.891 1032 90 2 997 2028 3004360 3003333 0.000000e+00 1382.0
15 TraesCS4A01G494200 chr7A 89.128 1113 101 9 930 2035 3379537 3380636 0.000000e+00 1367.0
16 TraesCS4A01G494200 chr7A 91.781 73 5 1 2268 2340 3582095 3582166 1.650000e-17 100.0
17 TraesCS4A01G494200 chr7A 93.750 64 4 0 2273 2336 3003193 3003130 2.130000e-16 97.1
18 TraesCS4A01G494200 chr7A 100.000 29 0 0 415 443 3360123 3360151 1.000000e-03 54.7


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 TraesCS4A01G494200 chr4A 742270059 742272664 2605 True 4813.000000 4813 100.000000 1 2606 1 chr4A.!!$R1 2605
1 TraesCS4A01G494200 chr4A 739830217 739832946 2729 False 2156.500000 3882 95.701000 29 2606 2 chr4A.!!$F2 2577
2 TraesCS4A01G494200 chr4A 740061665 740064341 2676 True 1958.000000 3528 94.501000 30 2606 2 chr4A.!!$R3 2576
3 TraesCS4A01G494200 chr4A 733927516 733930129 2613 True 1741.000000 3258 88.669500 30 2593 2 chr4A.!!$R2 2563
4 TraesCS4A01G494200 chr4A 739806203 739807230 1027 False 1365.000000 1365 90.601000 997 2028 1 chr4A.!!$F1 1031
5 TraesCS4A01G494200 chr7D 3730107 3731313 1206 True 1513.000000 1513 89.409000 957 2162 1 chr7D.!!$R1 1205
6 TraesCS4A01G494200 chr7D 3697390 3698403 1013 False 1376.000000 1376 91.168000 997 2013 1 chr7D.!!$F1 1016
7 TraesCS4A01G494200 chr7D 3582468 3583368 900 False 342.933333 715 90.743333 1780 2606 3 chr7D.!!$F2 826
8 TraesCS4A01G494200 chr7A 2553052 2554257 1205 True 1507.000000 1507 89.318000 957 2162 1 chr7A.!!$R1 1205
9 TraesCS4A01G494200 chr7A 3379537 3380636 1099 False 1367.000000 1367 89.128000 930 2035 1 chr7A.!!$F2 1105
10 TraesCS4A01G494200 chr7A 3003130 3004360 1230 True 739.550000 1382 92.320500 997 2336 2 chr7A.!!$R2 1339

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
933 1099 1.019673 CAACAACTGCTGAGCACTGT 58.98 50.0 1.4 7.35 32.92 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2443 2.589798 TCGACGAAACTTCCTTGTGT 57.41 45.0 0.0 0.0 0.0 3.72 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
25 26 1.843992 CGCAAGCATGGAAATTAGCC 58.156 50.000 0.00 0.00 0.00 3.93
26 27 1.134753 CGCAAGCATGGAAATTAGCCA 59.865 47.619 2.76 2.76 40.24 4.75
27 28 2.797087 CGCAAGCATGGAAATTAGCCAG 60.797 50.000 6.19 1.13 39.11 4.85
177 178 5.243207 AGTAAATTTCCACCCGAGTACAAG 58.757 41.667 0.00 0.00 0.00 3.16
212 213 5.732170 TCCCATAGGTAGGTTATTTGGTTGA 59.268 40.000 0.00 0.00 0.00 3.18
225 226 7.550196 GGTTATTTGGTTGAGGACGATTTAGTA 59.450 37.037 0.00 0.00 0.00 1.82
382 543 4.033776 GCTGCCCTGCCCAGTGTA 62.034 66.667 0.00 0.00 32.93 2.90
604 767 4.233632 TCCCATGAAGTGCATAACATCA 57.766 40.909 0.00 0.00 40.56 3.07
740 904 5.620206 TGATATTAGGTGGGTTGTATGCAG 58.380 41.667 0.00 0.00 0.00 4.41
762 926 4.460382 AGAAAATGCAGTCATCGGTGAAAT 59.540 37.500 0.00 0.00 35.80 2.17
793 957 8.793592 GTTTGTATAGTTTCTTTGATTGGAGGT 58.206 33.333 0.00 0.00 0.00 3.85
883 1049 2.961062 GCCATAATCAATGCTGACCCTT 59.039 45.455 0.00 0.00 33.30 3.95
933 1099 1.019673 CAACAACTGCTGAGCACTGT 58.980 50.000 1.40 7.35 32.92 3.55
960 1126 3.506810 GCACTTGCAAGTTACAACAACA 58.493 40.909 29.23 0.00 41.59 3.33
980 1146 4.868268 ACAGGAGGCAGATTGTAGTAGTA 58.132 43.478 0.00 0.00 0.00 1.82
1053 1226 3.645212 CCATGAGATCTCTCCTAGGCAAA 59.355 47.826 22.95 0.00 42.20 3.68
1094 1267 1.828832 GAGTACACTCTGATTCGCGG 58.171 55.000 6.13 0.00 39.81 6.46
1095 1268 0.179134 AGTACACTCTGATTCGCGGC 60.179 55.000 6.13 0.00 0.00 6.53
1096 1269 1.226575 TACACTCTGATTCGCGGCG 60.227 57.895 17.70 17.70 0.00 6.46
1097 1270 1.929806 TACACTCTGATTCGCGGCGT 61.930 55.000 22.90 3.24 0.00 5.68
1289 1471 1.383456 CCTCAGGACTCTCTCAGCGG 61.383 65.000 0.00 0.00 0.00 5.52
1566 1751 3.582647 TGAAGGTGGACATGAAGAAGCTA 59.417 43.478 0.00 0.00 0.00 3.32
1603 1788 5.163478 GCCAAACATGATAAAGGCTCTCATT 60.163 40.000 0.00 0.00 39.02 2.57
2262 2462 3.800506 AGTTACACAAGGAAGTTTCGTCG 59.199 43.478 0.00 0.00 0.00 5.12
2429 2679 8.990163 TGGACCTAAAAAGTAGAATCAAAACT 57.010 30.769 0.00 0.00 0.00 2.66
2518 2769 9.462174 GTTGAATTTGTGTTGAATCTGAATACA 57.538 29.630 0.00 0.00 0.00 2.29
2577 2855 7.831691 TTTCCTCAATGGTATGAACTTCAAA 57.168 32.000 0.00 0.00 37.07 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.203065 GCTAATTTCCATGCTTGCGC 58.797 50.000 0.00 0.00 0.00 6.09
6 7 1.134753 TGGCTAATTTCCATGCTTGCG 59.865 47.619 0.00 0.00 0.00 4.85
7 8 2.428171 TCTGGCTAATTTCCATGCTTGC 59.572 45.455 0.00 0.00 32.37 4.01
8 9 4.583489 AGATCTGGCTAATTTCCATGCTTG 59.417 41.667 0.00 0.00 32.37 4.01
9 10 4.801164 AGATCTGGCTAATTTCCATGCTT 58.199 39.130 0.00 0.00 32.37 3.91
10 11 4.450305 AGATCTGGCTAATTTCCATGCT 57.550 40.909 0.00 0.00 32.37 3.79
11 12 4.340381 ACAAGATCTGGCTAATTTCCATGC 59.660 41.667 0.00 0.00 32.37 4.06
12 13 5.221185 CCACAAGATCTGGCTAATTTCCATG 60.221 44.000 0.00 0.00 32.37 3.66
13 14 4.891756 CCACAAGATCTGGCTAATTTCCAT 59.108 41.667 0.00 0.00 32.37 3.41
14 15 4.263905 ACCACAAGATCTGGCTAATTTCCA 60.264 41.667 0.00 0.00 31.13 3.53
15 16 4.273318 ACCACAAGATCTGGCTAATTTCC 58.727 43.478 0.00 0.00 31.13 3.13
16 17 5.904362 AACCACAAGATCTGGCTAATTTC 57.096 39.130 0.00 0.00 31.13 2.17
17 18 7.961326 ATTAACCACAAGATCTGGCTAATTT 57.039 32.000 0.00 0.00 29.39 1.82
18 19 7.961326 AATTAACCACAAGATCTGGCTAATT 57.039 32.000 12.03 12.03 36.13 1.40
19 20 7.229506 GCTAATTAACCACAAGATCTGGCTAAT 59.770 37.037 0.00 0.00 33.34 1.73
20 21 6.542370 GCTAATTAACCACAAGATCTGGCTAA 59.458 38.462 0.00 0.00 31.13 3.09
21 22 6.055588 GCTAATTAACCACAAGATCTGGCTA 58.944 40.000 0.00 0.00 31.13 3.93
22 23 4.884164 GCTAATTAACCACAAGATCTGGCT 59.116 41.667 0.00 0.00 31.13 4.75
23 24 4.036852 GGCTAATTAACCACAAGATCTGGC 59.963 45.833 0.00 0.00 31.13 4.85
24 25 5.192927 TGGCTAATTAACCACAAGATCTGG 58.807 41.667 3.37 0.00 34.62 3.86
25 26 6.115446 TCTGGCTAATTAACCACAAGATCTG 58.885 40.000 3.37 0.00 0.00 2.90
26 27 6.313519 TCTGGCTAATTAACCACAAGATCT 57.686 37.500 3.37 0.00 0.00 2.75
27 28 6.995091 AGATCTGGCTAATTAACCACAAGATC 59.005 38.462 18.91 18.91 36.29 2.75
133 134 2.159240 TCACTGATAGACGACATGTGGC 60.159 50.000 1.15 0.00 0.00 5.01
177 178 5.010282 CCTACCTATGGGAAATATGGCAAC 58.990 45.833 0.25 0.00 36.25 4.17
382 543 3.306641 GGTCACTGAAGAGTCTTGAGCAT 60.307 47.826 18.06 0.00 36.13 3.79
713 877 6.746900 GCATACAACCCACCTAATATCATGGA 60.747 42.308 0.00 0.00 33.80 3.41
740 904 3.829886 TTCACCGATGACTGCATTTTC 57.170 42.857 0.00 0.00 34.11 2.29
960 1126 6.195700 TCTTTACTACTACAATCTGCCTCCT 58.804 40.000 0.00 0.00 0.00 3.69
980 1146 7.127032 ACTCCATCTTCCTTATCTGTGATCTTT 59.873 37.037 0.00 0.00 0.00 2.52
1053 1226 2.044946 GCAAGGAGACCGCCCAAT 60.045 61.111 0.00 0.00 0.00 3.16
1603 1788 3.253921 CCAATCAATGACACAACAGCTCA 59.746 43.478 0.00 0.00 0.00 4.26
2244 2443 2.589798 TCGACGAAACTTCCTTGTGT 57.410 45.000 0.00 0.00 0.00 3.72
2381 2581 8.545472 TCCAATTTTAGTATGTTACCTGCTACT 58.455 33.333 0.00 0.00 0.00 2.57
2455 2706 7.054491 ACCTATGTCCAAATTGCCATATTTC 57.946 36.000 4.74 0.00 0.00 2.17
2518 2769 5.221342 CGAACAGTCCAAGAGAGCCTTATAT 60.221 44.000 0.00 0.00 32.86 0.86
2557 2835 7.373493 AGCTTTTTGAAGTTCATACCATTGAG 58.627 34.615 6.36 0.00 0.00 3.02
2561 2839 7.669722 TCCTTAGCTTTTTGAAGTTCATACCAT 59.330 33.333 6.36 0.00 0.00 3.55
2574 2852 7.592903 GTGAGAAGAAACATCCTTAGCTTTTTG 59.407 37.037 0.00 0.00 0.00 2.44
2577 2855 6.538263 AGTGAGAAGAAACATCCTTAGCTTT 58.462 36.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.