Multiple sequence alignment - TraesCS2D01G241200

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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 TraesCS2D01G241200 chr2D 100.000 2360 0 0 1 2360 261212096 261209737 0.000000e+00 4359.0
1 TraesCS2D01G241200 chr2D 93.296 1969 101 10 308 2260 261321937 261319984 0.000000e+00 2876.0
2 TraesCS2D01G241200 chr2D 96.815 314 9 1 1 313 261322360 261322047 7.470000e-145 523.0
3 TraesCS2D01G241200 chr2D 91.071 112 6 2 2250 2360 261297675 261297567 5.260000e-32 148.0
4 TraesCS2D01G241200 chr2D 77.401 177 23 11 1033 1208 558717920 558718080 3.230000e-14 89.8
5 TraesCS2D01G241200 chr1A 90.490 1346 94 15 1040 2360 549076281 549077617 0.000000e+00 1746.0
6 TraesCS2D01G241200 chr2A 93.107 972 44 10 1402 2360 748989280 748990241 0.000000e+00 1402.0
7 TraesCS2D01G241200 chr2A 89.013 537 22 14 840 1340 748988518 748989053 4.280000e-177 630.0
8 TraesCS2D01G241200 chr2A 91.935 248 20 0 1 248 748986221 748986468 4.830000e-92 348.0
9 TraesCS2D01G241200 chr2A 90.798 163 10 3 407 565 748988111 748988272 1.840000e-51 213.0
10 TraesCS2D01G241200 chr3A 88.606 983 71 19 1409 2360 702264267 702263295 0.000000e+00 1157.0
11 TraesCS2D01G241200 chr3A 88.563 647 54 12 796 1423 702265101 702264456 0.000000e+00 767.0
12 TraesCS2D01G241200 chr7A 88.983 590 47 6 790 1361 701316399 701315810 0.000000e+00 713.0
13 TraesCS2D01G241200 chr6B 75.080 313 38 22 920 1208 608235667 608235963 2.480000e-20 110.0


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 TraesCS2D01G241200 chr2D 261209737 261212096 2359 True 4359.00 4359 100.00000 1 2360 1 chr2D.!!$R1 2359
1 TraesCS2D01G241200 chr2D 261319984 261322360 2376 True 1699.50 2876 95.05550 1 2260 2 chr2D.!!$R3 2259
2 TraesCS2D01G241200 chr1A 549076281 549077617 1336 False 1746.00 1746 90.49000 1040 2360 1 chr1A.!!$F1 1320
3 TraesCS2D01G241200 chr2A 748986221 748990241 4020 False 648.25 1402 91.21325 1 2360 4 chr2A.!!$F1 2359
4 TraesCS2D01G241200 chr3A 702263295 702265101 1806 True 962.00 1157 88.58450 796 2360 2 chr3A.!!$R1 1564
5 TraesCS2D01G241200 chr7A 701315810 701316399 589 True 713.00 713 88.98300 790 1361 1 chr7A.!!$R1 571

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
903 2486 0.106419 CGCTCTAGAACCCCCTCTCT 60.106 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 4131 1.604308 CCTTCACTGGGCATGCACA 60.604 57.895 23.75 23.75 0.0 4.57 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
31 32 6.126863 AGAATCAAGGAGTAAACCACATGA 57.873 37.500 0.00 0.00 0.00 3.07
38 39 3.751698 GGAGTAAACCACATGACAGGAAC 59.248 47.826 0.00 0.98 0.00 3.62
60 61 8.755018 GGAACAAAAATATCAGTCAACACTTTG 58.245 33.333 0.00 0.00 0.00 2.77
121 122 2.564947 AGAGTGTCATGAACTCCTCACC 59.435 50.000 23.15 10.89 44.27 4.02
294 467 5.828859 GTGAGTCTAAGCTAGGGTCATCTAA 59.171 44.000 0.00 0.00 0.00 2.10
548 2122 8.984764 CACCGGATTATACTATTCATTTTTCGA 58.015 33.333 9.46 0.00 0.00 3.71
631 2205 3.390003 TTTTTGAGTCGCTTCCCGT 57.610 47.368 0.00 0.00 38.35 5.28
690 2265 3.966543 CCTTGGCCAACCGTCCCT 61.967 66.667 16.05 0.00 39.70 4.20
783 2358 1.908340 GACAGCACTGCCTCCCAGAT 61.908 60.000 0.00 0.00 44.64 2.90
784 2359 1.153208 CAGCACTGCCTCCCAGATC 60.153 63.158 0.00 0.00 44.64 2.75
785 2360 2.191641 GCACTGCCTCCCAGATCC 59.808 66.667 0.00 0.00 44.64 3.36
786 2361 2.673200 GCACTGCCTCCCAGATCCA 61.673 63.158 0.00 0.00 44.64 3.41
787 2362 1.222936 CACTGCCTCCCAGATCCAC 59.777 63.158 0.00 0.00 44.64 4.02
788 2363 1.997874 ACTGCCTCCCAGATCCACC 60.998 63.158 0.00 0.00 44.64 4.61
831 2406 3.760035 GCCGCCCTCTCGAGACAA 61.760 66.667 12.08 0.00 0.00 3.18
855 2430 1.407936 GCTGCTCCTCTCACCTATCA 58.592 55.000 0.00 0.00 0.00 2.15
882 2457 1.007721 CCTTCCTCCTCTCTCCTCCAA 59.992 57.143 0.00 0.00 0.00 3.53
896 2479 0.175989 CTCCAACCGCTCTAGAACCC 59.824 60.000 0.00 0.00 0.00 4.11
903 2486 0.106419 CGCTCTAGAACCCCCTCTCT 60.106 60.000 0.00 0.00 0.00 3.10
953 2536 2.837947 AGTCTCTGAATCCCACATCCA 58.162 47.619 0.00 0.00 0.00 3.41
991 2574 0.835276 TATCCTCGACTCCTCCGACA 59.165 55.000 0.00 0.00 32.18 4.35
1001 2584 1.037579 TCCTCCGACATGCGTCTCAT 61.038 55.000 8.37 0.00 40.23 2.90
1116 2723 2.426522 CGGTGGACATTGTCTCACATT 58.573 47.619 25.92 0.00 36.33 2.71
1214 2824 2.111384 AGGCTGATGAGGAATGTACGT 58.889 47.619 0.00 0.00 0.00 3.57
1244 2857 7.200434 TCCTTTTCCTTTAGCAGATAGACAT 57.800 36.000 0.00 0.00 0.00 3.06
1406 3184 3.320826 GCAACACCAGGTGGACTAAATTT 59.679 43.478 24.13 3.26 37.94 1.82
1416 3194 7.393234 CCAGGTGGACTAAATTTCTTGACATTA 59.607 37.037 0.00 0.00 37.39 1.90
1560 3545 2.925966 TCGGGGGAGAGTTTAGGTTA 57.074 50.000 0.00 0.00 0.00 2.85
1688 3673 9.760077 ATACACTTGGTCTAAAATAATACGAGG 57.240 33.333 0.00 0.00 0.00 4.63
1737 3722 7.219535 GTGTCAATGTCATGATGCACTAATTTC 59.780 37.037 0.00 0.00 0.00 2.17
1763 3748 2.086869 AGAATGGTTGCATCTTCCACG 58.913 47.619 0.00 0.00 33.91 4.94
2141 4131 5.050126 TCTATCTACGGTTCATGACTCCT 57.950 43.478 12.47 4.76 0.00 3.69
2210 4212 5.936956 TGCTTTCATTTTGTGGAGTTTGTTT 59.063 32.000 0.00 0.00 0.00 2.83
2228 4230 2.986479 GTTTGCCATGTCGAACCATTTC 59.014 45.455 0.00 0.00 0.00 2.17
2270 4273 6.552859 TGTGTTATGTAACAGACCATTGTG 57.447 37.500 5.88 0.00 45.82 3.33
2326 4335 4.882427 TCCAAACAATGAAAACCACGACTA 59.118 37.500 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.431234 GTCATGTGGTTTACTCCTTGATTCTT 59.569 38.462 0.00 0.00 0.00 2.52
31 32 7.285401 AGTGTTGACTGATATTTTTGTTCCTGT 59.715 33.333 0.00 0.00 0.00 4.00
38 39 8.745837 GTCACAAAGTGTTGACTGATATTTTTG 58.254 33.333 0.00 0.00 38.20 2.44
121 122 8.693504 CAACAACTCATTATTACAAAGCTTGTG 58.306 33.333 0.00 3.34 45.03 3.33
209 210 8.297470 ACCATAGATTTATGAAGCAATGTGTT 57.703 30.769 4.85 0.00 39.22 3.32
309 482 3.699038 ACATTTATGCGTGGTGCCTTATT 59.301 39.130 0.00 0.00 45.60 1.40
313 486 0.810648 CACATTTATGCGTGGTGCCT 59.189 50.000 0.00 0.00 45.60 4.75
314 487 0.525761 ACACATTTATGCGTGGTGCC 59.474 50.000 0.00 0.00 45.60 5.01
315 488 1.068610 ACACACATTTATGCGTGGTGC 60.069 47.619 13.59 0.00 43.20 5.01
616 2190 0.105224 TTTCACGGGAAGCGACTCAA 59.895 50.000 0.00 0.00 33.82 3.02
622 2196 2.289547 TCTTTCTTTTTCACGGGAAGCG 59.710 45.455 0.00 0.00 33.82 4.68
652 2226 4.960469 AGGAATATCCCGTGACACTCTTTA 59.040 41.667 3.68 0.00 37.19 1.85
668 2242 1.409661 GGACGGTTGGCCAAGGAATAT 60.410 52.381 21.21 0.87 34.09 1.28
690 2265 4.466827 AGGCGGAGGTTTTCTTTTCTTTA 58.533 39.130 0.00 0.00 0.00 1.85
785 2360 3.775654 GAGGTGGAGGCGGAGGTG 61.776 72.222 0.00 0.00 0.00 4.00
831 2406 2.601666 TGAGAGGAGCAGCGGTGT 60.602 61.111 17.07 2.78 0.00 4.16
855 2430 1.076632 AGAGGAGGAAGGCGACGAT 60.077 57.895 0.00 0.00 0.00 3.73
882 2457 1.381463 GAGGGGGTTCTAGAGCGGT 60.381 63.158 0.05 0.00 0.00 5.68
896 2479 2.094100 TGCAGGGATCTAAGAGAGGG 57.906 55.000 0.00 0.00 0.00 4.30
903 2486 2.504175 GGTAGGTGTTGCAGGGATCTAA 59.496 50.000 0.00 0.00 0.00 2.10
991 2574 0.530211 GAGCTGAGCATGAGACGCAT 60.530 55.000 7.39 0.00 37.85 4.73
1001 2584 1.153025 GCATCCATGGAGCTGAGCA 60.153 57.895 21.33 0.00 0.00 4.26
1002 2585 0.885596 GAGCATCCATGGAGCTGAGC 60.886 60.000 31.04 22.96 39.02 4.26
1116 2723 1.286849 TCCCAGTCGGAGATCTGGTTA 59.713 52.381 0.00 0.00 46.71 2.85
1214 2824 6.636454 TCTGCTAAAGGAAAAGGAATAGGA 57.364 37.500 0.00 0.00 0.00 2.94
1406 3184 5.710513 ACTTGCTGCATTTAATGTCAAGA 57.289 34.783 26.28 8.57 37.50 3.02
1416 3194 4.142093 GGATGGTATCAACTTGCTGCATTT 60.142 41.667 1.84 0.00 0.00 2.32
1509 3494 3.862267 GCAGTGCTCAAGACAGTATACAG 59.138 47.826 8.18 0.00 0.00 2.74
1560 3545 0.254178 ACCATTGAGGCGATGCTTCT 59.746 50.000 2.60 0.00 43.14 2.85
1688 3673 6.369065 CACTTTCAAATGGTCTCCTACTACAC 59.631 42.308 0.00 0.00 0.00 2.90
1737 3722 2.625737 AGATGCAACCATTCTCTCACG 58.374 47.619 0.00 0.00 0.00 4.35
1802 3787 7.661437 ACACATCTACATTAGTTCTGCTGAAAA 59.339 33.333 7.68 0.37 33.52 2.29
1803 3788 7.161404 ACACATCTACATTAGTTCTGCTGAAA 58.839 34.615 7.68 0.00 33.52 2.69
1804 3789 6.701340 ACACATCTACATTAGTTCTGCTGAA 58.299 36.000 1.33 1.33 0.00 3.02
1805 3790 6.286240 ACACATCTACATTAGTTCTGCTGA 57.714 37.500 0.00 0.00 0.00 4.26
2141 4131 1.604308 CCTTCACTGGGCATGCACA 60.604 57.895 23.75 23.75 0.00 4.57
2210 4212 1.902938 TGAAATGGTTCGACATGGCA 58.097 45.000 0.00 0.00 36.46 4.92
2228 4230 2.615447 ACAAGACATCAAGCCGCATATG 59.385 45.455 0.00 0.00 0.00 1.78
2270 4273 6.336842 TGTGTAGTAGTAGAAAGGACCAAC 57.663 41.667 0.00 0.00 0.00 3.77
2326 4335 7.383300 GTCTGAAGTCAAATGCTTGCTAATTTT 59.617 33.333 0.00 0.00 32.14 1.82


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

AutoCloner maintained by Alex Coulton.