Multiple sequence alignment - TraesCS3D01G114400

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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 TraesCS3D01G114400 chr3D 100.000 2558 0 0 1 2558 68037813 68035256 0.000000e+00 4724
1 TraesCS3D01G114400 chr3D 84.770 1195 163 9 704 1894 127904077 127905256 0.000000e+00 1181
2 TraesCS3D01G114400 chr3D 82.071 647 69 18 119 755 127903471 127904080 2.270000e-140 508
3 TraesCS3D01G114400 chr3B 94.754 2440 82 19 138 2558 113983132 113985544 0.000000e+00 3755
4 TraesCS3D01G114400 chr3B 83.538 1713 232 26 165 1863 182202968 182204644 0.000000e+00 1555
5 TraesCS3D01G114400 chr3A 92.708 2578 134 22 1 2558 79905902 79903359 0.000000e+00 3670
6 TraesCS3D01G114400 chr3A 92.352 2602 113 29 1 2558 79876330 79873771 0.000000e+00 3624
7 TraesCS3D01G114400 chr3A 92.154 2600 127 25 5 2558 79803093 79800525 0.000000e+00 3600
8 TraesCS3D01G114400 chr3A 81.705 645 85 12 119 755 138806730 138807349 8.170000e-140 507
9 TraesCS3D01G114400 chr2A 78.504 842 160 19 1000 1828 545800752 545801585 1.350000e-147 532
10 TraesCS3D01G114400 chr2A 73.111 569 116 29 447 985 545800131 545800692 4.380000e-38 169
11 TraesCS3D01G114400 chr4D 83.399 253 34 6 1829 2075 416060703 416060953 7.120000e-56 228
12 TraesCS3D01G114400 chr1D 82.857 245 35 6 1840 2079 493485859 493486101 1.990000e-51 213
13 TraesCS3D01G114400 chr5B 81.673 251 44 2 1826 2075 327083530 327083779 9.280000e-50 207
14 TraesCS3D01G114400 chr1A 82.258 248 36 4 1829 2071 591612989 591613233 9.280000e-50 207
15 TraesCS3D01G114400 chr7A 81.395 258 38 6 1829 2078 163128931 163129186 4.320000e-48 202


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 TraesCS3D01G114400 chr3D 68035256 68037813 2557 True 4724.0 4724 100.0000 1 2558 1 chr3D.!!$R1 2557
1 TraesCS3D01G114400 chr3D 127903471 127905256 1785 False 844.5 1181 83.4205 119 1894 2 chr3D.!!$F1 1775
2 TraesCS3D01G114400 chr3B 113983132 113985544 2412 False 3755.0 3755 94.7540 138 2558 1 chr3B.!!$F1 2420
3 TraesCS3D01G114400 chr3B 182202968 182204644 1676 False 1555.0 1555 83.5380 165 1863 1 chr3B.!!$F2 1698
4 TraesCS3D01G114400 chr3A 79903359 79905902 2543 True 3670.0 3670 92.7080 1 2558 1 chr3A.!!$R3 2557
5 TraesCS3D01G114400 chr3A 79873771 79876330 2559 True 3624.0 3624 92.3520 1 2558 1 chr3A.!!$R2 2557
6 TraesCS3D01G114400 chr3A 79800525 79803093 2568 True 3600.0 3600 92.1540 5 2558 1 chr3A.!!$R1 2553
7 TraesCS3D01G114400 chr3A 138806730 138807349 619 False 507.0 507 81.7050 119 755 1 chr3A.!!$F1 636
8 TraesCS3D01G114400 chr2A 545800131 545801585 1454 False 350.5 532 75.8075 447 1828 2 chr2A.!!$F1 1381

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
778 890 0.035317 AGCATTGAGAGGCACGACAA 59.965 50.0 0.0 0.0 34.36 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 2708 0.75085 TTTCGGCTCTTAGGGATCGG 59.249 55.0 0.0 0.0 0.0 4.18 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
79 80 4.943093 TCAATGATGAAGGCAATCTTTCGA 59.057 37.500 0.00 0.00 35.50 3.71
83 84 7.756395 ATGATGAAGGCAATCTTTCGATTAT 57.244 32.000 0.00 0.00 37.77 1.28
155 157 3.055530 TGGACAATCTTTGCTCTCTCTCC 60.056 47.826 0.00 0.00 0.00 3.71
186 188 4.039004 CCTCTCTCTCTCTCTCTCTCTCTG 59.961 54.167 0.00 0.00 0.00 3.35
239 253 7.472543 CAATACTAGTTTTGACCTATTGTGCC 58.527 38.462 18.10 0.00 0.00 5.01
242 256 6.717289 ACTAGTTTTGACCTATTGTGCCATA 58.283 36.000 0.00 0.00 0.00 2.74
244 258 8.491134 ACTAGTTTTGACCTATTGTGCCATATA 58.509 33.333 0.00 0.00 0.00 0.86
245 259 9.507329 CTAGTTTTGACCTATTGTGCCATATAT 57.493 33.333 0.00 0.00 0.00 0.86
649 683 5.475909 CACATAAGCATCAAAGGCATCCTAT 59.524 40.000 0.00 0.00 31.13 2.57
685 719 8.250143 TCTATTCTCCATAACATCTACTGCAA 57.750 34.615 0.00 0.00 0.00 4.08
686 720 8.874156 TCTATTCTCCATAACATCTACTGCAAT 58.126 33.333 0.00 0.00 0.00 3.56
687 721 7.976135 ATTCTCCATAACATCTACTGCAATC 57.024 36.000 0.00 0.00 0.00 2.67
688 722 6.737720 TCTCCATAACATCTACTGCAATCT 57.262 37.500 0.00 0.00 0.00 2.40
689 723 6.519382 TCTCCATAACATCTACTGCAATCTG 58.481 40.000 0.00 0.00 0.00 2.90
690 724 5.059161 TCCATAACATCTACTGCAATCTGC 58.941 41.667 0.00 0.00 45.29 4.26
778 890 0.035317 AGCATTGAGAGGCACGACAA 59.965 50.000 0.00 0.00 34.36 3.18
902 1014 5.084818 ACTGTGATGTCGGTCAATGATAA 57.915 39.130 0.00 0.00 0.00 1.75
988 1145 5.844516 ACAATCCCTATTCCTTTATCCTCGA 59.155 40.000 0.00 0.00 0.00 4.04
1154 1312 6.509418 TCATTCCCAACTTAACACTAATGC 57.491 37.500 0.00 0.00 0.00 3.56
1155 1313 5.123186 TCATTCCCAACTTAACACTAATGCG 59.877 40.000 0.00 0.00 0.00 4.73
1159 1317 3.119990 CCAACTTAACACTAATGCGGTGG 60.120 47.826 0.00 0.00 38.83 4.61
1362 1522 0.661552 CTTCTCCAGCCATGCAATCG 59.338 55.000 0.00 0.00 0.00 3.34
1440 1600 7.490402 TCTGATAGTGCTATTATGCATGATTCG 59.510 37.037 10.16 2.93 45.23 3.34
1500 1660 3.485633 CACATTCAACACATCTCAAGCG 58.514 45.455 0.00 0.00 0.00 4.68
1611 1775 8.429237 TTGATACTTGTGGGACCAATATTTTT 57.571 30.769 0.00 0.00 0.00 1.94
1875 2045 3.490526 GTGCATTAGTTTTTGTGCCAGTG 59.509 43.478 0.00 0.00 36.79 3.66
1902 2072 8.650143 AACTTATGTACATTTGACCAGGATTT 57.350 30.769 14.77 0.00 0.00 2.17
1903 2073 8.650143 ACTTATGTACATTTGACCAGGATTTT 57.350 30.769 14.77 0.00 0.00 1.82
2001 2178 6.952773 TTTGGTATTGCAGATATTGGTACC 57.047 37.500 4.43 4.43 0.00 3.34
2147 2349 6.137794 TCACGCTTTTTAATGAAGGTTTGA 57.862 33.333 0.00 0.00 0.00 2.69
2260 2462 5.987347 AGTGAAAGCATCTCAACCATTTTTG 59.013 36.000 0.00 0.00 0.00 2.44
2440 2652 6.189677 TGATAAAAGTTAACCCATGCTTCG 57.810 37.500 0.88 0.00 0.00 3.79
2486 2698 5.124776 TGAACAAAAGAAAACGGACACTCAT 59.875 36.000 0.00 0.00 0.00 2.90
2490 2702 7.540299 ACAAAAGAAAACGGACACTCATAAAA 58.460 30.769 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.959606 ACCATATCAACCTTATGCTCCTAT 57.040 37.500 0.00 0.00 0.00 2.57
155 157 2.370189 GAGAGAGAGAGAGGGAGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
186 188 3.248602 GGATCTTTGAGACACACACACAC 59.751 47.826 0.00 0.00 0.00 3.82
328 349 8.306761 GCATCTTCTCTTTTATTGGAAGGAAAA 58.693 33.333 0.00 0.00 36.71 2.29
564 593 2.290916 ACTATAGACGTGCATGGACTCG 59.709 50.000 15.82 5.73 0.00 4.18
649 683 9.039165 TGTTATGGAGAATAGAGATGCATATGA 57.961 33.333 6.97 0.00 29.08 2.15
685 719 8.004087 ACTAGCAATATCAACAATTTGCAGAT 57.996 30.769 8.92 8.60 45.26 2.90
686 720 7.395190 ACTAGCAATATCAACAATTTGCAGA 57.605 32.000 8.92 0.00 45.26 4.26
687 721 7.377928 GCTACTAGCAATATCAACAATTTGCAG 59.622 37.037 2.96 6.77 45.26 4.41
688 722 7.067372 AGCTACTAGCAATATCAACAATTTGCA 59.933 33.333 10.73 0.00 45.56 4.08
689 723 7.420800 AGCTACTAGCAATATCAACAATTTGC 58.579 34.615 10.73 0.00 45.56 3.68
778 890 5.335113 CGAAATCATTCAATATCGGCATGGT 60.335 40.000 0.00 0.00 35.15 3.55
902 1014 7.886970 CACTAGATTGGTATGGAATCATGGATT 59.113 37.037 0.00 0.00 34.71 3.01
988 1145 3.314080 TGCGAGAACATTCCTTTTTCGTT 59.686 39.130 0.00 0.00 0.00 3.85
1154 1312 0.035534 TGAACCATCATCCACCACCG 60.036 55.000 0.00 0.00 0.00 4.94
1155 1313 1.004745 AGTGAACCATCATCCACCACC 59.995 52.381 0.00 0.00 38.01 4.61
1159 1317 6.173339 TCTTAAAGAGTGAACCATCATCCAC 58.827 40.000 0.00 0.00 38.01 4.02
1440 1600 5.670341 GCATGTGTATTTACGTGAGGTTGTC 60.670 44.000 0.00 0.00 39.39 3.18
1500 1660 2.930040 CGAACTCATGTGACCACCATAC 59.070 50.000 0.94 0.00 0.00 2.39
1611 1775 3.998913 TCATCCATTGTGTGCTTAGGA 57.001 42.857 0.00 0.00 0.00 2.94
1778 1948 8.410673 TGTTGTTTACATAGGGAAATAGCAAA 57.589 30.769 0.00 0.00 0.00 3.68
1804 1974 7.004555 AGTACACAACCATCAAAGATGACTA 57.995 36.000 8.49 0.00 38.69 2.59
1875 2045 7.681939 TCCTGGTCAAATGTACATAAGTTTC 57.318 36.000 9.21 0.00 0.00 2.78
2205 2407 6.266131 TGGCAAATTATCAGGGACTCTTAT 57.734 37.500 0.00 0.00 34.60 1.73
2426 2638 6.041637 ACATCTATAGACGAAGCATGGGTTAA 59.958 38.462 4.10 0.00 0.00 2.01
2490 2702 3.744530 CGGCTCTTAGGGATCGGAAATTT 60.745 47.826 0.00 0.00 0.00 1.82
2496 2708 0.750850 TTTCGGCTCTTAGGGATCGG 59.249 55.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.