Multiple sequence alignment - TraesCS4D01G154800

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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 TraesCS4D01G154800 chr4D 100.000 2264 0 0 1 2264 206902777 206900514 0 4181
1 TraesCS4D01G154800 chr5A 95.489 1729 62 9 549 2264 559030945 559029220 0 2747
2 TraesCS4D01G154800 chr5B 95.428 1728 65 6 549 2264 57514120 57512395 0 2741
3 TraesCS4D01G154800 chr1A 95.329 1734 61 9 549 2264 554483020 554484751 0 2736
4 TraesCS4D01G154800 chr5D 95.740 1690 60 6 549 2227 299970985 299969297 0 2712
5 TraesCS4D01G154800 chr5D 95.078 1727 71 7 549 2264 503340448 503342171 0 2706
6 TraesCS4D01G154800 chr5D 94.844 1726 76 6 549 2264 6252268 6250546 0 2682
7 TraesCS4D01G154800 chr5D 92.491 546 35 6 7 548 130690224 130689681 0 776
8 TraesCS4D01G154800 chr3A 95.078 1727 72 6 549 2264 105555954 105554230 0 2706
9 TraesCS4D01G154800 chrUn 95.020 1727 73 6 549 2264 261567687 261565963 0 2700
10 TraesCS4D01G154800 chrUn 95.005 1101 41 7 549 1637 386224622 386225720 0 1716
11 TraesCS4D01G154800 chr1D 94.841 1725 75 5 549 2264 254460412 254462131 0 2680
12 TraesCS4D01G154800 chr1D 93.333 555 28 5 1 550 294940851 294941401 0 811
13 TraesCS4D01G154800 chr1D 92.532 549 32 8 7 548 164994705 164994159 0 778
14 TraesCS4D01G154800 chr2B 95.332 1478 61 3 795 2264 683728694 683730171 0 2340
15 TraesCS4D01G154800 chr1B 94.459 1516 65 8 549 2052 633717974 633719482 0 2316
16 TraesCS4D01G154800 chr7B 95.163 765 29 3 1508 2264 662753104 662752340 0 1201
17 TraesCS4D01G154800 chr2D 93.978 548 27 1 7 548 276422989 276422442 0 824
18 TraesCS4D01G154800 chr2D 92.935 552 32 5 1 548 274880590 274881138 0 797
19 TraesCS4D01G154800 chr7D 92.793 555 31 8 1 548 315369864 315370416 0 795
20 TraesCS4D01G154800 chr7D 92.350 549 34 5 7 550 424880238 424879693 0 774
21 TraesCS4D01G154800 chr6D 92.446 556 33 7 1 548 243609961 243610515 0 785
22 TraesCS4D01G154800 chr3D 92.182 550 39 4 1 548 227915154 227915701 0 774


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 TraesCS4D01G154800 chr4D 206900514 206902777 2263 True 4181 4181 100.000 1 2264 1 chr4D.!!$R1 2263
1 TraesCS4D01G154800 chr5A 559029220 559030945 1725 True 2747 2747 95.489 549 2264 1 chr5A.!!$R1 1715
2 TraesCS4D01G154800 chr5B 57512395 57514120 1725 True 2741 2741 95.428 549 2264 1 chr5B.!!$R1 1715
3 TraesCS4D01G154800 chr1A 554483020 554484751 1731 False 2736 2736 95.329 549 2264 1 chr1A.!!$F1 1715
4 TraesCS4D01G154800 chr5D 299969297 299970985 1688 True 2712 2712 95.740 549 2227 1 chr5D.!!$R3 1678
5 TraesCS4D01G154800 chr5D 503340448 503342171 1723 False 2706 2706 95.078 549 2264 1 chr5D.!!$F1 1715
6 TraesCS4D01G154800 chr5D 6250546 6252268 1722 True 2682 2682 94.844 549 2264 1 chr5D.!!$R1 1715
7 TraesCS4D01G154800 chr5D 130689681 130690224 543 True 776 776 92.491 7 548 1 chr5D.!!$R2 541
8 TraesCS4D01G154800 chr3A 105554230 105555954 1724 True 2706 2706 95.078 549 2264 1 chr3A.!!$R1 1715
9 TraesCS4D01G154800 chrUn 261565963 261567687 1724 True 2700 2700 95.020 549 2264 1 chrUn.!!$R1 1715
10 TraesCS4D01G154800 chrUn 386224622 386225720 1098 False 1716 1716 95.005 549 1637 1 chrUn.!!$F1 1088
11 TraesCS4D01G154800 chr1D 254460412 254462131 1719 False 2680 2680 94.841 549 2264 1 chr1D.!!$F1 1715
12 TraesCS4D01G154800 chr1D 294940851 294941401 550 False 811 811 93.333 1 550 1 chr1D.!!$F2 549
13 TraesCS4D01G154800 chr1D 164994159 164994705 546 True 778 778 92.532 7 548 1 chr1D.!!$R1 541
14 TraesCS4D01G154800 chr2B 683728694 683730171 1477 False 2340 2340 95.332 795 2264 1 chr2B.!!$F1 1469
15 TraesCS4D01G154800 chr1B 633717974 633719482 1508 False 2316 2316 94.459 549 2052 1 chr1B.!!$F1 1503
16 TraesCS4D01G154800 chr7B 662752340 662753104 764 True 1201 1201 95.163 1508 2264 1 chr7B.!!$R1 756
17 TraesCS4D01G154800 chr2D 276422442 276422989 547 True 824 824 93.978 7 548 1 chr2D.!!$R1 541
18 TraesCS4D01G154800 chr2D 274880590 274881138 548 False 797 797 92.935 1 548 1 chr2D.!!$F1 547
19 TraesCS4D01G154800 chr7D 315369864 315370416 552 False 795 795 92.793 1 548 1 chr7D.!!$F1 547
20 TraesCS4D01G154800 chr7D 424879693 424880238 545 True 774 774 92.350 7 550 1 chr7D.!!$R1 543
21 TraesCS4D01G154800 chr6D 243609961 243610515 554 False 785 785 92.446 1 548 1 chr6D.!!$F1 547
22 TraesCS4D01G154800 chr3D 227915154 227915701 547 False 774 774 92.182 1 548 1 chr3D.!!$F1 547

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
940 979 2.763039 TGCATAGAGGGACCATTGAGA 58.237 47.619 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 1913 1.238439 GCTACTGCTGTTTTGCCAGA 58.762 50.0 0.09 0.0 34.23 3.86 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
340 360 6.402226 GGTGGATGTCGTTTGAGTTTCTATTC 60.402 42.308 0.00 0.00 0.00 1.75
358 378 7.107639 TCTATTCGTGTTTCATCCATAGTCA 57.892 36.000 0.00 0.00 0.00 3.41
473 496 6.663093 TGTAATGATATCCACCTTGCAAAAGT 59.337 34.615 0.00 0.00 0.00 2.66
501 525 5.305902 TCAATATGCGGTTCTATCCTTGGTA 59.694 40.000 0.00 0.00 0.00 3.25
521 545 4.221482 GGTAGGACCTTCGAGTTCCTTTAA 59.779 45.833 14.65 0.00 34.73 1.52
565 589 8.495148 GGCGTGACATTTTTCTTAATGAAATTT 58.505 29.630 0.00 0.00 43.34 1.82
593 618 7.684937 TTACTAACTAGCGGGCAAATAAAAA 57.315 32.000 0.00 0.00 0.00 1.94
789 827 4.225942 AGGAGTGTGAGAGCCAAATGAATA 59.774 41.667 0.00 0.00 0.00 1.75
801 840 6.746120 AGCCAAATGAATAGAAGATTCATGC 58.254 36.000 12.29 11.39 45.07 4.06
830 869 4.876107 TCGGGAAGAGATCATAAAAGTTGC 59.124 41.667 0.00 0.00 0.00 4.17
940 979 2.763039 TGCATAGAGGGACCATTGAGA 58.237 47.619 0.00 0.00 0.00 3.27
952 991 5.048013 GGGACCATTGAGAAACTCGAAAAAT 60.048 40.000 0.00 0.00 32.35 1.82
976 1015 5.124936 TCTCGGATTCGATTACAGAAAGTCA 59.875 40.000 0.00 0.00 45.04 3.41
987 1026 7.116376 CGATTACAGAAAGTCAAACTAGAAGCA 59.884 37.037 0.00 0.00 0.00 3.91
1106 1145 8.757789 GTCTAAAAACGAAACCCTTTATTTTGG 58.242 33.333 0.00 0.00 0.00 3.28
1125 1164 3.802866 TGGAAAACAAAGGGCAATGAAC 58.197 40.909 0.00 0.00 0.00 3.18
1179 1218 4.594675 ACAAGGAGCTCTAGGAACTCTA 57.405 45.455 14.64 0.00 41.75 2.43
1209 1248 9.275398 AGTTGTTTGAATACCGAGTTACATTTA 57.725 29.630 0.00 0.00 0.00 1.40
1240 1279 6.772360 TTTGTGCTAATATTGGCATTCTCA 57.228 33.333 26.54 17.62 46.33 3.27
1395 1434 7.333423 AGTCGACGAAATTCATAAAATTCTCCA 59.667 33.333 10.46 0.00 0.00 3.86
1446 1485 8.798975 AAAGTAGGGATTGAGAATATAGGTCA 57.201 34.615 0.00 0.00 0.00 4.02
1488 1527 3.391049 GGATTGCTCGTATTGTAGGTCC 58.609 50.000 0.00 0.00 0.00 4.46
1547 1586 4.409247 CAGAAGGTACTAGGGGTATTGCTT 59.591 45.833 0.00 0.00 38.49 3.91
1550 1589 4.109320 AGGTACTAGGGGTATTGCTTTGT 58.891 43.478 0.00 0.00 36.02 2.83
1589 1636 3.482436 TGTATTAATGGGCGATGGGTTC 58.518 45.455 0.00 0.00 0.00 3.62
1610 1657 6.094186 GGTTCATGATACAAGAGGGAAGTTTC 59.906 42.308 0.00 0.00 0.00 2.78
1646 1693 2.973945 AGAATTGCTCAGTTACCCGTC 58.026 47.619 0.00 0.00 0.00 4.79
1668 1715 0.606604 TGAGGCTTACTTGGGTCGTC 59.393 55.000 0.00 0.00 0.00 4.20
1676 1723 4.512571 GCTTACTTGGGTCGTCTTGTAAAA 59.487 41.667 0.00 0.00 0.00 1.52
1727 1774 4.451096 GGCGAAATTATAGCTTCCGAATCA 59.549 41.667 0.00 0.00 0.00 2.57
1865 1912 6.657541 GTGAGTTAATTATTGGGGACAGACAA 59.342 38.462 0.00 0.00 44.54 3.18
1866 1913 7.339466 GTGAGTTAATTATTGGGGACAGACAAT 59.661 37.037 0.00 0.00 44.54 2.71
1914 1961 8.742777 CAGATACAATTCTCAATCAAAAAGGGA 58.257 33.333 0.00 0.00 0.00 4.20
2104 2151 4.385865 CCTGGCTGGGTATTTTATGTACCA 60.386 45.833 1.84 0.00 42.74 3.25
2108 2155 4.510340 GCTGGGTATTTTATGTACCACGAG 59.490 45.833 4.87 0.00 42.74 4.18
2150 2197 2.625314 TGATGATCTCTCCTAACAGGCG 59.375 50.000 0.00 0.00 34.61 5.52
2172 2219 2.684881 CAAGCTTATCGCCAAATGTCCT 59.315 45.455 0.00 0.00 40.39 3.85
2175 2222 3.129287 AGCTTATCGCCAAATGTCCTTTG 59.871 43.478 0.00 0.00 43.27 2.77
2253 2300 2.066262 CACGCCTTTTAGAAAGAGCGA 58.934 47.619 26.94 0.00 46.03 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.062934 CGGTCGCAAACTAGTAATGATGAAA 59.937 40.000 11.66 0.00 0.00 2.69
5 6 3.863424 ACGGTCGCAAACTAGTAATGATG 59.137 43.478 11.66 4.53 0.00 3.07
58 59 4.638421 GCAATGTATGGTGGCTAACTTACA 59.362 41.667 14.79 14.79 34.27 2.41
340 360 5.111989 ACATCTGACTATGGATGAAACACG 58.888 41.667 9.47 0.00 41.05 4.49
358 378 9.842775 AATACATCATACATGAGAACAACATCT 57.157 29.630 0.00 0.00 40.64 2.90
473 496 4.100963 AGGATAGAACCGCATATTGACACA 59.899 41.667 0.00 0.00 34.73 3.72
521 545 3.601443 GCCCAATATGCGACTCTATCT 57.399 47.619 0.00 0.00 0.00 1.98
565 589 8.961294 TTATTTGCCCGCTAGTTAGTAATTTA 57.039 30.769 0.00 0.00 0.00 1.40
593 618 5.146010 TGGTCAGCAAAGTTGTTTCTTTT 57.854 34.783 0.00 0.00 35.77 2.27
771 809 6.053632 TCTTCTATTCATTTGGCTCTCACA 57.946 37.500 0.00 0.00 0.00 3.58
789 827 3.012518 CCGAACCAAGCATGAATCTTCT 58.987 45.455 0.00 0.00 0.00 2.85
801 840 3.550437 ATGATCTCTTCCCGAACCAAG 57.450 47.619 0.00 0.00 0.00 3.61
866 905 7.871973 AGATCCTCTGTTTTCGATTATCTCATG 59.128 37.037 0.00 0.00 0.00 3.07
869 908 7.923344 TCAAGATCCTCTGTTTTCGATTATCTC 59.077 37.037 0.00 0.00 0.00 2.75
923 962 4.100189 CGAGTTTCTCAATGGTCCCTCTAT 59.900 45.833 0.00 0.00 0.00 1.98
940 979 4.927425 TCGAATCCGAGATTTTTCGAGTTT 59.073 37.500 2.80 0.00 43.37 2.66
976 1015 6.701145 TCGATACTCATCTGCTTCTAGTTT 57.299 37.500 0.00 0.00 0.00 2.66
987 1026 8.359875 AGTATCCATTCATTCGATACTCATCT 57.640 34.615 3.67 0.00 43.19 2.90
1106 1145 3.802866 TGGTTCATTGCCCTTTGTTTTC 58.197 40.909 0.00 0.00 0.00 2.29
1179 1218 9.275398 TGTAACTCGGTATTCAAACAACTATTT 57.725 29.630 0.00 0.00 0.00 1.40
1209 1248 8.180706 TGCCAATATTAGCACAAATCATACAT 57.819 30.769 4.32 0.00 33.08 2.29
1210 1249 7.579761 TGCCAATATTAGCACAAATCATACA 57.420 32.000 4.32 0.00 33.08 2.29
1219 1258 4.823442 CCTGAGAATGCCAATATTAGCACA 59.177 41.667 10.84 4.04 42.84 4.57
1240 1279 1.081174 TCTCTTCCATTCCAGGGACCT 59.919 52.381 0.00 0.00 33.18 3.85
1395 1434 9.970395 TCCTATTATATTGTTCAATACGTTCGT 57.030 29.630 7.30 2.91 0.00 3.85
1446 1485 1.278127 CATCCCCCACTTGAACTACGT 59.722 52.381 0.00 0.00 0.00 3.57
1488 1527 6.764308 ATTCACCTGACATTATTTCACCAG 57.236 37.500 0.00 0.00 0.00 4.00
1589 1636 5.178797 ACGAAACTTCCCTCTTGTATCATG 58.821 41.667 0.00 0.00 0.00 3.07
1610 1657 4.382754 GCAATTCTTCCTGTTGCTTTTACG 59.617 41.667 2.36 0.00 43.56 3.18
1638 1685 1.547372 GTAAGCCTCACTGACGGGTAA 59.453 52.381 0.00 0.00 0.00 2.85
1646 1693 1.673033 CGACCCAAGTAAGCCTCACTG 60.673 57.143 0.00 0.00 0.00 3.66
1727 1774 3.873952 GAGCAGGAGATTCAATTAAGCGT 59.126 43.478 0.00 0.00 0.00 5.07
1841 1888 6.381498 TGTCTGTCCCCAATAATTAACTCA 57.619 37.500 0.00 0.00 0.00 3.41
1865 1912 1.815003 GCTACTGCTGTTTTGCCAGAT 59.185 47.619 0.09 0.00 34.23 2.90
1866 1913 1.238439 GCTACTGCTGTTTTGCCAGA 58.762 50.000 0.09 0.00 34.23 3.86
1914 1961 9.681062 AGCTACATAAACACATATTACACCTTT 57.319 29.630 0.00 0.00 0.00 3.11
1999 2046 7.116948 CAGCTACTACAATAGTGTATTCCATGC 59.883 40.741 3.10 3.76 39.51 4.06
2089 2136 3.492011 CCGCTCGTGGTACATAAAATACC 59.508 47.826 0.00 0.00 44.52 2.73
2104 2151 6.613755 AAATTATTAAAGTATGCCGCTCGT 57.386 33.333 0.00 0.00 0.00 4.18
2142 2189 1.286501 CGATAAGCTTGCGCCTGTTA 58.713 50.000 9.86 0.00 36.60 2.41


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

AutoCloner maintained by Alex Coulton.