Multiple sequence alignment - TraesCS5A01G258000

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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 TraesCS5A01G258000 chr5A 100.000 2847 0 0 1 2847 473012563 473015409 0 5258
1 TraesCS5A01G258000 chr5D 92.255 1756 91 19 1 1740 370465629 370467355 0 2447
2 TraesCS5A01G258000 chr5B 89.570 1745 86 26 1 1668 439718672 439720397 0 2126
3 TraesCS5A01G258000 chr6A 98.236 1077 19 0 1771 2847 579434261 579433185 0 1884
4 TraesCS5A01G258000 chr3D 92.732 1087 66 11 1769 2847 36832645 36831564 0 1557
5 TraesCS5A01G258000 chr3D 92.364 1087 70 11 1769 2847 459074132 459075213 0 1535
6 TraesCS5A01G258000 chr2D 92.421 1082 69 11 1774 2847 87410616 87409540 0 1531
7 TraesCS5A01G258000 chr2D 91.959 1082 75 7 1771 2847 35554696 35553622 0 1506
8 TraesCS5A01G258000 chr3A 92.322 1081 71 7 1771 2847 704108238 704109310 0 1526
9 TraesCS5A01G258000 chr6B 92.137 1081 74 6 1771 2847 164742830 164743903 0 1515
10 TraesCS5A01G258000 chr6B 92.044 1081 75 6 1771 2847 218002345 218001272 0 1509
11 TraesCS5A01G258000 chr3B 91.790 1084 81 7 1771 2847 745462298 745463380 0 1502


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 TraesCS5A01G258000 chr5A 473012563 473015409 2846 False 5258 5258 100.000 1 2847 1 chr5A.!!$F1 2846
1 TraesCS5A01G258000 chr5D 370465629 370467355 1726 False 2447 2447 92.255 1 1740 1 chr5D.!!$F1 1739
2 TraesCS5A01G258000 chr5B 439718672 439720397 1725 False 2126 2126 89.570 1 1668 1 chr5B.!!$F1 1667
3 TraesCS5A01G258000 chr6A 579433185 579434261 1076 True 1884 1884 98.236 1771 2847 1 chr6A.!!$R1 1076
4 TraesCS5A01G258000 chr3D 36831564 36832645 1081 True 1557 1557 92.732 1769 2847 1 chr3D.!!$R1 1078
5 TraesCS5A01G258000 chr3D 459074132 459075213 1081 False 1535 1535 92.364 1769 2847 1 chr3D.!!$F1 1078
6 TraesCS5A01G258000 chr2D 87409540 87410616 1076 True 1531 1531 92.421 1774 2847 1 chr2D.!!$R2 1073
7 TraesCS5A01G258000 chr2D 35553622 35554696 1074 True 1506 1506 91.959 1771 2847 1 chr2D.!!$R1 1076
8 TraesCS5A01G258000 chr3A 704108238 704109310 1072 False 1526 1526 92.322 1771 2847 1 chr3A.!!$F1 1076
9 TraesCS5A01G258000 chr6B 164742830 164743903 1073 False 1515 1515 92.137 1771 2847 1 chr6B.!!$F1 1076
10 TraesCS5A01G258000 chr6B 218001272 218002345 1073 True 1509 1509 92.044 1771 2847 1 chr6B.!!$R1 1076
11 TraesCS5A01G258000 chr3B 745462298 745463380 1082 False 1502 1502 91.790 1771 2847 1 chr3B.!!$F1 1076

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
913 978 0.390078 CAGCTCTCTGCAGTCACTGG 60.39 60.0 14.67 0.0 45.94 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2358 1.067974 CAATCCGTCGGTGGCACTATA 59.932 52.381 18.45 0.0 0.0 1.31 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
57 58 2.523507 CGAGATGGCGCTGCTGAAG 61.524 63.158 7.64 0.00 0.00 3.02
116 117 2.051345 CGGGTTGTTTGACAGCGC 60.051 61.111 0.00 0.00 38.53 5.92
219 220 1.745489 GCTGGCGAAGGTGGTTAGG 60.745 63.158 0.00 0.00 0.00 2.69
240 241 4.401837 AGGTACCGGAGTAAAATCTGAGAC 59.598 45.833 9.46 0.00 0.00 3.36
384 385 8.160106 TCACTGAGATAGCTAGTCTGATTATGA 58.840 37.037 15.58 8.62 0.00 2.15
385 386 8.959548 CACTGAGATAGCTAGTCTGATTATGAT 58.040 37.037 15.58 0.00 0.00 2.45
386 387 9.177608 ACTGAGATAGCTAGTCTGATTATGATC 57.822 37.037 15.58 0.00 0.00 2.92
387 388 9.399797 CTGAGATAGCTAGTCTGATTATGATCT 57.600 37.037 0.00 0.00 33.28 2.75
388 389 9.176460 TGAGATAGCTAGTCTGATTATGATCTG 57.824 37.037 0.00 0.00 33.28 2.90
430 433 5.983118 ACAACTTATTTAACCAACTTGCTGC 59.017 36.000 0.00 0.00 0.00 5.25
455 458 6.017770 CGTACAGTCCAGTCTCCTAAATCTAG 60.018 46.154 0.00 0.00 0.00 2.43
542 571 5.536538 CCTGGAGATGTTATGTGCTAGTAGA 59.463 44.000 0.00 0.00 0.00 2.59
584 613 7.099764 TGCTGAACATTTTACTCCTAGAAGAG 58.900 38.462 0.00 0.00 39.91 2.85
586 615 7.276878 GCTGAACATTTTACTCCTAGAAGAGAC 59.723 40.741 3.32 0.00 37.33 3.36
603 632 3.829601 AGAGACTGTAACTCCAGTGAAGG 59.170 47.826 0.00 0.00 45.46 3.46
679 715 1.203287 GCAGTCTTCCCTTGCAATTCC 59.797 52.381 0.00 0.00 37.75 3.01
698 734 4.471904 TCCGATGCTGAATTTAGTCTGT 57.528 40.909 0.00 0.00 0.00 3.41
702 738 5.985530 CCGATGCTGAATTTAGTCTGTCATA 59.014 40.000 0.00 0.00 0.00 2.15
743 782 2.864946 GCACAGAGTAGCAGACATGATG 59.135 50.000 0.00 0.00 0.00 3.07
784 823 2.415168 TGCTTCTTCCTTATCGCAAACG 59.585 45.455 0.00 0.00 42.01 3.60
831 870 0.395724 ATGGATGGGGAAACGAAGGC 60.396 55.000 0.00 0.00 0.00 4.35
889 935 4.634443 TGATCATGCATCAAGTCTGAACTG 59.366 41.667 0.00 0.00 38.68 3.16
913 978 0.390078 CAGCTCTCTGCAGTCACTGG 60.390 60.000 14.67 0.00 45.94 4.00
981 1053 8.737175 GTGCATTCTCATCCATGATATAAATGT 58.263 33.333 0.00 0.00 36.02 2.71
1012 1084 1.117142 ATGCTTGCCTGGTTGTGCTT 61.117 50.000 0.00 0.00 0.00 3.91
1051 1126 2.050351 CCTTCGTGTGCTCGTCGT 60.050 61.111 0.00 0.00 0.00 4.34
1052 1127 2.081212 CCTTCGTGTGCTCGTCGTC 61.081 63.158 0.00 0.00 0.00 4.20
1053 1128 2.418333 CTTCGTGTGCTCGTCGTCG 61.418 63.158 0.00 0.00 38.55 5.12
1099 1174 1.006571 GGCTTCTTCGACACCGTCA 60.007 57.895 0.00 0.00 37.05 4.35
1113 1188 1.012086 CCGTCATGGACATCAAGCAG 58.988 55.000 0.00 0.00 42.00 4.24
1303 1393 1.552792 GTCAGGAGAAGAAGAGTGGGG 59.447 57.143 0.00 0.00 0.00 4.96
1557 1647 2.126071 CGGTCGTTCGAGTGGCAT 60.126 61.111 0.00 0.00 0.00 4.40
1608 1698 2.680352 GAGGGCTCCGTCACCAGA 60.680 66.667 3.92 0.00 0.00 3.86
1707 1797 5.065914 AGCTCTCTTGCATCAAACAACTTA 58.934 37.500 0.00 0.00 34.99 2.24
1713 1805 4.582701 TGCATCAAACAACTTACCCAAG 57.417 40.909 0.00 0.00 37.81 3.61
1716 1808 4.783242 CATCAAACAACTTACCCAAGACG 58.217 43.478 0.00 0.00 35.60 4.18
1721 1813 5.900865 AACAACTTACCCAAGACGAAAAA 57.099 34.783 0.00 0.00 35.60 1.94
1740 1832 8.060090 ACGAAAAATCGTAACTTCAAACTACTG 58.940 33.333 1.50 0.00 45.19 2.74
1741 1833 8.270799 CGAAAAATCGTAACTTCAAACTACTGA 58.729 33.333 0.00 0.00 0.00 3.41
1742 1834 9.582223 GAAAAATCGTAACTTCAAACTACTGAG 57.418 33.333 0.00 0.00 0.00 3.35
1743 1835 8.658499 AAAATCGTAACTTCAAACTACTGAGT 57.342 30.769 0.00 0.00 37.59 3.41
1744 1836 9.754382 AAAATCGTAACTTCAAACTACTGAGTA 57.246 29.630 0.00 0.00 33.58 2.59
1745 1837 8.967552 AATCGTAACTTCAAACTACTGAGTAG 57.032 34.615 17.61 17.61 41.43 2.57
1746 1838 6.906659 TCGTAACTTCAAACTACTGAGTAGG 58.093 40.000 22.40 6.34 40.13 3.18
1747 1839 6.712095 TCGTAACTTCAAACTACTGAGTAGGA 59.288 38.462 22.40 8.52 40.13 2.94
1748 1840 7.022384 CGTAACTTCAAACTACTGAGTAGGAG 58.978 42.308 22.40 12.04 40.13 3.69
1760 1852 9.869667 ACTACTGAGTAGGAGTATGTCATTATT 57.130 33.333 22.40 0.00 46.47 1.40
1831 1923 6.471233 TTTGTCCACCAAATTACACAATGA 57.529 33.333 0.00 0.00 38.12 2.57
1962 2055 2.781595 CTACAACCCACGCTCGCCTT 62.782 60.000 0.00 0.00 0.00 4.35
1979 2073 2.648059 CCTTCAGCAAATCGATTCCCT 58.352 47.619 11.83 7.84 0.00 4.20
1996 2090 1.246737 CCTCCAAGGCTCCAGCAAAC 61.247 60.000 0.03 0.00 44.36 2.93
2041 2136 1.337728 CGCTCACTTCACCACCACATA 60.338 52.381 0.00 0.00 0.00 2.29
2241 2337 0.534412 AGGTTCATGAGAGCTGGACG 59.466 55.000 0.00 0.00 0.00 4.79
2262 2358 2.826725 GTCCTACTACAACCAGCTGACT 59.173 50.000 17.39 0.00 0.00 3.41
2568 2668 5.351458 TCTGTTCATGTCTCATATCCGTTG 58.649 41.667 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.510012 TTCAGCAGCGCCATCTCG 60.510 61.111 2.29 0.00 0.00 4.04
116 117 3.385384 TCCTGCACAGCTCCTCCG 61.385 66.667 0.00 0.00 0.00 4.63
139 140 0.176680 ATGACCGTCCTGATGCTGAC 59.823 55.000 0.00 0.00 0.00 3.51
204 205 3.448267 GTACCTAACCACCTTCGCC 57.552 57.895 0.00 0.00 0.00 5.54
219 220 4.095483 TCGTCTCAGATTTTACTCCGGTAC 59.905 45.833 0.00 0.00 0.00 3.34
223 224 3.099362 CGTCGTCTCAGATTTTACTCCG 58.901 50.000 0.00 0.00 0.00 4.63
384 385 6.939622 TGTCAAGTTACACATGATCTCAGAT 58.060 36.000 0.00 0.00 28.08 2.90
385 386 6.345096 TGTCAAGTTACACATGATCTCAGA 57.655 37.500 0.00 0.00 28.08 3.27
386 387 6.648310 AGTTGTCAAGTTACACATGATCTCAG 59.352 38.462 0.00 0.00 28.08 3.35
387 388 6.524734 AGTTGTCAAGTTACACATGATCTCA 58.475 36.000 0.00 0.00 28.08 3.27
388 389 7.426929 AAGTTGTCAAGTTACACATGATCTC 57.573 36.000 0.00 0.00 28.08 2.75
430 433 4.641094 AGATTTAGGAGACTGGACTGTACG 59.359 45.833 0.00 0.00 43.88 3.67
467 470 7.385752 TCCAATTTGCTCAGAATTTCATCAAAC 59.614 33.333 0.00 0.00 0.00 2.93
586 615 7.439655 GCTAAATATCCTTCACTGGAGTTACAG 59.560 40.741 0.00 0.00 44.03 2.74
603 632 7.992754 AATCACAGATCCCTTGCTAAATATC 57.007 36.000 0.00 0.00 0.00 1.63
679 715 5.980698 ATGACAGACTAAATTCAGCATCG 57.019 39.130 0.00 0.00 0.00 3.84
698 734 4.225942 AGGAGAACTTTGCTGGTGATATGA 59.774 41.667 0.00 0.00 0.00 2.15
702 738 2.787994 CAGGAGAACTTTGCTGGTGAT 58.212 47.619 0.00 0.00 33.40 3.06
784 823 0.312416 ATCGGCGTGTCAGCTAGATC 59.688 55.000 6.85 0.00 37.29 2.75
791 830 0.865111 TCACAAAATCGGCGTGTCAG 59.135 50.000 6.85 0.00 32.42 3.51
792 831 0.865111 CTCACAAAATCGGCGTGTCA 59.135 50.000 6.85 0.00 32.42 3.58
794 833 1.464608 CATCTCACAAAATCGGCGTGT 59.535 47.619 6.85 0.00 32.42 4.49
889 935 2.187424 CTGCAGAGAGCTGAGGGC 59.813 66.667 8.42 0.00 45.17 5.19
913 978 2.738314 GTTGCCAACCAGCATGAATTTC 59.262 45.455 0.00 0.00 43.64 2.17
938 1003 3.005205 ACTGCGTGTGAGCATTTGA 57.995 47.368 0.00 0.00 46.97 2.69
1149 1224 1.079750 GTCGTGGAAGAGGGACAGC 60.080 63.158 0.00 0.00 0.00 4.40
1493 1583 0.249322 TATGAAGAAGTAGCCGCCGC 60.249 55.000 0.00 0.00 0.00 6.53
1578 1668 2.688794 GCCCTCGAAGACGACGACT 61.689 63.158 0.00 0.00 43.81 4.18
1633 1723 1.421268 ACAGATTTGCAGTCCAGTCCA 59.579 47.619 0.00 0.00 0.00 4.02
1635 1725 3.126000 GCTAACAGATTTGCAGTCCAGTC 59.874 47.826 0.00 0.00 36.67 3.51
1636 1726 3.077359 GCTAACAGATTTGCAGTCCAGT 58.923 45.455 0.00 0.00 36.67 4.00
1673 1763 4.960938 TGCAAGAGAGCTTCTAGTTTGAA 58.039 39.130 0.00 0.00 34.14 2.69
1674 1764 4.607293 TGCAAGAGAGCTTCTAGTTTGA 57.393 40.909 0.00 0.00 34.14 2.69
1675 1765 4.934001 TGATGCAAGAGAGCTTCTAGTTTG 59.066 41.667 0.00 0.00 38.90 2.93
1677 1767 4.815533 TGATGCAAGAGAGCTTCTAGTT 57.184 40.909 0.00 0.00 38.90 2.24
1678 1768 4.815533 TTGATGCAAGAGAGCTTCTAGT 57.184 40.909 0.00 0.00 38.90 2.57
1679 1769 4.934001 TGTTTGATGCAAGAGAGCTTCTAG 59.066 41.667 0.00 0.00 38.90 2.43
1681 1771 3.748083 TGTTTGATGCAAGAGAGCTTCT 58.252 40.909 0.00 0.00 38.90 2.85
1682 1772 4.023365 AGTTGTTTGATGCAAGAGAGCTTC 60.023 41.667 0.00 0.00 38.68 3.86
1683 1773 3.887716 AGTTGTTTGATGCAAGAGAGCTT 59.112 39.130 0.00 0.00 34.99 3.74
1684 1774 3.484407 AGTTGTTTGATGCAAGAGAGCT 58.516 40.909 0.00 0.00 34.99 4.09
1685 1775 3.911661 AGTTGTTTGATGCAAGAGAGC 57.088 42.857 0.00 0.00 0.00 4.09
1686 1776 5.335191 GGGTAAGTTGTTTGATGCAAGAGAG 60.335 44.000 0.00 0.00 0.00 3.20
1687 1777 4.518970 GGGTAAGTTGTTTGATGCAAGAGA 59.481 41.667 0.00 0.00 0.00 3.10
1690 1780 4.582701 TGGGTAAGTTGTTTGATGCAAG 57.417 40.909 0.00 0.00 0.00 4.01
1707 1797 4.383173 AGTTACGATTTTTCGTCTTGGGT 58.617 39.130 4.07 0.00 45.81 4.51
1713 1805 8.271487 AGTAGTTTGAAGTTACGATTTTTCGTC 58.729 33.333 4.07 0.00 45.81 4.20
1716 1808 9.582223 CTCAGTAGTTTGAAGTTACGATTTTTC 57.418 33.333 0.00 0.00 0.00 2.29
1721 1813 7.392673 TCCTACTCAGTAGTTTGAAGTTACGAT 59.607 37.037 11.06 0.00 37.15 3.73
1727 1819 7.670559 ACATACTCCTACTCAGTAGTTTGAAGT 59.329 37.037 11.06 8.23 37.15 3.01
1831 1923 3.686016 AGTGGACGGCTACAAATGAATT 58.314 40.909 7.78 0.00 0.00 2.17
1962 2055 1.559219 TGGAGGGAATCGATTTGCTGA 59.441 47.619 12.81 0.00 0.00 4.26
1979 2073 1.228552 GGTTTGCTGGAGCCTTGGA 60.229 57.895 0.00 0.00 41.18 3.53
1996 2090 3.460868 GCCTTGGCGGGGAATTGG 61.461 66.667 0.00 0.00 0.00 3.16
2241 2337 2.826725 AGTCAGCTGGTTGTAGTAGGAC 59.173 50.000 15.13 0.00 0.00 3.85
2262 2358 1.067974 CAATCCGTCGGTGGCACTATA 59.932 52.381 18.45 0.00 0.00 1.31
2820 2925 9.109393 GGCAAGCGATCAATAAGGATAATAATA 57.891 33.333 0.00 0.00 0.00 0.98
2821 2926 7.989826 GGCAAGCGATCAATAAGGATAATAAT 58.010 34.615 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.