Multiple sequence alignment - TraesCS2D01G513400

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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 TraesCS2D01G513400 chr2D 100.000 2603 0 0 1 2603 605328927 605326325 0.000000e+00 4807
1 TraesCS2D01G513400 chr2D 94.259 749 38 4 1860 2603 50939666 50938918 0.000000e+00 1140
2 TraesCS2D01G513400 chr2D 92.699 767 34 4 1857 2603 401276999 401276235 0.000000e+00 1086
3 TraesCS2D01G513400 chr2D 89.726 584 36 7 1846 2407 637025164 637024583 0.000000e+00 725
4 TraesCS2D01G513400 chr2D 92.562 121 8 1 766 886 605181199 605181080 3.440000e-39 172
5 TraesCS2D01G513400 chr2D 88.806 134 7 1 643 776 605246296 605246171 9.640000e-35 158
6 TraesCS2D01G513400 chr2A 96.312 1600 22 10 263 1854 736463707 736462137 0.000000e+00 2593
7 TraesCS2D01G513400 chr2A 91.667 228 10 4 4 230 736463918 736463699 9.050000e-80 307
8 TraesCS2D01G513400 chr2A 93.443 122 8 0 761 882 736371915 736371794 5.720000e-42 182
9 TraesCS2D01G513400 chr2A 89.552 134 5 1 643 776 736376857 736376733 7.450000e-36 161
10 TraesCS2D01G513400 chr2A 89.552 134 5 1 643 776 736379701 736379577 7.450000e-36 161
11 TraesCS2D01G513400 chr3D 93.992 749 41 4 1857 2603 20533465 20532719 0.000000e+00 1131
12 TraesCS2D01G513400 chr3D 92.016 764 43 4 1857 2603 567370341 567369579 0.000000e+00 1057
13 TraesCS2D01G513400 chr6D 93.464 765 33 5 1856 2603 55115527 55116291 0.000000e+00 1120
14 TraesCS2D01G513400 chr5D 93.256 771 30 9 1855 2603 45170051 45169281 0.000000e+00 1116
15 TraesCS2D01G513400 chr5D 93.054 763 37 4 1857 2603 526965519 526966281 0.000000e+00 1101
16 TraesCS2D01G513400 chr7D 93.229 768 32 5 1856 2603 44653318 44652551 0.000000e+00 1112
17 TraesCS2D01G513400 chr7D 88.005 767 51 13 1856 2603 379289231 379288487 0.000000e+00 869
18 TraesCS2D01G513400 chr4D 93.333 750 34 6 1857 2603 456039247 456038511 0.000000e+00 1094
19 TraesCS2D01G513400 chr7A 89.921 764 52 7 1855 2603 51648988 51648235 0.000000e+00 961
20 TraesCS2D01G513400 chr4A 90.998 611 23 8 30 637 466153427 466154008 0.000000e+00 795


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 TraesCS2D01G513400 chr2D 605326325 605328927 2602 True 4807 4807 100.0000 1 2603 1 chr2D.!!$R5 2602
1 TraesCS2D01G513400 chr2D 50938918 50939666 748 True 1140 1140 94.2590 1860 2603 1 chr2D.!!$R1 743
2 TraesCS2D01G513400 chr2D 401276235 401276999 764 True 1086 1086 92.6990 1857 2603 1 chr2D.!!$R2 746
3 TraesCS2D01G513400 chr2D 637024583 637025164 581 True 725 725 89.7260 1846 2407 1 chr2D.!!$R6 561
4 TraesCS2D01G513400 chr2A 736462137 736463918 1781 True 1450 2593 93.9895 4 1854 2 chr2A.!!$R3 1850
5 TraesCS2D01G513400 chr3D 20532719 20533465 746 True 1131 1131 93.9920 1857 2603 1 chr3D.!!$R1 746
6 TraesCS2D01G513400 chr3D 567369579 567370341 762 True 1057 1057 92.0160 1857 2603 1 chr3D.!!$R2 746
7 TraesCS2D01G513400 chr6D 55115527 55116291 764 False 1120 1120 93.4640 1856 2603 1 chr6D.!!$F1 747
8 TraesCS2D01G513400 chr5D 45169281 45170051 770 True 1116 1116 93.2560 1855 2603 1 chr5D.!!$R1 748
9 TraesCS2D01G513400 chr5D 526965519 526966281 762 False 1101 1101 93.0540 1857 2603 1 chr5D.!!$F1 746
10 TraesCS2D01G513400 chr7D 44652551 44653318 767 True 1112 1112 93.2290 1856 2603 1 chr7D.!!$R1 747
11 TraesCS2D01G513400 chr7D 379288487 379289231 744 True 869 869 88.0050 1856 2603 1 chr7D.!!$R2 747
12 TraesCS2D01G513400 chr4D 456038511 456039247 736 True 1094 1094 93.3330 1857 2603 1 chr4D.!!$R1 746
13 TraesCS2D01G513400 chr7A 51648235 51648988 753 True 961 961 89.9210 1855 2603 1 chr7A.!!$R1 748
14 TraesCS2D01G513400 chr4A 466153427 466154008 581 False 795 795 90.9980 30 637 1 chr4A.!!$F1 607

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
620 644 0.104671 GGAGCATCTGAGACTGAGCC 59.895 60.0 0.0 0.0 33.73 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2318 0.787183 GCTCTCGGCAAAGATATCGC 59.213 55.0 0.0 0.0 41.35 4.58 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
23 24 2.250939 TGACGCAGGTTTGAAGCCG 61.251 57.895 0.00 0.00 0.00 5.52
28 29 0.884704 GCAGGTTTGAAGCCGTCTGA 60.885 55.000 0.00 0.00 0.00 3.27
87 89 4.696078 GCATGTGCCAATAGTGCG 57.304 55.556 0.00 0.00 34.31 5.34
88 90 1.587088 GCATGTGCCAATAGTGCGC 60.587 57.895 0.00 0.00 39.63 6.09
89 91 1.297819 CATGTGCCAATAGTGCGCG 60.298 57.895 0.00 0.00 42.03 6.86
90 92 3.112126 ATGTGCCAATAGTGCGCGC 62.112 57.895 27.26 27.26 42.03 6.86
91 93 4.536687 GTGCCAATAGTGCGCGCC 62.537 66.667 30.77 19.97 0.00 6.53
174 176 3.005539 TCAGCCTCCTGGTCCTGC 61.006 66.667 0.00 0.00 39.61 4.85
183 185 3.883744 CTGGTCCTGCCGCTCGTTT 62.884 63.158 0.00 0.00 41.21 3.60
221 223 1.270732 GGCAGGCTAGTGATCAGGATG 60.271 57.143 0.00 0.00 37.54 3.51
231 233 2.895680 TCAGGATGACGCAGAGGC 59.104 61.111 0.00 0.00 42.56 4.70
251 253 3.429141 CTGCTGCTGCGTGGGAAG 61.429 66.667 11.21 0.00 43.34 3.46
340 362 2.882876 CGTCGGGACAACGGAGAT 59.117 61.111 0.00 0.00 0.00 2.75
524 546 6.208402 TGTGGCAGACATATTTGTGTTACAAT 59.792 34.615 0.00 0.00 38.00 2.71
620 644 0.104671 GGAGCATCTGAGACTGAGCC 59.895 60.000 0.00 0.00 33.73 4.70
624 648 0.464870 CATCTGAGACTGAGCCCAGG 59.535 60.000 0.00 0.00 44.60 4.45
654 678 0.393132 CCCGCTTCTTCCTCCTTTCC 60.393 60.000 0.00 0.00 0.00 3.13
660 684 2.743131 TCTTCCTCCTTTCCCCTTCT 57.257 50.000 0.00 0.00 0.00 2.85
692 716 4.445452 CACAAATTGCATGTAGGAAGCT 57.555 40.909 0.00 0.00 0.00 3.74
721 745 3.006003 AGTTTCACGTCTTCTTCCTCCTC 59.994 47.826 0.00 0.00 0.00 3.71
935 959 1.512734 CGCGTCCTTGAAATGCAGC 60.513 57.895 0.00 0.00 0.00 5.25
1061 1085 4.096003 CCCATCGGTGGCGTCCTT 62.096 66.667 9.99 0.00 44.62 3.36
1248 1278 0.466007 CATGGCGGATGATTGTGGGA 60.466 55.000 0.00 0.00 33.31 4.37
1655 1687 3.390639 CAGTTAGATCCTCAATGAGCCCT 59.609 47.826 4.40 3.92 0.00 5.19
1656 1688 3.390639 AGTTAGATCCTCAATGAGCCCTG 59.609 47.826 4.40 0.00 0.00 4.45
1657 1689 2.187239 AGATCCTCAATGAGCCCTGA 57.813 50.000 4.40 0.00 0.00 3.86
1658 1690 1.767681 AGATCCTCAATGAGCCCTGAC 59.232 52.381 4.40 0.00 0.00 3.51
1659 1691 0.467384 ATCCTCAATGAGCCCTGACG 59.533 55.000 4.40 0.00 0.00 4.35
1660 1692 1.153289 CCTCAATGAGCCCTGACGG 60.153 63.158 4.40 0.00 0.00 4.79
1669 1701 2.187946 CCCTGACGGCTCACCATC 59.812 66.667 0.00 0.00 34.57 3.51
1670 1702 2.362369 CCCTGACGGCTCACCATCT 61.362 63.158 0.00 0.00 34.57 2.90
1671 1703 1.153489 CCTGACGGCTCACCATCTG 60.153 63.158 0.00 0.00 34.57 2.90
1672 1704 1.812922 CTGACGGCTCACCATCTGC 60.813 63.158 0.00 0.00 34.57 4.26
1673 1705 2.512515 GACGGCTCACCATCTGCC 60.513 66.667 0.00 0.00 42.94 4.85
1674 1706 4.101448 ACGGCTCACCATCTGCCC 62.101 66.667 0.00 0.00 43.42 5.36
1753 1785 3.046280 GTCCGGATGAAAGACGACC 57.954 57.895 7.81 0.00 0.00 4.79
1796 1828 3.220110 ACAGTTTACACTCGGAGTCTCA 58.780 45.455 7.89 0.00 0.00 3.27
1830 1862 2.355209 GCTCTTGGGTCTTCTTCCGAAT 60.355 50.000 0.00 0.00 0.00 3.34
1891 1923 1.032014 ACGTACGCCGGGTGTAATAT 58.968 50.000 21.24 7.77 42.24 1.28
1894 1926 2.407090 GTACGCCGGGTGTAATATTCC 58.593 52.381 21.24 5.15 30.12 3.01
2114 2162 0.449388 CGTACTTTACCGAGAGCCGT 59.551 55.000 0.00 0.00 36.31 5.68
2430 2497 3.191888 ACAGTAGGTCTCCCAGACAAT 57.808 47.619 6.03 0.00 46.79 2.71
2444 2511 4.142816 CCCAGACAATCATGTTTTCGAGAC 60.143 45.833 0.00 0.00 40.74 3.36
2494 2561 4.137543 AGTGTTGCTCTCGGAAATCTTTT 58.862 39.130 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.865111 TTCAAACCTGCGTCACGATG 59.135 50.000 0.00 0.00 0.00 3.84
1 2 1.148310 CTTCAAACCTGCGTCACGAT 58.852 50.000 0.00 0.00 0.00 3.73
2 3 1.495584 GCTTCAAACCTGCGTCACGA 61.496 55.000 0.00 0.00 0.00 4.35
23 24 0.903454 TCCCCCTCGTCCTTTCAGAC 60.903 60.000 0.00 0.00 0.00 3.51
28 29 1.612739 GGACTCCCCCTCGTCCTTT 60.613 63.158 0.00 0.00 44.90 3.11
91 93 4.969196 ACAGTCACCACCGCGCAG 62.969 66.667 8.75 0.00 0.00 5.18
205 207 1.604185 GCGTCATCCTGATCACTAGCC 60.604 57.143 0.00 0.00 0.00 3.93
234 236 3.429141 CTTCCCACGCAGCAGCAG 61.429 66.667 0.82 0.00 42.27 4.24
328 350 1.153628 CCCGTCATCTCCGTTGTCC 60.154 63.158 0.00 0.00 0.00 4.02
340 362 4.308458 CAACCTCACCGCCCGTCA 62.308 66.667 0.00 0.00 0.00 4.35
421 443 0.613572 TGGACCATACTGAGCCGACA 60.614 55.000 0.00 0.00 0.00 4.35
524 546 5.773176 TGGATGTATCTCAAGCGTATAGGAA 59.227 40.000 0.00 0.00 0.00 3.36
624 648 1.106285 AGAAGCGGGGAAATGCATTC 58.894 50.000 13.38 6.38 37.31 2.67
654 678 0.391793 GTGCCTCGGAAGAAGAAGGG 60.392 60.000 0.00 0.00 41.32 3.95
692 716 2.029964 GACGTGAAACTGGGCCGA 59.970 61.111 0.00 0.00 31.75 5.54
826 850 4.018490 ACAAATTGCATGTAGGCAGATCA 58.982 39.130 0.00 0.00 45.88 2.92
935 959 2.290896 TGTGAGCTTTTGATGGGTAGGG 60.291 50.000 0.00 0.00 0.00 3.53
1061 1085 0.172127 CTACGAGCAGCAGAAGCAGA 59.828 55.000 0.00 0.00 45.49 4.26
1205 1235 1.503542 GCAGCCCATGAAACAGTCG 59.496 57.895 0.00 0.00 0.00 4.18
1238 1268 1.702182 TGCAAAAGCTCCCACAATCA 58.298 45.000 0.00 0.00 0.00 2.57
1248 1278 0.319405 GGCTTGTCCATGCAAAAGCT 59.681 50.000 11.37 0.00 43.58 3.74
1660 1692 4.864334 CGGGGGCAGATGGTGAGC 62.864 72.222 0.00 0.00 0.00 4.26
1661 1693 4.864334 GCGGGGGCAGATGGTGAG 62.864 72.222 0.00 0.00 0.00 3.51
1796 1828 1.134965 CCAAGAGCTCGGTCGAAATCT 60.135 52.381 8.37 0.00 0.00 2.40
2114 2162 1.795768 CTTTGCCGAGTGTCAAGCTA 58.204 50.000 0.00 0.00 0.00 3.32
2118 2166 2.177394 TATGCTTTGCCGAGTGTCAA 57.823 45.000 0.00 0.00 0.00 3.18
2119 2167 2.009051 CATATGCTTTGCCGAGTGTCA 58.991 47.619 0.00 0.00 0.00 3.58
2254 2318 0.787183 GCTCTCGGCAAAGATATCGC 59.213 55.000 0.00 0.00 41.35 4.58
2430 2497 2.229062 AGAGCTCGTCTCGAAAACATGA 59.771 45.455 8.37 0.00 46.44 3.07


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

AutoCloner maintained by Alex Coulton.