Multiple sequence alignment - TraesCS5D01G023700

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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 TraesCS5D01G023700 chr5D 100.000 2378 0 0 1 2378 18750796 18748419 0 4392
1 TraesCS5D01G023700 chr5D 94.790 2380 114 6 1 2378 18999673 18997302 0 3699
2 TraesCS5D01G023700 chrUn 94.916 2380 111 7 1 2378 245706817 245704446 0 3716
3 TraesCS5D01G023700 chrUn 94.874 2380 112 7 1 2378 67500259 67502630 0 3711
4 TraesCS5D01G023700 chrUn 94.790 2380 114 7 1 2378 291536189 291533818 0 3699
5 TraesCS5D01G023700 chrUn 94.496 2380 121 6 1 2378 229309478 229311849 0 3661
6 TraesCS5D01G023700 chrUn 94.325 2379 125 7 1 2377 199905493 199903123 0 3637
7 TraesCS5D01G023700 chr6B 94.538 2380 120 7 1 2378 111686040 111688411 0 3666
8 TraesCS5D01G023700 chr1B 94.286 2380 126 7 1 2378 544624385 544622014 0 3633
9 TraesCS5D01G023700 chr1B 94.244 2380 126 7 1 2378 544610088 544607718 0 3626


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 TraesCS5D01G023700 chr5D 18748419 18750796 2377 True 4392 4392 100.000 1 2378 1 chr5D.!!$R1 2377
1 TraesCS5D01G023700 chr5D 18997302 18999673 2371 True 3699 3699 94.790 1 2378 1 chr5D.!!$R2 2377
2 TraesCS5D01G023700 chrUn 245704446 245706817 2371 True 3716 3716 94.916 1 2378 1 chrUn.!!$R2 2377
3 TraesCS5D01G023700 chrUn 67500259 67502630 2371 False 3711 3711 94.874 1 2378 1 chrUn.!!$F1 2377
4 TraesCS5D01G023700 chrUn 291533818 291536189 2371 True 3699 3699 94.790 1 2378 1 chrUn.!!$R3 2377
5 TraesCS5D01G023700 chrUn 229309478 229311849 2371 False 3661 3661 94.496 1 2378 1 chrUn.!!$F2 2377
6 TraesCS5D01G023700 chrUn 199903123 199905493 2370 True 3637 3637 94.325 1 2377 1 chrUn.!!$R1 2376
7 TraesCS5D01G023700 chr6B 111686040 111688411 2371 False 3666 3666 94.538 1 2378 1 chr6B.!!$F1 2377
8 TraesCS5D01G023700 chr1B 544622014 544624385 2371 True 3633 3633 94.286 1 2378 1 chr1B.!!$R2 2377
9 TraesCS5D01G023700 chr1B 544607718 544610088 2370 True 3626 3626 94.244 1 2378 1 chr1B.!!$R1 2377

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
342 344 0.400213 TCAGGGCAAGTTGATTCGGT 59.6 50.0 7.16 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2189 0.460109 CGTCATCCAATCTGTCGGCA 60.46 55.0 0.0 0.0 0.0 5.69 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
196 198 2.260822 ACTACCACCAAGATCTGCACT 58.739 47.619 0.00 0.00 0.00 4.40
198 200 1.059098 ACCACCAAGATCTGCACTGA 58.941 50.000 0.00 0.00 0.00 3.41
205 207 1.375908 GATCTGCACTGAACGGCCA 60.376 57.895 2.24 0.00 0.00 5.36
261 263 2.416260 CCGCGCCCTCCTACTTAC 59.584 66.667 0.00 0.00 0.00 2.34
263 265 2.420568 CGCGCCCTCCTACTTACCA 61.421 63.158 0.00 0.00 0.00 3.25
271 273 0.837272 TCCTACTTACCAGGGCATGC 59.163 55.000 9.90 9.90 33.66 4.06
325 327 1.035923 TTCAGCGCAACCCATTTTCA 58.964 45.000 11.47 0.00 0.00 2.69
342 344 0.400213 TCAGGGCAAGTTGATTCGGT 59.600 50.000 7.16 0.00 0.00 4.69
374 376 4.463539 TGTTACACACTCCTTAGCGGATTA 59.536 41.667 0.00 0.00 42.12 1.75
396 398 1.078426 CTTCCATGACCACCGTCCC 60.078 63.158 0.00 0.00 38.32 4.46
409 411 1.153449 CGTCCCGCTGCCTTAATCA 60.153 57.895 0.00 0.00 0.00 2.57
419 421 1.883275 TGCCTTAATCAACCAACACCG 59.117 47.619 0.00 0.00 0.00 4.94
479 481 2.674754 GGCTTCCGGTTCATCCCA 59.325 61.111 0.00 0.00 0.00 4.37
580 582 6.238648 CGCCATCCTACCTATTTAAAGTTTGG 60.239 42.308 0.00 0.00 0.00 3.28
611 613 2.428187 ACGTTGCGTCCCCAATGA 59.572 55.556 1.55 0.00 33.69 2.57
636 638 6.769822 ACTCTAATCATTGGCTTAACCTGATG 59.230 38.462 0.00 0.00 34.42 3.07
648 650 5.234543 GCTTAACCTGATGGAACTCGTAATC 59.765 44.000 0.00 0.00 37.04 1.75
662 664 1.542030 CGTAATCGGCTCCAGCTATCT 59.458 52.381 0.00 0.00 41.70 1.98
734 736 2.339769 GCCCCTATACCCAAGTCAGAT 58.660 52.381 0.00 0.00 0.00 2.90
738 740 4.599241 CCCCTATACCCAAGTCAGATGAAT 59.401 45.833 0.00 0.00 0.00 2.57
750 752 5.178061 AGTCAGATGAATGATTTGCACGTA 58.822 37.500 0.00 0.00 0.00 3.57
753 755 5.874261 TCAGATGAATGATTTGCACGTAAGA 59.126 36.000 0.00 0.00 43.62 2.10
754 756 6.036408 TCAGATGAATGATTTGCACGTAAGAG 59.964 38.462 0.00 0.00 43.62 2.85
756 758 5.940192 TGAATGATTTGCACGTAAGAGTT 57.060 34.783 0.00 0.00 43.62 3.01
757 759 6.312399 TGAATGATTTGCACGTAAGAGTTT 57.688 33.333 0.00 0.00 43.62 2.66
758 760 6.370593 TGAATGATTTGCACGTAAGAGTTTC 58.629 36.000 0.00 0.00 43.62 2.78
759 761 5.940192 ATGATTTGCACGTAAGAGTTTCA 57.060 34.783 0.00 0.00 43.62 2.69
760 762 5.940192 TGATTTGCACGTAAGAGTTTCAT 57.060 34.783 0.00 0.00 43.62 2.57
761 763 5.927030 TGATTTGCACGTAAGAGTTTCATC 58.073 37.500 0.00 0.00 43.62 2.92
762 764 5.700832 TGATTTGCACGTAAGAGTTTCATCT 59.299 36.000 0.00 0.00 43.62 2.90
763 765 4.990543 TTGCACGTAAGAGTTTCATCTG 57.009 40.909 0.00 0.00 43.62 2.90
828 830 3.620488 GGGCATAGTTCACCATCTTTCA 58.380 45.455 0.00 0.00 0.00 2.69
837 839 1.210478 CACCATCTTTCAGGTCCCGAT 59.790 52.381 0.00 0.00 35.52 4.18
866 868 1.487142 TCCAACTCGAACCCTTCACAA 59.513 47.619 0.00 0.00 0.00 3.33
979 981 1.204704 CGCATGTCAGACTCCTTGGTA 59.795 52.381 1.31 0.00 0.00 3.25
1212 1214 3.743017 ACATCGCCAGCCCCCATT 61.743 61.111 0.00 0.00 0.00 3.16
1239 1241 0.602562 CTCCCGGCAATTTCAAGCAA 59.397 50.000 0.00 0.00 0.00 3.91
1500 1503 2.422479 CTCCAGACTACAATTCGGACGA 59.578 50.000 0.00 0.00 0.00 4.20
1607 1610 8.988934 CCGCTTATTTATATGCTTAAACTCAGA 58.011 33.333 6.20 0.00 32.93 3.27
1693 1696 3.826221 GCCATAATGTCGGCTGCA 58.174 55.556 0.50 0.00 45.29 4.41
1719 1722 1.396996 GATGCACCGCGTTGATAAAGT 59.603 47.619 8.22 0.00 0.00 2.66
1769 1772 2.434359 GTACACCGGCAGCCTGAC 60.434 66.667 10.32 0.00 0.00 3.51
1774 1777 4.020617 CCGGCAGCCTGACCTTCA 62.021 66.667 10.54 0.00 0.00 3.02
1852 1855 0.394488 TGGTTGGGAGCGTGTTTTGA 60.394 50.000 0.00 0.00 0.00 2.69
1917 1920 2.797491 GCAACTTGCGTTCAAAGACTT 58.203 42.857 0.00 0.00 31.71 3.01
1927 1930 3.247648 CGTTCAAAGACTTGATGGTTCGT 59.752 43.478 0.00 0.00 41.22 3.85
1947 1950 2.821969 GTGGGATTCTGCAATTCACACT 59.178 45.455 14.95 0.00 31.78 3.55
1967 1970 2.882927 AGGTATCGCATTTCGCTACA 57.117 45.000 0.00 0.00 40.44 2.74
2015 2018 1.660575 CGTTGCCGAGAGTCGTGTT 60.661 57.895 0.00 0.00 38.40 3.32
2038 2041 7.168972 TGTTGATTAAATAGCTTTGCAACACAC 59.831 33.333 0.00 0.00 37.33 3.82
2042 2045 1.169661 TAGCTTTGCAACACACGGGG 61.170 55.000 0.00 0.00 0.00 5.73
2074 2077 4.450612 GCCATGCCCCCGGGTTAA 62.451 66.667 21.85 3.88 37.65 2.01
2155 2158 4.348495 GGGGAGGGGAGGTGGTCA 62.348 72.222 0.00 0.00 0.00 4.02
2163 2166 0.623723 GGGAGGTGGTCAAGGCATTA 59.376 55.000 0.00 0.00 0.00 1.90
2206 2209 0.460284 GCCGACAGATTGGATGACGT 60.460 55.000 0.00 0.00 34.74 4.34
2225 2228 3.959975 TGCGCGGTCTGTTTTGGC 61.960 61.111 8.83 0.00 0.00 4.52
2239 2242 2.063015 TTTGGCCAGGGTCACGACAT 62.063 55.000 5.11 0.00 0.00 3.06
2321 2324 3.771577 AAGGTTCAATGGACTTCTCGT 57.228 42.857 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 1.336131 GATCCTAAGGGACGGGGTAC 58.664 60.000 0.00 0.00 45.43 3.34
271 273 4.899239 GGCCATCTGGACGAGCGG 62.899 72.222 0.00 0.00 37.39 5.52
278 280 3.716195 CACACCCGGCCATCTGGA 61.716 66.667 2.24 0.00 41.45 3.86
305 307 1.269517 TGAAAATGGGTTGCGCTGAAC 60.270 47.619 9.73 5.37 0.00 3.18
314 316 2.101640 ACTTGCCCTGAAAATGGGTT 57.898 45.000 0.00 0.00 46.22 4.11
325 327 1.065418 CCTACCGAATCAACTTGCCCT 60.065 52.381 0.00 0.00 0.00 5.19
330 332 4.202326 ACAACTCACCTACCGAATCAACTT 60.202 41.667 0.00 0.00 0.00 2.66
374 376 1.292223 CGGTGGTCATGGAAGTCGT 59.708 57.895 0.00 0.00 0.00 4.34
396 398 1.539388 TGTTGGTTGATTAAGGCAGCG 59.461 47.619 0.00 0.00 0.00 5.18
401 403 4.202070 ACAAACGGTGTTGGTTGATTAAGG 60.202 41.667 0.00 0.00 37.01 2.69
409 411 2.194460 CCCACAAACGGTGTTGGTT 58.806 52.632 0.18 0.00 46.44 3.67
419 421 2.740447 CGCTAACCTAGAACCCACAAAC 59.260 50.000 0.00 0.00 0.00 2.93
479 481 1.676014 GGTAAGCAGAACTGGCGATGT 60.676 52.381 3.99 0.00 36.08 3.06
580 582 2.007608 GCAACGTCCTTGACCTATTCC 58.992 52.381 0.00 0.00 30.42 3.01
611 613 6.313519 TCAGGTTAAGCCAATGATTAGAGT 57.686 37.500 0.00 0.00 40.61 3.24
628 630 3.430374 CCGATTACGAGTTCCATCAGGTT 60.430 47.826 0.00 0.00 42.66 3.50
636 638 0.458669 TGGAGCCGATTACGAGTTCC 59.541 55.000 0.00 0.00 42.66 3.62
648 650 0.033228 CCTCAAGATAGCTGGAGCCG 59.967 60.000 6.89 0.00 40.33 5.52
662 664 0.690762 CCCTCCGAAGTTTCCCTCAA 59.309 55.000 0.00 0.00 0.00 3.02
693 695 3.245519 GCGAAAGACTAATCGAACCATCC 59.754 47.826 13.14 0.00 41.43 3.51
734 736 5.940192 AACTCTTACGTGCAAATCATTCA 57.060 34.783 0.00 0.00 0.00 2.57
738 740 5.700832 AGATGAAACTCTTACGTGCAAATCA 59.299 36.000 0.00 0.00 0.00 2.57
750 752 3.594134 CTCGAAGCCAGATGAAACTCTT 58.406 45.455 0.00 0.00 0.00 2.85
753 755 1.731720 GCTCGAAGCCAGATGAAACT 58.268 50.000 0.00 0.00 34.48 2.66
807 809 3.620488 TGAAAGATGGTGAACTATGCCC 58.380 45.455 0.00 0.00 0.00 5.36
828 830 3.537874 GCACGCCTATCGGGACCT 61.538 66.667 0.00 0.00 46.58 3.85
837 839 1.529152 TTCGAGTTGGAGCACGCCTA 61.529 55.000 0.00 0.00 0.00 3.93
866 868 1.604378 CTGGCCGACCCTGATCTTT 59.396 57.895 0.00 0.00 34.66 2.52
948 950 1.874019 GACATGCGTGCGAGTCGAT 60.874 57.895 18.61 0.00 0.00 3.59
979 981 0.872881 CGACCCGTCTTGAAACACGT 60.873 55.000 0.00 0.00 34.06 4.49
1169 1171 3.234390 CGTATGCGGAATGGCTCG 58.766 61.111 0.00 0.00 0.00 5.03
1195 1197 3.721370 GAATGGGGGCTGGCGATGT 62.721 63.158 0.00 0.00 0.00 3.06
1203 1205 4.129148 GGGAAGCGAATGGGGGCT 62.129 66.667 0.00 0.00 42.33 5.19
1500 1503 3.665675 GAGAATCGGGCGGCTGTGT 62.666 63.158 18.34 6.70 0.00 3.72
1706 1709 1.320555 CGTCCTCACTTTATCAACGCG 59.679 52.381 3.53 3.53 0.00 6.01
1719 1722 4.408821 GCATGGTGGGCGTCCTCA 62.409 66.667 7.97 6.35 0.00 3.86
1766 1769 2.741092 GCGGTGGACTGAAGGTCA 59.259 61.111 0.00 0.00 46.16 4.02
1769 1772 4.410400 GGGGCGGTGGACTGAAGG 62.410 72.222 0.00 0.00 0.00 3.46
1917 1920 1.678728 GCAGAATCCCACGAACCATCA 60.679 52.381 0.00 0.00 0.00 3.07
1927 1930 3.159213 AGTGTGAATTGCAGAATCCCA 57.841 42.857 0.00 0.00 0.00 4.37
1967 1970 2.402305 GCTCTCGCATCGATGAAGAAT 58.598 47.619 29.20 0.00 34.61 2.40
2015 2018 5.855925 CGTGTGTTGCAAAGCTATTTAATCA 59.144 36.000 0.00 0.00 0.00 2.57
2074 2077 1.160329 GCGTCAAGGAACACTGTGCT 61.160 55.000 7.90 0.00 0.00 4.40
2139 2142 2.204090 TTGACCACCTCCCCTCCC 60.204 66.667 0.00 0.00 0.00 4.30
2186 2189 0.460109 CGTCATCCAATCTGTCGGCA 60.460 55.000 0.00 0.00 0.00 5.69
2193 2196 1.361668 GCGCACACGTCATCCAATCT 61.362 55.000 0.30 0.00 42.83 2.40
2206 2209 2.712539 CAAAACAGACCGCGCACA 59.287 55.556 8.75 0.00 0.00 4.57
2225 2228 1.656652 GATCAATGTCGTGACCCTGG 58.343 55.000 0.00 0.00 0.00 4.45
2263 2266 4.374399 GAGAAGTCGTAACAAGGTTTCCA 58.626 43.478 0.00 0.00 0.00 3.53
2351 2354 1.445582 GAAGTGTTCGGATCGCGGT 60.446 57.895 6.13 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.