Multiple sequence alignment - TraesCS7D01G119300

Loading Multiple Alignment...

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 TraesCS7D01G119300 chr7D 100.000 2297 0 0 1 2297 74090970 74093266 0 4242
1 TraesCS7D01G119300 chrUn 96.543 2285 77 2 1 2285 245706068 245708350 0 3781
2 TraesCS7D01G119300 chrUn 96.543 2285 78 1 1 2285 291535440 291537723 0 3781
3 TraesCS7D01G119300 chrUn 96.500 2286 78 2 1 2285 274341282 274338998 0 3777
4 TraesCS7D01G119300 chrUn 96.499 2285 79 1 1 2285 199874824 199877107 0 3775
5 TraesCS7D01G119300 chrUn 96.499 2285 79 1 1 2285 229310227 229307944 0 3775
6 TraesCS7D01G119300 chrUn 96.368 2285 82 1 1 2285 237311709 237313992 0 3759
7 TraesCS7D01G119300 chr1B 96.499 2285 77 2 1 2285 544593697 544595978 0 3773
8 TraesCS7D01G119300 chr1B 96.293 2293 83 2 1 2292 544623636 544625927 0 3762
9 TraesCS7D01G119300 chr5D 96.455 2285 80 1 1 2285 18998924 19001207 0 3770


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 TraesCS7D01G119300 chr7D 74090970 74093266 2296 False 4242 4242 100.000 1 2297 1 chr7D.!!$F1 2296
1 TraesCS7D01G119300 chrUn 245706068 245708350 2282 False 3781 3781 96.543 1 2285 1 chrUn.!!$F3 2284
2 TraesCS7D01G119300 chrUn 291535440 291537723 2283 False 3781 3781 96.543 1 2285 1 chrUn.!!$F4 2284
3 TraesCS7D01G119300 chrUn 274338998 274341282 2284 True 3777 3777 96.500 1 2285 1 chrUn.!!$R2 2284
4 TraesCS7D01G119300 chrUn 199874824 199877107 2283 False 3775 3775 96.499 1 2285 1 chrUn.!!$F1 2284
5 TraesCS7D01G119300 chrUn 229307944 229310227 2283 True 3775 3775 96.499 1 2285 1 chrUn.!!$R1 2284
6 TraesCS7D01G119300 chrUn 237311709 237313992 2283 False 3759 3759 96.368 1 2285 1 chrUn.!!$F2 2284
7 TraesCS7D01G119300 chr1B 544593697 544595978 2281 False 3773 3773 96.499 1 2285 1 chr1B.!!$F1 2284
8 TraesCS7D01G119300 chr1B 544623636 544625927 2291 False 3762 3762 96.293 1 2292 1 chr1B.!!$F2 2291
9 TraesCS7D01G119300 chr5D 18998924 19001207 2283 False 3770 3770 96.455 1 2285 1 chr5D.!!$F1 2284

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
409 410 0.105964 TGCGTAACAACTCACCTGCT 59.894 50.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1744 0.03759 TTTAACAGATGTGCCGCCCT 59.962 50.0 0.0 0.0 0.0 5.19 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
32 33 3.445857 GTTCGTCTGACTTGGGTATAGC 58.554 50.000 6.21 0.00 0.00 2.97
109 110 1.717032 TAGCTGGAGCCCATTACGAT 58.283 50.000 0.00 0.00 43.38 3.73
153 154 1.754234 GAGGCATTGGGGACGCAAT 60.754 57.895 8.57 8.57 31.30 3.56
263 264 4.219725 GGCCATTTTTGGTAAGCAGAACTA 59.780 41.667 0.00 0.00 0.00 2.24
308 309 1.894756 GTTACGGTGCCCAACTGCA 60.895 57.895 0.00 0.00 38.92 4.41
370 371 4.480480 AGGACGGTGGTCATGGAT 57.520 55.556 0.00 0.00 45.28 3.41
380 381 3.270027 GTGGTCATGGATGTCGAAATCA 58.730 45.455 17.32 4.27 0.00 2.57
392 393 2.605366 GTCGAAATCAGCTAAGGAGTGC 59.395 50.000 0.00 0.00 0.00 4.40
409 410 0.105964 TGCGTAACAACTCACCTGCT 59.894 50.000 0.00 0.00 0.00 4.24
566 567 2.456119 CGTCGGTGCAGATCTTGGC 61.456 63.158 0.00 0.00 0.00 4.52
567 568 2.109126 GTCGGTGCAGATCTTGGCC 61.109 63.158 0.00 0.00 0.00 5.36
600 601 9.206870 GCAAATATTCAAATGAGAACTTGGAAA 57.793 29.630 0.00 0.00 0.00 3.13
651 652 1.538047 CACTTGCACATGGGTAAGCT 58.462 50.000 23.81 9.86 34.33 3.74
656 657 0.940126 GCACATGGGTAAGCTGATCG 59.060 55.000 0.00 0.00 0.00 3.69
704 705 4.592192 CGATCACGCGCATCCCCT 62.592 66.667 5.73 0.00 0.00 4.79
709 710 2.033448 ACGCGCATCCCCTGAAAA 59.967 55.556 5.73 0.00 0.00 2.29
710 711 1.378514 ACGCGCATCCCCTGAAAAT 60.379 52.632 5.73 0.00 0.00 1.82
809 810 4.262617 GCCTCGGGAAGAGTTATCTTTTT 58.737 43.478 0.00 0.00 45.98 1.94
920 921 4.141876 CCCCGGTGGCCCATGAAT 62.142 66.667 0.00 0.00 0.00 2.57
925 926 0.110295 CGGTGGCCCATGAATATCCA 59.890 55.000 0.00 0.00 0.00 3.41
964 965 2.037144 ACGCCCGGTCTTACTCATAAT 58.963 47.619 0.00 0.00 0.00 1.28
965 966 2.433239 ACGCCCGGTCTTACTCATAATT 59.567 45.455 0.00 0.00 0.00 1.40
989 990 2.123589 TCAGGTCTCCAAGGTGAACAA 58.876 47.619 8.73 0.00 0.00 2.83
1040 1041 0.250553 AAGTCGGCAAAACGGATCCA 60.251 50.000 13.41 0.00 0.00 3.41
1058 1059 4.644163 TCCATAACTTCGGGAAAAGGAA 57.356 40.909 0.00 0.00 0.00 3.36
1182 1183 3.858225 GGGACGGACCGGGAATCC 61.858 72.222 20.00 15.42 40.11 3.01
1316 1317 0.813184 CGCAATGTGATTTCTGCCCT 59.187 50.000 0.00 0.00 0.00 5.19
1621 1623 5.562113 GCGCAAGTGAAATACCACTACTTTT 60.562 40.000 0.30 0.00 45.82 2.27
1686 1689 0.251519 CTCCTTTTGGCTCCAAGGCT 60.252 55.000 1.26 0.00 41.96 4.58
1687 1690 0.188342 TCCTTTTGGCTCCAAGGCTT 59.812 50.000 0.00 0.00 41.96 4.35
1721 1724 1.587547 GATCCGGGCAGAAGACATTC 58.412 55.000 0.00 0.00 35.52 2.67
1735 1738 1.208293 GACATTCTCAGGTGGGGAGTC 59.792 57.143 0.00 0.00 34.04 3.36
1741 1744 1.306141 CAGGTGGGGAGTCTGGCTA 60.306 63.158 0.00 0.00 0.00 3.93
1791 1794 3.387374 CAGGTGTCCTAAGATGAGCTCAT 59.613 47.826 29.09 29.09 33.51 2.90
1792 1795 4.036518 AGGTGTCCTAAGATGAGCTCATT 58.963 43.478 29.26 18.12 31.42 2.57
1807 1810 6.939622 TGAGCTCATTGAGAACAGAAATCTA 58.060 36.000 13.74 0.00 0.00 1.98
1836 1839 4.563337 ACAAAAGGGTAAAAGCTCGTTC 57.437 40.909 0.00 0.00 0.00 3.95
1837 1840 3.949113 ACAAAAGGGTAAAAGCTCGTTCA 59.051 39.130 0.00 0.00 0.00 3.18
1841 1844 5.784578 AAGGGTAAAAGCTCGTTCAATTT 57.215 34.783 0.00 0.00 0.00 1.82
1843 1846 5.769367 AGGGTAAAAGCTCGTTCAATTTTC 58.231 37.500 0.00 0.00 0.00 2.29
1850 1853 5.712152 AGCTCGTTCAATTTTCATTTCCT 57.288 34.783 0.00 0.00 0.00 3.36
1864 1867 7.655236 TTTCATTTCCTGTACGAATACGAAA 57.345 32.000 0.00 0.00 42.66 3.46
1948 1951 2.844348 AGTTACCACAGGGATAACTGGG 59.156 50.000 0.00 0.00 42.75 4.45
2061 2064 3.332187 TGGATTGTTCACCCACCAATAGA 59.668 43.478 0.00 0.00 0.00 1.98
2062 2065 4.202620 TGGATTGTTCACCCACCAATAGAA 60.203 41.667 0.00 0.00 0.00 2.10
2131 2134 1.195347 CTGATGACAGTGTCGCGATC 58.805 55.000 14.06 15.15 39.11 3.69
2224 2227 2.048597 CGAAGCTACCGTGTGCCA 60.049 61.111 0.00 0.00 0.00 4.92
2239 2242 4.002982 GTGTGCCAGATTATGACTGAACA 58.997 43.478 0.00 0.00 37.54 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.587034 GGTTCGATTAGTCTTTCGCCG 59.413 52.381 0.00 0.00 35.39 6.46
109 110 9.342308 CTAATCATTGGCTTTACCTGATAGAAA 57.658 33.333 0.00 0.00 40.22 2.52
153 154 4.087182 AGTTTGAGAATAGGTCGAGGACA 58.913 43.478 0.00 0.00 33.68 4.02
263 264 2.203070 GGTTCATCCCGCATCGCT 60.203 61.111 0.00 0.00 0.00 4.93
308 309 1.636148 TGTGGGTTCTAGGTTAGCGT 58.364 50.000 0.00 0.00 0.00 5.07
370 371 3.849911 CACTCCTTAGCTGATTTCGACA 58.150 45.455 0.00 0.00 0.00 4.35
380 381 2.299297 AGTTGTTACGCACTCCTTAGCT 59.701 45.455 0.00 0.00 0.00 3.32
392 393 2.061773 CTCAGCAGGTGAGTTGTTACG 58.938 52.381 19.84 0.00 46.89 3.18
409 410 1.860641 TTTCGGGGCTAGATGACTCA 58.139 50.000 0.00 0.00 0.00 3.41
412 413 2.158813 TCCATTTTCGGGGCTAGATGAC 60.159 50.000 0.00 0.00 0.00 3.06
416 417 1.142870 CCATCCATTTTCGGGGCTAGA 59.857 52.381 0.00 0.00 0.00 2.43
566 567 8.365399 TCTCATTTGAATATTTGCTACTACGG 57.635 34.615 0.00 0.00 0.00 4.02
567 568 9.638300 GTTCTCATTTGAATATTTGCTACTACG 57.362 33.333 0.00 0.00 0.00 3.51
596 597 2.351455 CTTTCTCCTCTTCGGCTTTCC 58.649 52.381 0.00 0.00 0.00 3.13
600 601 1.276705 GAACCTTTCTCCTCTTCGGCT 59.723 52.381 0.00 0.00 0.00 5.52
656 657 1.907739 GGGTTACCCCGTCCCTTAC 59.092 63.158 9.81 0.00 42.41 2.34
686 687 4.891727 GGGGATGCGCGTGATCGT 62.892 66.667 6.97 0.00 39.49 3.73
704 705 7.363443 GGGAAATCTTAACCCGATTCATTTTCA 60.363 37.037 0.00 0.00 34.03 2.69
734 735 3.315140 TCAACCGCCACATCCCGA 61.315 61.111 0.00 0.00 0.00 5.14
754 755 0.606401 TCCGGACTTCCTAACGTCGT 60.606 55.000 0.00 0.00 0.00 4.34
809 810 0.955905 GTTGGCAGGCCGTTAAGAAA 59.044 50.000 5.74 0.00 39.42 2.52
811 812 1.302993 GGTTGGCAGGCCGTTAAGA 60.303 57.895 5.74 0.00 39.42 2.10
855 856 2.203788 TCTTCCGGCCACTGGACT 60.204 61.111 2.24 0.00 34.56 3.85
909 910 1.706866 CCTCTGGATATTCATGGGCCA 59.293 52.381 9.61 9.61 0.00 5.36
920 921 1.202734 CGGTACTCGGTCCTCTGGATA 60.203 57.143 0.00 0.00 32.73 2.59
954 955 6.126796 TGGAGACCTGATGCAATTATGAGTAA 60.127 38.462 0.00 0.00 0.00 2.24
964 965 1.067295 ACCTTGGAGACCTGATGCAA 58.933 50.000 0.00 0.00 0.00 4.08
965 966 0.325933 CACCTTGGAGACCTGATGCA 59.674 55.000 0.00 0.00 0.00 3.96
989 990 0.482446 TTGTTCCATTGGCCAGAGGT 59.518 50.000 21.07 1.32 0.00 3.85
1040 1041 3.699538 GCCATTCCTTTTCCCGAAGTTAT 59.300 43.478 0.00 0.00 0.00 1.89
1058 1059 2.373707 GCCCAGTCCTCAGAGCCAT 61.374 63.158 0.00 0.00 0.00 4.40
1100 1101 1.522355 CAATCTGCCGACAGCCGAT 60.522 57.895 0.00 0.00 46.25 4.18
1113 1114 0.459934 GTGAGCAGCTCGAGCAATCT 60.460 55.000 36.87 28.04 45.16 2.40
1316 1317 3.807553 TCACTTTGACATTCAGAGCACA 58.192 40.909 0.00 0.00 32.38 4.57
1425 1426 7.607991 GTGGGAATCTCGTTAATCCATTCATAT 59.392 37.037 0.00 0.00 33.48 1.78
1426 1427 6.934645 GTGGGAATCTCGTTAATCCATTCATA 59.065 38.462 0.00 0.00 33.48 2.15
1621 1623 7.821846 ACCCACGGAATAAGTAAAATAACGTTA 59.178 33.333 11.02 11.02 0.00 3.18
1686 1689 1.963464 GATCGGCCCGGTAAGACCAA 61.963 60.000 1.90 0.00 38.47 3.67
1687 1690 2.364579 ATCGGCCCGGTAAGACCA 60.365 61.111 1.90 0.00 38.47 4.02
1711 1714 1.912043 CCCCACCTGAGAATGTCTTCT 59.088 52.381 0.00 0.00 44.53 2.85
1721 1724 2.664081 GCCAGACTCCCCACCTGAG 61.664 68.421 0.00 0.00 35.92 3.35
1735 1738 4.181010 ATGTGCCGCCCTAGCCAG 62.181 66.667 0.00 0.00 34.57 4.85
1741 1744 0.037590 TTTAACAGATGTGCCGCCCT 59.962 50.000 0.00 0.00 0.00 5.19
1791 1794 6.419484 TCCACACTAGATTTCTGTTCTCAA 57.581 37.500 0.00 0.00 0.00 3.02
1792 1795 6.183360 TGTTCCACACTAGATTTCTGTTCTCA 60.183 38.462 0.00 0.00 0.00 3.27
1807 1810 4.142026 GCTTTTACCCTTTTGTTCCACACT 60.142 41.667 0.00 0.00 0.00 3.55
1836 1839 8.172484 TCGTATTCGTACAGGAAATGAAAATTG 58.828 33.333 0.00 0.00 38.33 2.32
1837 1840 8.259049 TCGTATTCGTACAGGAAATGAAAATT 57.741 30.769 0.00 0.00 38.33 1.82
1841 1844 6.645827 TGTTTCGTATTCGTACAGGAAATGAA 59.354 34.615 0.00 0.00 38.33 2.57
1843 1846 6.397831 TGTTTCGTATTCGTACAGGAAATG 57.602 37.500 0.00 0.00 38.33 2.32
1850 1853 5.443562 CGCTTTCATGTTTCGTATTCGTACA 60.444 40.000 0.00 5.34 37.22 2.90
1864 1867 1.668419 GATAGGCCACGCTTTCATGT 58.332 50.000 5.01 0.00 0.00 3.21
1899 1902 5.077564 TGACACCTCTAGCTTCAAACTCTA 58.922 41.667 0.00 0.00 0.00 2.43
1900 1903 3.898123 TGACACCTCTAGCTTCAAACTCT 59.102 43.478 0.00 0.00 0.00 3.24
1948 1951 3.137637 AACGCTTGGCTGCCACAAC 62.138 57.895 23.30 12.63 30.78 3.32
2061 2064 2.367567 TCTAAACCCAGCTCACGTTCTT 59.632 45.455 0.00 0.00 0.00 2.52
2062 2065 1.968493 TCTAAACCCAGCTCACGTTCT 59.032 47.619 0.00 0.00 0.00 3.01
2131 2134 5.295292 TCCTCTCGTACTAGGTTGAATTACG 59.705 44.000 0.00 0.00 37.47 3.18
2224 2227 7.397476 TGACTTAGAGGTGTTCAGTCATAATCT 59.603 37.037 0.00 0.00 31.07 2.40
2239 2242 4.100373 AGCTTGGATTCTGACTTAGAGGT 58.900 43.478 0.00 0.00 36.61 3.85


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

AutoCloner maintained by Alex Coulton.