Multiple sequence alignment - TraesCS7A01G164900

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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 TraesCS7A01G164900 chr7A 100.000 2723 0 0 1 2723 120904321 120901599 0 5029
1 TraesCS7A01G164900 chrUn 99.150 1765 14 1 1 1764 189394035 189395799 0 3175
2 TraesCS7A01G164900 chrUn 99.135 925 8 0 1799 2723 186169267 186170191 0 1664
3 TraesCS7A01G164900 chrUn 98.919 925 10 0 1799 2723 86500133 86499209 0 1653
4 TraesCS7A01G164900 chr2A 99.150 1764 15 0 1 1764 618278460 618276697 0 3175
5 TraesCS7A01G164900 chr5B 99.036 1764 17 0 1 1764 679660393 679662156 0 3164
6 TraesCS7A01G164900 chr5B 99.135 925 8 0 1799 2723 130542770 130543694 0 1664
7 TraesCS7A01G164900 chr5B 99.135 925 8 0 1799 2723 130600915 130601839 0 1664
8 TraesCS7A01G164900 chr5B 99.027 925 9 0 1799 2723 130619849 130620773 0 1659
9 TraesCS7A01G164900 chr7B 98.980 1764 18 0 1 1764 743087695 743089458 0 3158
10 TraesCS7A01G164900 chr7B 99.135 925 8 0 1799 2723 716852309 716853233 0 1664
11 TraesCS7A01G164900 chr7B 99.135 925 8 0 1799 2723 743028210 743027286 0 1664
12 TraesCS7A01G164900 chr5A 98.923 1764 19 0 1 1764 16601427 16599664 0 3153
13 TraesCS7A01G164900 chr5A 98.923 1764 19 0 1 1764 300074475 300076238 0 3153
14 TraesCS7A01G164900 chr4D 98.923 1764 19 0 1 1764 123414378 123416141 0 3153
15 TraesCS7A01G164900 chr4D 99.135 925 8 0 1799 2723 6633818 6632894 0 1664
16 TraesCS7A01G164900 chr7D 98.923 1764 18 1 2 1764 203554849 203553086 0 3151
17 TraesCS7A01G164900 chr6A 98.810 1764 21 0 1 1764 289130126 289131889 0 3142
18 TraesCS7A01G164900 chr3A 99.135 925 7 1 1799 2723 66016111 66015188 0 1663


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 TraesCS7A01G164900 chr7A 120901599 120904321 2722 True 5029 5029 100.000 1 2723 1 chr7A.!!$R1 2722
1 TraesCS7A01G164900 chrUn 189394035 189395799 1764 False 3175 3175 99.150 1 1764 1 chrUn.!!$F2 1763
2 TraesCS7A01G164900 chrUn 186169267 186170191 924 False 1664 1664 99.135 1799 2723 1 chrUn.!!$F1 924
3 TraesCS7A01G164900 chrUn 86499209 86500133 924 True 1653 1653 98.919 1799 2723 1 chrUn.!!$R1 924
4 TraesCS7A01G164900 chr2A 618276697 618278460 1763 True 3175 3175 99.150 1 1764 1 chr2A.!!$R1 1763
5 TraesCS7A01G164900 chr5B 679660393 679662156 1763 False 3164 3164 99.036 1 1764 1 chr5B.!!$F4 1763
6 TraesCS7A01G164900 chr5B 130542770 130543694 924 False 1664 1664 99.135 1799 2723 1 chr5B.!!$F1 924
7 TraesCS7A01G164900 chr5B 130600915 130601839 924 False 1664 1664 99.135 1799 2723 1 chr5B.!!$F2 924
8 TraesCS7A01G164900 chr5B 130619849 130620773 924 False 1659 1659 99.027 1799 2723 1 chr5B.!!$F3 924
9 TraesCS7A01G164900 chr7B 743087695 743089458 1763 False 3158 3158 98.980 1 1764 1 chr7B.!!$F2 1763
10 TraesCS7A01G164900 chr7B 716852309 716853233 924 False 1664 1664 99.135 1799 2723 1 chr7B.!!$F1 924
11 TraesCS7A01G164900 chr7B 743027286 743028210 924 True 1664 1664 99.135 1799 2723 1 chr7B.!!$R1 924
12 TraesCS7A01G164900 chr5A 16599664 16601427 1763 True 3153 3153 98.923 1 1764 1 chr5A.!!$R1 1763
13 TraesCS7A01G164900 chr5A 300074475 300076238 1763 False 3153 3153 98.923 1 1764 1 chr5A.!!$F1 1763
14 TraesCS7A01G164900 chr4D 123414378 123416141 1763 False 3153 3153 98.923 1 1764 1 chr4D.!!$F1 1763
15 TraesCS7A01G164900 chr4D 6632894 6633818 924 True 1664 1664 99.135 1799 2723 1 chr4D.!!$R1 924
16 TraesCS7A01G164900 chr7D 203553086 203554849 1763 True 3151 3151 98.923 2 1764 1 chr7D.!!$R1 1762
17 TraesCS7A01G164900 chr6A 289130126 289131889 1763 False 3142 3142 98.810 1 1764 1 chr6A.!!$F1 1763
18 TraesCS7A01G164900 chr3A 66015188 66016111 923 True 1663 1663 99.135 1799 2723 1 chr3A.!!$R1 924

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
324 325 0.89553 CGGTTTCCTCTGTAGCCAGA 59.104 55.0 0.0 0.0 45.44 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 1783 0.039618 GATGGCAGAACCCCCAAGAA 59.96 55.0 0.0 0.0 37.83 2.52 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
33 34 1.153449 CCGCCCGCTCTCAATACAA 60.153 57.895 0.00 0.00 0.00 2.41
40 41 3.067106 CCGCTCTCAATACAACAAGTGT 58.933 45.455 0.00 0.00 44.82 3.55
324 325 0.895530 CGGTTTCCTCTGTAGCCAGA 59.104 55.000 0.00 0.00 45.44 3.86
460 461 2.369394 CTTGTGGTAGAAGATTGGGCC 58.631 52.381 0.00 0.00 0.00 5.80
807 808 2.365237 GTAAGAGGGGACGGGCCT 60.365 66.667 0.84 0.00 36.66 5.19
1251 1253 6.239572 CCTTGTTCCCATTAACAAAACATCCT 60.240 38.462 4.00 0.00 45.88 3.24
1267 1269 4.249661 ACATCCTCTTTTTCTTCGCTCTC 58.750 43.478 0.00 0.00 0.00 3.20
1764 1767 3.601443 AGTTCACTCGCTAAAGCATCT 57.399 42.857 2.44 0.00 42.21 2.90
1765 1768 4.720649 AGTTCACTCGCTAAAGCATCTA 57.279 40.909 2.44 0.00 42.21 1.98
1766 1769 5.073311 AGTTCACTCGCTAAAGCATCTAA 57.927 39.130 2.44 0.00 42.21 2.10
1767 1770 4.865365 AGTTCACTCGCTAAAGCATCTAAC 59.135 41.667 2.44 0.43 42.21 2.34
1768 1771 3.782046 TCACTCGCTAAAGCATCTAACC 58.218 45.455 2.44 0.00 42.21 2.85
1769 1772 3.194755 TCACTCGCTAAAGCATCTAACCA 59.805 43.478 2.44 0.00 42.21 3.67
1770 1773 3.932710 CACTCGCTAAAGCATCTAACCAA 59.067 43.478 2.44 0.00 42.21 3.67
1771 1774 4.033358 CACTCGCTAAAGCATCTAACCAAG 59.967 45.833 2.44 0.00 42.21 3.61
1772 1775 4.184629 CTCGCTAAAGCATCTAACCAAGT 58.815 43.478 2.44 0.00 42.21 3.16
1773 1776 3.932710 TCGCTAAAGCATCTAACCAAGTG 59.067 43.478 2.44 0.00 42.21 3.16
1774 1777 3.063997 CGCTAAAGCATCTAACCAAGTGG 59.936 47.826 2.44 0.00 42.21 4.00
1775 1778 4.010349 GCTAAAGCATCTAACCAAGTGGT 58.990 43.478 0.00 0.00 45.76 4.16
1776 1779 4.142600 GCTAAAGCATCTAACCAAGTGGTG 60.143 45.833 3.14 0.00 44.15 4.17
1777 1780 7.110224 GCTAAAGCATCTAACCAAGTGGTGG 62.110 48.000 3.14 0.74 46.81 4.61
1788 1791 1.895131 CAAGTGGTGGATTTCTTGGGG 59.105 52.381 0.00 0.00 35.21 4.96
1789 1792 0.409484 AGTGGTGGATTTCTTGGGGG 59.591 55.000 0.00 0.00 0.00 5.40
1790 1793 0.114364 GTGGTGGATTTCTTGGGGGT 59.886 55.000 0.00 0.00 0.00 4.95
1791 1794 0.863956 TGGTGGATTTCTTGGGGGTT 59.136 50.000 0.00 0.00 0.00 4.11
1792 1795 1.203125 TGGTGGATTTCTTGGGGGTTC 60.203 52.381 0.00 0.00 0.00 3.62
1793 1796 1.077169 GGTGGATTTCTTGGGGGTTCT 59.923 52.381 0.00 0.00 0.00 3.01
1794 1797 2.171003 GTGGATTTCTTGGGGGTTCTG 58.829 52.381 0.00 0.00 0.00 3.02
1795 1798 1.186200 GGATTTCTTGGGGGTTCTGC 58.814 55.000 0.00 0.00 0.00 4.26
1796 1799 1.186200 GATTTCTTGGGGGTTCTGCC 58.814 55.000 0.00 0.00 0.00 4.85
1797 1800 0.486879 ATTTCTTGGGGGTTCTGCCA 59.513 50.000 0.00 0.00 39.65 4.92
1806 1809 1.379527 GGGTTCTGCCATCTTAACCG 58.620 55.000 0.00 0.00 41.90 4.44
2221 2224 3.838244 AGACCAACTACAACAAGCTCA 57.162 42.857 0.00 0.00 0.00 4.26
2222 2225 4.357918 AGACCAACTACAACAAGCTCAT 57.642 40.909 0.00 0.00 0.00 2.90
2316 2319 4.202284 ACCTGACCTTACGCTGAAAAACTA 60.202 41.667 0.00 0.00 0.00 2.24
2333 2336 1.140852 ACTACACTTGTTGGCTCTGCA 59.859 47.619 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.037446 GTCTTGTGAGAGAGAGACACTTGT 59.963 45.833 0.00 0.00 38.64 3.16
324 325 5.581874 GTCGGCAAATGATTTGGAATTGAAT 59.418 36.000 18.52 0.00 40.94 2.57
405 406 4.157849 TGTTGTACTTGATTCACCCACA 57.842 40.909 0.00 0.00 0.00 4.17
705 706 7.186570 ACTAATTTTTACGGCCTCCTTAGTA 57.813 36.000 0.00 0.00 0.00 1.82
1251 1253 1.337823 CCGGGAGAGCGAAGAAAAAGA 60.338 52.381 0.00 0.00 0.00 2.52
1331 1334 0.552615 ACCCCACATAGGCCTTCCTT 60.553 55.000 12.58 0.00 40.66 3.36
1332 1335 0.345502 TACCCCACATAGGCCTTCCT 59.654 55.000 12.58 0.00 46.57 3.36
1768 1771 1.895131 CCCCAAGAAATCCACCACTTG 59.105 52.381 0.00 0.00 39.24 3.16
1769 1772 1.203174 CCCCCAAGAAATCCACCACTT 60.203 52.381 0.00 0.00 0.00 3.16
1770 1773 0.409484 CCCCCAAGAAATCCACCACT 59.591 55.000 0.00 0.00 0.00 4.00
1771 1774 0.114364 ACCCCCAAGAAATCCACCAC 59.886 55.000 0.00 0.00 0.00 4.16
1772 1775 0.863956 AACCCCCAAGAAATCCACCA 59.136 50.000 0.00 0.00 0.00 4.17
1773 1776 1.077169 AGAACCCCCAAGAAATCCACC 59.923 52.381 0.00 0.00 0.00 4.61
1774 1777 2.171003 CAGAACCCCCAAGAAATCCAC 58.829 52.381 0.00 0.00 0.00 4.02
1775 1778 1.549950 GCAGAACCCCCAAGAAATCCA 60.550 52.381 0.00 0.00 0.00 3.41
1776 1779 1.186200 GCAGAACCCCCAAGAAATCC 58.814 55.000 0.00 0.00 0.00 3.01
1777 1780 1.186200 GGCAGAACCCCCAAGAAATC 58.814 55.000 0.00 0.00 0.00 2.17
1778 1781 0.486879 TGGCAGAACCCCCAAGAAAT 59.513 50.000 0.00 0.00 37.83 2.17
1779 1782 0.486879 ATGGCAGAACCCCCAAGAAA 59.513 50.000 0.00 0.00 37.83 2.52
1780 1783 0.039618 GATGGCAGAACCCCCAAGAA 59.960 55.000 0.00 0.00 37.83 2.52
1781 1784 0.846427 AGATGGCAGAACCCCCAAGA 60.846 55.000 0.00 0.00 37.83 3.02
1782 1785 0.040204 AAGATGGCAGAACCCCCAAG 59.960 55.000 0.00 0.00 37.83 3.61
1783 1786 1.377690 TAAGATGGCAGAACCCCCAA 58.622 50.000 0.00 0.00 37.83 4.12
1784 1787 1.005450 GTTAAGATGGCAGAACCCCCA 59.995 52.381 0.00 0.00 37.83 4.96
1785 1788 1.685180 GGTTAAGATGGCAGAACCCCC 60.685 57.143 10.65 0.00 36.18 5.40
1786 1789 1.763968 GGTTAAGATGGCAGAACCCC 58.236 55.000 10.65 0.00 36.18 4.95
1787 1790 1.379527 CGGTTAAGATGGCAGAACCC 58.620 55.000 14.24 0.76 38.50 4.11
1788 1791 0.733150 GCGGTTAAGATGGCAGAACC 59.267 55.000 11.39 11.39 38.38 3.62
1789 1792 1.739067 AGCGGTTAAGATGGCAGAAC 58.261 50.000 0.00 0.00 0.00 3.01
1790 1793 2.356135 GAAGCGGTTAAGATGGCAGAA 58.644 47.619 0.00 0.00 0.00 3.02
1791 1794 1.406887 GGAAGCGGTTAAGATGGCAGA 60.407 52.381 0.00 0.00 0.00 4.26
1792 1795 1.017387 GGAAGCGGTTAAGATGGCAG 58.983 55.000 0.00 0.00 0.00 4.85
1793 1796 0.393808 GGGAAGCGGTTAAGATGGCA 60.394 55.000 0.00 0.00 0.00 4.92
1794 1797 0.393808 TGGGAAGCGGTTAAGATGGC 60.394 55.000 0.00 0.00 0.00 4.40
1795 1798 2.122783 TTGGGAAGCGGTTAAGATGG 57.877 50.000 0.00 0.00 0.00 3.51
1796 1799 3.947834 AGAATTGGGAAGCGGTTAAGATG 59.052 43.478 0.00 0.00 0.00 2.90
1797 1800 4.236527 AGAATTGGGAAGCGGTTAAGAT 57.763 40.909 0.00 0.00 0.00 2.40
1806 1809 5.926542 GGTTTCAGTTTAAGAATTGGGAAGC 59.073 40.000 0.00 0.00 0.00 3.86
2221 2224 4.681074 GCAGAGAGCTAACCTAAGGAAT 57.319 45.455 0.00 0.00 41.15 3.01
2316 2319 1.242076 GATGCAGAGCCAACAAGTGT 58.758 50.000 0.00 0.00 0.00 3.55
2376 2379 2.290768 GGGGGTTAGGGAACTCTTGAAC 60.291 54.545 0.00 0.00 43.67 3.18


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

AutoCloner maintained by Alex Coulton.