Multiple sequence alignment - TraesCS7B01G273200

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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 TraesCS7B01G273200 chr7B 100.000 2589 0 0 1 2589 501321325 501318737 0.000000e+00 4782
1 TraesCS7B01G273200 chr7D 93.983 1878 63 21 1 1858 476759940 476758093 0.000000e+00 2796
2 TraesCS7B01G273200 chr7D 93.438 381 16 7 1 376 476777036 476776660 8.090000e-155 556
3 TraesCS7B01G273200 chr4B 99.045 733 7 0 1857 2589 661635436 661636168 0.000000e+00 1315
4 TraesCS7B01G273200 chr7A 99.042 731 7 0 1859 2589 317174179 317173449 0.000000e+00 1312
5 TraesCS7B01G273200 chr7A 82.824 1473 108 57 450 1847 519091633 519093035 0.000000e+00 1184
6 TraesCS7B01G273200 chr7A 89.738 458 30 11 6 453 519091144 519091594 1.040000e-158 569
7 TraesCS7B01G273200 chr5B 99.042 731 7 0 1859 2589 224614631 224613901 0.000000e+00 1312
8 TraesCS7B01G273200 chr5B 98.774 734 9 0 1856 2589 253176817 253177550 0.000000e+00 1306
9 TraesCS7B01G273200 chr5A 99.042 731 7 0 1859 2589 180307202 180307932 0.000000e+00 1312
10 TraesCS7B01G273200 chr4A 99.042 731 7 0 1859 2589 16029670 16028940 0.000000e+00 1312
11 TraesCS7B01G273200 chr4A 98.906 731 8 0 1859 2589 423443174 423442444 0.000000e+00 1306
12 TraesCS7B01G273200 chr6A 98.906 731 8 0 1859 2589 384878618 384879348 0.000000e+00 1306
13 TraesCS7B01G273200 chr2A 98.645 738 8 2 1852 2589 456651274 456650539 0.000000e+00 1306
14 TraesCS7B01G273200 chr4D 78.693 352 27 20 1460 1803 329666582 329666893 9.460000e-45 191
15 TraesCS7B01G273200 chr4D 79.137 278 36 12 518 790 329665291 329665551 3.430000e-39 172
16 TraesCS7B01G273200 chr4D 83.824 136 12 7 741 876 329665545 329665670 1.260000e-23 121


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 TraesCS7B01G273200 chr7B 501318737 501321325 2588 True 4782.0 4782 100.000 1 2589 1 chr7B.!!$R1 2588
1 TraesCS7B01G273200 chr7D 476758093 476759940 1847 True 2796.0 2796 93.983 1 1858 1 chr7D.!!$R1 1857
2 TraesCS7B01G273200 chr4B 661635436 661636168 732 False 1315.0 1315 99.045 1857 2589 1 chr4B.!!$F1 732
3 TraesCS7B01G273200 chr7A 317173449 317174179 730 True 1312.0 1312 99.042 1859 2589 1 chr7A.!!$R1 730
4 TraesCS7B01G273200 chr7A 519091144 519093035 1891 False 876.5 1184 86.281 6 1847 2 chr7A.!!$F1 1841
5 TraesCS7B01G273200 chr5B 224613901 224614631 730 True 1312.0 1312 99.042 1859 2589 1 chr5B.!!$R1 730
6 TraesCS7B01G273200 chr5B 253176817 253177550 733 False 1306.0 1306 98.774 1856 2589 1 chr5B.!!$F1 733
7 TraesCS7B01G273200 chr5A 180307202 180307932 730 False 1312.0 1312 99.042 1859 2589 1 chr5A.!!$F1 730
8 TraesCS7B01G273200 chr4A 16028940 16029670 730 True 1312.0 1312 99.042 1859 2589 1 chr4A.!!$R1 730
9 TraesCS7B01G273200 chr4A 423442444 423443174 730 True 1306.0 1306 98.906 1859 2589 1 chr4A.!!$R2 730
10 TraesCS7B01G273200 chr6A 384878618 384879348 730 False 1306.0 1306 98.906 1859 2589 1 chr6A.!!$F1 730
11 TraesCS7B01G273200 chr2A 456650539 456651274 735 True 1306.0 1306 98.645 1852 2589 1 chr2A.!!$R1 737


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
812 894 0.179161 CGGTCGGTTGCTACAGAGAG 60.179 60.0 0.93 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 2702 1.13458 CGGAGAGCTTGATGGTGATGT 60.135 52.381 0.0 0.0 0.0 3.06 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
87 89 2.962421 ACATCTCCCTTTTCGGCAAAAA 59.038 40.909 0.00 0.00 35.56 1.94
150 153 3.896648 ACCGAAGTGTGCAAATGTAAG 57.103 42.857 0.00 0.00 0.00 2.34
246 253 2.086869 CAGCGTTGACAGATGGGATTT 58.913 47.619 0.00 0.00 0.00 2.17
247 254 2.096496 CAGCGTTGACAGATGGGATTTC 59.904 50.000 0.00 0.00 0.00 2.17
267 274 2.964978 GCTGAAAAGGGCGCACAT 59.035 55.556 14.57 0.00 0.00 3.21
294 301 2.038295 AGCTGGAAACTCTCTCTTGGTG 59.962 50.000 0.00 0.00 0.00 4.17
319 331 1.349026 CTGTGAAGTGTGATCCCCACT 59.651 52.381 8.84 8.84 45.86 4.00
488 551 2.035530 AGCTCAGCTTCATTGCTACC 57.964 50.000 0.00 0.00 41.98 3.18
624 700 3.951332 CAGTGGTGGTACTGCGTG 58.049 61.111 0.00 0.00 41.31 5.34
708 788 1.213013 GCGACGGAAGCTTCTCTGA 59.787 57.895 25.05 0.00 0.00 3.27
724 804 2.583593 GAGTCGCAGCATCGTCCC 60.584 66.667 0.00 0.00 0.00 4.46
809 891 1.287815 CACGGTCGGTTGCTACAGA 59.712 57.895 0.00 0.00 0.00 3.41
810 892 0.732880 CACGGTCGGTTGCTACAGAG 60.733 60.000 0.93 0.00 0.00 3.35
811 893 0.892358 ACGGTCGGTTGCTACAGAGA 60.892 55.000 0.93 0.00 0.00 3.10
812 894 0.179161 CGGTCGGTTGCTACAGAGAG 60.179 60.000 0.93 0.00 0.00 3.20
813 895 1.174783 GGTCGGTTGCTACAGAGAGA 58.825 55.000 0.93 0.00 0.00 3.10
814 896 1.133407 GGTCGGTTGCTACAGAGAGAG 59.867 57.143 0.93 0.00 0.00 3.20
815 897 2.085320 GTCGGTTGCTACAGAGAGAGA 58.915 52.381 0.93 0.00 0.00 3.10
816 898 2.085320 TCGGTTGCTACAGAGAGAGAC 58.915 52.381 0.00 0.00 0.00 3.36
894 977 4.158579 GCCACCATTAAAGAAAGGAAGGAG 59.841 45.833 0.00 0.00 0.00 3.69
895 978 4.706962 CCACCATTAAAGAAAGGAAGGAGG 59.293 45.833 0.00 0.00 0.00 4.30
1113 1215 0.970937 TCGGTCCTGTTCCTAGCTGG 60.971 60.000 0.00 0.00 37.10 4.85
1475 1589 2.140717 GGTTGACGATCGAAACCTTGT 58.859 47.619 31.85 9.61 40.22 3.16
1485 1599 6.647895 ACGATCGAAACCTTGTATTTTGTAGT 59.352 34.615 24.34 0.00 0.00 2.73
1495 1609 7.717875 ACCTTGTATTTTGTAGTACATGTGTGT 59.282 33.333 9.11 0.00 42.39 3.72
1536 1650 5.491982 ACAGACATGGATTTACTTGTCTCC 58.508 41.667 8.05 0.00 45.19 3.71
1574 1689 2.365293 TCTGCCGCTGCTTCTCATAATA 59.635 45.455 0.70 0.00 38.71 0.98
1595 1710 4.547406 ATGATGTGATTGACATTCGCTG 57.453 40.909 11.11 0.00 45.90 5.18
1597 1712 3.125658 TGATGTGATTGACATTCGCTGTG 59.874 43.478 11.11 0.00 45.90 3.66
1598 1713 1.805943 TGTGATTGACATTCGCTGTGG 59.194 47.619 11.11 0.00 38.54 4.17
1599 1714 2.076100 GTGATTGACATTCGCTGTGGA 58.924 47.619 4.10 0.00 38.54 4.02
1600 1715 2.483877 GTGATTGACATTCGCTGTGGAA 59.516 45.455 4.10 0.00 38.54 3.53
1601 1716 3.127548 GTGATTGACATTCGCTGTGGAAT 59.872 43.478 4.10 0.00 38.54 3.01
1602 1717 3.758023 TGATTGACATTCGCTGTGGAATT 59.242 39.130 0.00 0.00 38.54 2.17
1603 1718 3.829886 TTGACATTCGCTGTGGAATTC 57.170 42.857 0.00 0.00 38.54 2.17
1763 1901 1.137872 GTGATGATCCCGAGAAGCACT 59.862 52.381 0.00 0.00 0.00 4.40
1808 1951 6.094603 ACAGGATTTTCTCATGATTGTACTGC 59.905 38.462 0.00 0.00 37.89 4.40
1847 1990 3.366171 CCATGCGATGTTTGTTCATGTGA 60.366 43.478 0.00 0.00 34.36 3.58
1848 1991 3.978718 TGCGATGTTTGTTCATGTGAA 57.021 38.095 0.00 0.00 0.00 3.18
2129 2272 1.071814 GCCACCACCGGTTTCACTA 59.928 57.895 2.97 0.00 31.02 2.74
2559 2702 1.790755 CCGTTTCACTTCGGTCATCA 58.209 50.000 0.00 0.00 41.58 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.233757 GCCTAATCTCCAATCTAGAAAGTAGGA 59.766 40.741 0.00 0.00 32.76 2.94
87 89 6.880942 TTAATTGCCGGTACTACAACTTTT 57.119 33.333 1.90 0.00 0.00 2.27
88 90 6.262720 TGTTTAATTGCCGGTACTACAACTTT 59.737 34.615 1.90 0.00 0.00 2.66
132 135 4.211389 GTGTCTTACATTTGCACACTTCG 58.789 43.478 0.00 0.00 35.50 3.79
207 214 4.684485 CGCTGGATGGAGTAAAGAGGAATT 60.684 45.833 0.00 0.00 0.00 2.17
267 274 7.106239 CCAAGAGAGAGTTTCCAGCTAATTTA 58.894 38.462 0.00 0.00 0.00 1.40
294 301 1.160137 GATCACACTTCACAGGCACC 58.840 55.000 0.00 0.00 0.00 5.01
624 700 3.127352 CTCGTACCTCTCTGGGCGC 62.127 68.421 0.00 0.00 41.11 6.53
708 788 3.071206 AGGGACGATGCTGCGACT 61.071 61.111 5.82 0.00 34.83 4.18
724 804 2.230025 CCTCGCATCCATCTAGTACCAG 59.770 54.545 0.00 0.00 0.00 4.00
809 891 4.614475 TCTCTCTCTCTCTCTGTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
810 892 5.069648 TGATCTCTCTCTCTCTCTGTCTCTC 59.930 48.000 0.00 0.00 0.00 3.20
811 893 4.964897 TGATCTCTCTCTCTCTCTGTCTCT 59.035 45.833 0.00 0.00 0.00 3.10
812 894 5.282055 TGATCTCTCTCTCTCTCTGTCTC 57.718 47.826 0.00 0.00 0.00 3.36
813 895 4.444022 GCTGATCTCTCTCTCTCTCTGTCT 60.444 50.000 0.00 0.00 0.00 3.41
814 896 3.812053 GCTGATCTCTCTCTCTCTCTGTC 59.188 52.174 0.00 0.00 0.00 3.51
815 897 3.457380 AGCTGATCTCTCTCTCTCTCTGT 59.543 47.826 0.00 0.00 0.00 3.41
816 898 3.813724 CAGCTGATCTCTCTCTCTCTCTG 59.186 52.174 8.42 0.00 0.00 3.35
848 931 0.390472 CCCTCTTCTCTCGCAACACC 60.390 60.000 0.00 0.00 0.00 4.16
851 934 1.448717 GGCCCTCTTCTCTCGCAAC 60.449 63.158 0.00 0.00 0.00 4.17
852 935 1.610673 AGGCCCTCTTCTCTCGCAA 60.611 57.895 0.00 0.00 0.00 4.85
894 977 3.151022 CTGGCCGTCTCCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
895 978 2.363147 ACTGGCCGTCTCCTCCTC 60.363 66.667 0.00 0.00 0.00 3.71
1188 1290 3.069318 GGGCTCGGACTCGGAGTT 61.069 66.667 12.67 0.00 36.95 3.01
1475 1589 9.549078 TTCTTCACACACATGTACTACAAAATA 57.451 29.630 0.00 0.00 36.72 1.40
1485 1599 4.452114 GTGCAGATTCTTCACACACATGTA 59.548 41.667 10.98 0.00 36.72 2.29
1495 1609 1.699083 TGTCCCAGTGCAGATTCTTCA 59.301 47.619 0.00 0.00 0.00 3.02
1536 1650 2.675519 GAGCATCTGCGTCAGAAGG 58.324 57.895 12.43 9.48 44.04 3.46
1574 1689 3.943381 ACAGCGAATGTCAATCACATCAT 59.057 39.130 0.00 0.00 45.77 2.45
1595 1710 3.064545 CAGAAGAAGCATCCGAATTCCAC 59.935 47.826 0.00 0.00 0.00 4.02
1597 1712 3.535561 TCAGAAGAAGCATCCGAATTCC 58.464 45.455 0.00 0.00 0.00 3.01
1598 1713 4.437239 TCTCAGAAGAAGCATCCGAATTC 58.563 43.478 0.00 0.00 0.00 2.17
1599 1714 4.478206 TCTCAGAAGAAGCATCCGAATT 57.522 40.909 0.00 0.00 0.00 2.17
1600 1715 4.478206 TTCTCAGAAGAAGCATCCGAAT 57.522 40.909 0.00 0.00 36.59 3.34
1601 1716 3.961480 TTCTCAGAAGAAGCATCCGAA 57.039 42.857 0.00 0.00 36.59 4.30
1703 1835 3.671928 GCTGTACTGTAACCACGTACTTG 59.328 47.826 1.46 0.00 36.49 3.16
1763 1901 2.395360 GCAATTACAGCGCACCGGA 61.395 57.895 9.46 0.00 0.00 5.14
1795 1938 3.119743 CCAACCACAGCAGTACAATCATG 60.120 47.826 0.00 0.00 0.00 3.07
2559 2702 1.134580 CGGAGAGCTTGATGGTGATGT 60.135 52.381 0.00 0.00 0.00 3.06



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

AutoCloner maintained by Alex Coulton.