Multiple sequence alignment - TraesCS4A01G472900

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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 TraesCS4A01G472900 chr4A 100.000 2297 0 0 1 2297 732918817 732921113 0 4242
1 TraesCS4A01G472900 chr4A 97.564 862 21 0 3 864 702869742 702868881 0 1476
2 TraesCS4A01G472900 chr4A 90.609 788 66 6 912 1692 742890032 742889246 0 1038
3 TraesCS4A01G472900 chr4B 97.567 863 21 0 3 865 593142366 593141504 0 1478
4 TraesCS4A01G472900 chr4B 97.448 862 22 0 3 864 323836418 323835557 0 1471
5 TraesCS4A01G472900 chr4B 89.721 788 72 6 912 1692 640482137 640482922 0 998
6 TraesCS4A01G472900 chr1B 97.564 862 21 0 3 864 600010631 600011492 0 1476
7 TraesCS4A01G472900 chr1B 97.558 860 21 0 3 862 569557301 569558160 0 1472
8 TraesCS4A01G472900 chr7B 97.564 862 20 1 3 864 687159599 687160459 0 1474
9 TraesCS4A01G472900 chr7B 96.807 877 27 1 3 879 375112474 375111599 0 1463
10 TraesCS4A01G472900 chr7B 89.003 782 77 9 912 1692 504953352 504952579 0 959
11 TraesCS4A01G472900 chr6B 97.448 862 22 0 3 864 698484238 698483377 0 1471
12 TraesCS4A01G472900 chr5B 97.448 862 22 0 3 864 577779396 577778535 0 1471
13 TraesCS4A01G472900 chr5B 90.269 781 71 4 912 1692 633760978 633761753 0 1016
14 TraesCS4A01G472900 chr5B 89.822 786 71 5 912 1690 691759155 691758372 0 1000
15 TraesCS4A01G472900 chr5B 89.367 790 72 7 912 1692 556717530 556718316 0 983
16 TraesCS4A01G472900 chr2B 89.974 778 69 5 922 1692 735935205 735934430 0 996
17 TraesCS4A01G472900 chr1D 89.629 781 72 3 912 1692 251717841 251717070 0 985
18 TraesCS4A01G472900 chr1D 89.427 785 73 4 912 1692 474021192 474020414 0 981
19 TraesCS4A01G472900 chr7D 95.410 610 27 1 1689 2297 133270641 133271250 0 970
20 TraesCS4A01G472900 chr7D 95.530 604 26 1 1693 2295 183525055 183525658 0 965
21 TraesCS4A01G472900 chr7D 95.230 608 28 1 1691 2297 451643101 451643708 0 961
22 TraesCS4A01G472900 chr4D 95.695 604 25 1 1695 2297 373785520 373786123 0 970
23 TraesCS4A01G472900 chr4D 95.372 605 27 1 1694 2297 124182576 124183180 0 961
24 TraesCS4A01G472900 chr4D 95.372 605 27 1 1694 2297 495747833 495748437 0 961
25 TraesCS4A01G472900 chr3D 95.269 613 27 2 1687 2297 442819742 442820354 0 970
26 TraesCS4A01G472900 chr5D 95.530 604 26 1 1695 2297 57617848 57617245 0 965
27 TraesCS4A01G472900 chr2D 95.530 604 26 1 1695 2297 27733074 27733677 0 965


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 TraesCS4A01G472900 chr4A 732918817 732921113 2296 False 4242 4242 100.000 1 2297 1 chr4A.!!$F1 2296
1 TraesCS4A01G472900 chr4A 702868881 702869742 861 True 1476 1476 97.564 3 864 1 chr4A.!!$R1 861
2 TraesCS4A01G472900 chr4A 742889246 742890032 786 True 1038 1038 90.609 912 1692 1 chr4A.!!$R2 780
3 TraesCS4A01G472900 chr4B 593141504 593142366 862 True 1478 1478 97.567 3 865 1 chr4B.!!$R2 862
4 TraesCS4A01G472900 chr4B 323835557 323836418 861 True 1471 1471 97.448 3 864 1 chr4B.!!$R1 861
5 TraesCS4A01G472900 chr4B 640482137 640482922 785 False 998 998 89.721 912 1692 1 chr4B.!!$F1 780
6 TraesCS4A01G472900 chr1B 600010631 600011492 861 False 1476 1476 97.564 3 864 1 chr1B.!!$F2 861
7 TraesCS4A01G472900 chr1B 569557301 569558160 859 False 1472 1472 97.558 3 862 1 chr1B.!!$F1 859
8 TraesCS4A01G472900 chr7B 687159599 687160459 860 False 1474 1474 97.564 3 864 1 chr7B.!!$F1 861
9 TraesCS4A01G472900 chr7B 375111599 375112474 875 True 1463 1463 96.807 3 879 1 chr7B.!!$R1 876
10 TraesCS4A01G472900 chr7B 504952579 504953352 773 True 959 959 89.003 912 1692 1 chr7B.!!$R2 780
11 TraesCS4A01G472900 chr6B 698483377 698484238 861 True 1471 1471 97.448 3 864 1 chr6B.!!$R1 861
12 TraesCS4A01G472900 chr5B 577778535 577779396 861 True 1471 1471 97.448 3 864 1 chr5B.!!$R1 861
13 TraesCS4A01G472900 chr5B 633760978 633761753 775 False 1016 1016 90.269 912 1692 1 chr5B.!!$F2 780
14 TraesCS4A01G472900 chr5B 691758372 691759155 783 True 1000 1000 89.822 912 1690 1 chr5B.!!$R2 778
15 TraesCS4A01G472900 chr5B 556717530 556718316 786 False 983 983 89.367 912 1692 1 chr5B.!!$F1 780
16 TraesCS4A01G472900 chr2B 735934430 735935205 775 True 996 996 89.974 922 1692 1 chr2B.!!$R1 770
17 TraesCS4A01G472900 chr1D 251717070 251717841 771 True 985 985 89.629 912 1692 1 chr1D.!!$R1 780
18 TraesCS4A01G472900 chr1D 474020414 474021192 778 True 981 981 89.427 912 1692 1 chr1D.!!$R2 780
19 TraesCS4A01G472900 chr7D 133270641 133271250 609 False 970 970 95.410 1689 2297 1 chr7D.!!$F1 608
20 TraesCS4A01G472900 chr7D 183525055 183525658 603 False 965 965 95.530 1693 2295 1 chr7D.!!$F2 602
21 TraesCS4A01G472900 chr7D 451643101 451643708 607 False 961 961 95.230 1691 2297 1 chr7D.!!$F3 606
22 TraesCS4A01G472900 chr4D 373785520 373786123 603 False 970 970 95.695 1695 2297 1 chr4D.!!$F2 602
23 TraesCS4A01G472900 chr4D 124182576 124183180 604 False 961 961 95.372 1694 2297 1 chr4D.!!$F1 603
24 TraesCS4A01G472900 chr4D 495747833 495748437 604 False 961 961 95.372 1694 2297 1 chr4D.!!$F3 603
25 TraesCS4A01G472900 chr3D 442819742 442820354 612 False 970 970 95.269 1687 2297 1 chr3D.!!$F1 610
26 TraesCS4A01G472900 chr5D 57617245 57617848 603 True 965 965 95.530 1695 2297 1 chr5D.!!$R1 602
27 TraesCS4A01G472900 chr2D 27733074 27733677 603 False 965 965 95.530 1695 2297 1 chr2D.!!$F1 602

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
908 910 0.112218 TGGGATCTGGTGGTTGTTGG 59.888 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2055 2.492025 ACTGGTCCACCCACATATCAT 58.508 47.619 0.0 0.0 38.72 2.45 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
333 335 2.044946 GAGGAACCCGCCTTGCAT 60.045 61.111 0.00 0.00 38.73 3.96
607 609 5.078256 CCCTCTCCGGTGTCTATATAAACT 58.922 45.833 0.00 0.00 0.00 2.66
608 610 6.243900 CCCTCTCCGGTGTCTATATAAACTA 58.756 44.000 0.00 0.00 0.00 2.24
613 615 8.162085 TCTCCGGTGTCTATATAAACTAGATGT 58.838 37.037 0.00 0.00 0.00 3.06
629 631 9.440761 AAACTAGATGTCTTTAGTCCATAGGAT 57.559 33.333 0.00 0.00 32.73 3.24
866 868 1.652563 GGTTTTGACACCGACAGCC 59.347 57.895 0.00 0.00 0.00 4.85
898 900 4.996434 GCGGGCGATGGGATCTGG 62.996 72.222 0.00 0.00 0.00 3.86
899 901 3.550431 CGGGCGATGGGATCTGGT 61.550 66.667 0.00 0.00 0.00 4.00
900 902 2.111878 GGGCGATGGGATCTGGTG 59.888 66.667 0.00 0.00 0.00 4.17
901 903 2.111878 GGCGATGGGATCTGGTGG 59.888 66.667 0.00 0.00 0.00 4.61
902 904 2.746375 GGCGATGGGATCTGGTGGT 61.746 63.158 0.00 0.00 0.00 4.16
903 905 1.224592 GCGATGGGATCTGGTGGTT 59.775 57.895 0.00 0.00 0.00 3.67
904 906 1.097547 GCGATGGGATCTGGTGGTTG 61.098 60.000 0.00 0.00 0.00 3.77
905 907 0.253044 CGATGGGATCTGGTGGTTGT 59.747 55.000 0.00 0.00 0.00 3.32
906 908 1.340017 CGATGGGATCTGGTGGTTGTT 60.340 52.381 0.00 0.00 0.00 2.83
907 909 2.094675 GATGGGATCTGGTGGTTGTTG 58.905 52.381 0.00 0.00 0.00 3.33
908 910 0.112218 TGGGATCTGGTGGTTGTTGG 59.888 55.000 0.00 0.00 0.00 3.77
909 911 1.250840 GGGATCTGGTGGTTGTTGGC 61.251 60.000 0.00 0.00 0.00 4.52
910 912 1.586154 GGATCTGGTGGTTGTTGGCG 61.586 60.000 0.00 0.00 0.00 5.69
934 936 2.997315 CGCCACTCCTCCTCACCA 60.997 66.667 0.00 0.00 0.00 4.17
1095 1104 2.358247 CACGGCCGGCTAACAGTT 60.358 61.111 31.76 0.57 0.00 3.16
1166 1185 2.126228 CGTTGGCGGCGTCTTCTA 60.126 61.111 14.51 0.00 0.00 2.10
1315 1334 2.598787 TTCGGGCGAAATCCCTGGT 61.599 57.895 0.00 0.00 44.30 4.00
1317 1336 2.674754 GGGCGAAATCCCTGGTCA 59.325 61.111 0.00 0.00 43.13 4.02
1364 1383 2.045045 CTGAGGGCGCCATTTCCA 60.045 61.111 30.85 15.11 0.00 3.53
1496 1515 4.634703 TGAAGGCGCCGCTTTGGA 62.635 61.111 23.20 0.00 42.00 3.53
1501 1520 3.972276 GCGCCGCTTTGGAAACCA 61.972 61.111 0.00 0.00 42.00 3.67
1563 1582 1.453928 GCGGCCCTTTCCTAGCATT 60.454 57.895 0.00 0.00 0.00 3.56
1564 1583 0.179029 GCGGCCCTTTCCTAGCATTA 60.179 55.000 0.00 0.00 0.00 1.90
1609 1628 1.968493 GAGTTGTGTAGGTGGAGGTCA 59.032 52.381 0.00 0.00 0.00 4.02
1713 1732 5.127194 GTGACTGATGACCCACAAGTATAGA 59.873 44.000 0.00 0.00 0.00 1.98
1767 1786 1.079127 CGAACCCAACGAGGAGCAT 60.079 57.895 0.00 0.00 41.22 3.79
1900 1920 0.467106 TAAAGTGCAGCAAGGTGGCA 60.467 50.000 0.00 0.00 35.83 4.92
1991 2011 5.527214 CACATGGGAATTATCGTCAAGCTAA 59.473 40.000 0.00 0.00 0.00 3.09
2009 2029 6.925610 AGCTAATTTTCATCACGCTCATAA 57.074 33.333 0.00 0.00 0.00 1.90
2016 2036 4.307443 TCATCACGCTCATAAGATTCGT 57.693 40.909 0.00 0.00 34.60 3.85
2026 2046 5.287752 GCTCATAAGATTCGTGTTCGTTACA 59.712 40.000 0.00 0.00 38.33 2.41
2035 2055 9.524106 AGATTCGTGTTCGTTACATTGATAATA 57.476 29.630 0.00 0.00 39.39 0.98
2119 2139 2.834638 AACCCCTATTGCAAGCATCT 57.165 45.000 4.94 0.00 0.00 2.90
2184 2204 6.964807 TGAAACATATGGATCCAAATCAGG 57.035 37.500 20.67 8.70 33.21 3.86
2187 2207 2.566833 TATGGATCCAAATCAGGCCG 57.433 50.000 20.67 0.00 33.21 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.154205 CGGCGCTTGGGAGATAAGTG 61.154 60.000 7.64 0.00 38.38 3.16
1 2 1.144057 CGGCGCTTGGGAGATAAGT 59.856 57.895 7.64 0.00 0.00 2.24
134 136 7.598493 CGAATTGTTTTTATTGTTCCACCTCAT 59.402 33.333 0.00 0.00 0.00 2.90
333 335 0.376852 GCGCATATTGTCTTCGGCAA 59.623 50.000 0.30 0.00 0.00 4.52
607 609 8.861086 GTTCATCCTATGGACTAAAGACATCTA 58.139 37.037 0.00 0.00 35.82 1.98
608 610 7.345653 TGTTCATCCTATGGACTAAAGACATCT 59.654 37.037 0.33 0.00 39.59 2.90
613 615 7.252612 TGTTGTTCATCCTATGGACTAAAGA 57.747 36.000 0.33 0.00 39.59 2.52
629 631 5.754782 AGCCTATGGTATGATTGTTGTTCA 58.245 37.500 0.00 0.00 0.00 3.18
881 883 4.996434 CCAGATCCCATCGCCCGC 62.996 72.222 0.00 0.00 0.00 6.13
882 884 3.550431 ACCAGATCCCATCGCCCG 61.550 66.667 0.00 0.00 0.00 6.13
883 885 2.111878 CACCAGATCCCATCGCCC 59.888 66.667 0.00 0.00 0.00 6.13
884 886 2.111878 CCACCAGATCCCATCGCC 59.888 66.667 0.00 0.00 0.00 5.54
885 887 1.097547 CAACCACCAGATCCCATCGC 61.098 60.000 0.00 0.00 0.00 4.58
886 888 0.253044 ACAACCACCAGATCCCATCG 59.747 55.000 0.00 0.00 0.00 3.84
887 889 2.094675 CAACAACCACCAGATCCCATC 58.905 52.381 0.00 0.00 0.00 3.51
888 890 1.272648 CCAACAACCACCAGATCCCAT 60.273 52.381 0.00 0.00 0.00 4.00
889 891 0.112218 CCAACAACCACCAGATCCCA 59.888 55.000 0.00 0.00 0.00 4.37
890 892 1.250840 GCCAACAACCACCAGATCCC 61.251 60.000 0.00 0.00 0.00 3.85
891 893 1.586154 CGCCAACAACCACCAGATCC 61.586 60.000 0.00 0.00 0.00 3.36
892 894 1.875963 CGCCAACAACCACCAGATC 59.124 57.895 0.00 0.00 0.00 2.75
893 895 2.268076 GCGCCAACAACCACCAGAT 61.268 57.895 0.00 0.00 0.00 2.90
894 896 2.904866 GCGCCAACAACCACCAGA 60.905 61.111 0.00 0.00 0.00 3.86
895 897 3.977244 GGCGCCAACAACCACCAG 61.977 66.667 24.80 0.00 0.00 4.00
896 898 3.121406 TAGGCGCCAACAACCACCA 62.121 57.895 31.54 0.00 0.00 4.17
897 899 2.281900 TAGGCGCCAACAACCACC 60.282 61.111 31.54 0.00 0.00 4.61
898 900 2.978018 GCTAGGCGCCAACAACCAC 61.978 63.158 31.54 4.76 0.00 4.16
899 901 2.671619 GCTAGGCGCCAACAACCA 60.672 61.111 31.54 2.99 0.00 3.67
910 912 4.228567 GAGGAGTGGCGGCTAGGC 62.229 72.222 11.43 6.15 46.95 3.93
934 936 3.369388 GAGGGAGGAGGGGAGGGT 61.369 72.222 0.00 0.00 0.00 4.34
1019 1027 2.113774 CACAGGAGCAGGGCAACA 59.886 61.111 0.00 0.00 39.74 3.33
1095 1104 4.028490 GGATCCACCACCCGCACA 62.028 66.667 6.95 0.00 38.79 4.57
1159 1178 1.471684 ACATCGACCACCGTAGAAGAC 59.528 52.381 0.00 0.00 39.75 3.01
1248 1267 0.600782 GTACAGAACCGGCGACCAAA 60.601 55.000 9.30 0.00 0.00 3.28
1288 1307 3.492829 GGATTTCGCCCGAACTAGATCTT 60.493 47.826 0.00 0.00 33.41 2.40
1334 1353 3.785499 CTCAGTCGTCGCCGTCGA 61.785 66.667 1.66 1.66 43.28 4.20
1346 1365 2.044946 GGAAATGGCGCCCTCAGT 60.045 61.111 26.77 0.30 0.00 3.41
1364 1383 1.349026 CATACCGATGCCTCCAAGGAT 59.651 52.381 0.00 0.00 37.67 3.24
1474 1493 2.010582 AAAGCGGCGCCTTCACAAAA 62.011 50.000 30.40 0.00 0.00 2.44
1477 1496 3.659092 CAAAGCGGCGCCTTCACA 61.659 61.111 30.40 0.00 0.00 3.58
1478 1497 4.404654 CCAAAGCGGCGCCTTCAC 62.405 66.667 30.40 11.27 0.00 3.18
1650 1669 1.576356 CTCCACCTATGCGAGCTTTC 58.424 55.000 0.00 0.00 0.00 2.62
1653 1672 1.381872 ACCTCCACCTATGCGAGCT 60.382 57.895 0.00 0.00 0.00 4.09
1713 1732 4.970711 TCGAAAGGACTACGATAGATCCT 58.029 43.478 0.00 0.61 37.69 3.24
1767 1786 4.580995 TGAAAACCGCTTGTCATTTCCTTA 59.419 37.500 0.00 0.00 30.80 2.69
1936 1956 7.201617 CGGGAGTGTTTTCCTTCATATAAGAAC 60.202 40.741 0.00 0.00 37.40 3.01
1937 1957 6.821665 CGGGAGTGTTTTCCTTCATATAAGAA 59.178 38.462 0.00 0.00 37.40 2.52
1991 2011 6.258727 ACGAATCTTATGAGCGTGATGAAAAT 59.741 34.615 8.03 0.00 36.36 1.82
2009 2029 7.821595 TTATCAATGTAACGAACACGAATCT 57.178 32.000 0.00 0.00 42.09 2.40
2026 2046 8.055181 GGTCCACCCACATATCATATTATCAAT 58.945 37.037 0.00 0.00 0.00 2.57
2035 2055 2.492025 ACTGGTCCACCCACATATCAT 58.508 47.619 0.00 0.00 38.72 2.45
2142 2162 6.943146 TGTTTCATGCTATGGTTAGGTTTACA 59.057 34.615 0.00 0.00 0.00 2.41
2187 2207 4.061570 AGTTTATGCGTTGCTTCGTAAC 57.938 40.909 0.00 0.00 0.00 2.50
2222 2242 2.840038 TGATGGGTTGCTAGAGTGACAT 59.160 45.455 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.