Multiple sequence alignment - TraesCS3A01G536700

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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 TraesCS3A01G536700 chr3A 100.000 3404 0 0 1 3404 748233515 748236918 0.000000e+00 6287.0
1 TraesCS3A01G536700 chr3A 97.709 2488 39 4 919 3404 750213195 750215666 0.000000e+00 4263.0
2 TraesCS3A01G536700 chr3A 94.655 898 45 3 1 897 489603199 489602304 0.000000e+00 1389.0
3 TraesCS3A01G536700 chr3A 94.549 899 46 3 1 898 686233493 686234389 0.000000e+00 1386.0
4 TraesCS3A01G536700 chr3A 91.111 135 12 0 1564 1698 739542986 739542852 2.090000e-42 183.0
5 TraesCS3A01G536700 chr3A 72.020 604 133 29 1795 2386 740333684 740333105 2.740000e-31 147.0
6 TraesCS3A01G536700 chr3D 92.303 1507 105 4 1223 2726 614667887 614669385 0.000000e+00 2130.0
7 TraesCS3A01G536700 chr3D 88.327 1405 158 3 1123 2521 607080614 607079210 0.000000e+00 1681.0
8 TraesCS3A01G536700 chr3D 70.770 1259 291 59 1155 2386 608038393 608037185 7.400000e-52 215.0
9 TraesCS3A01G536700 chr3D 84.706 170 19 1 3146 3308 614643943 614644112 2.720000e-36 163.0
10 TraesCS3A01G536700 chr3D 96.774 93 3 0 2776 2868 614669945 614670037 4.550000e-34 156.0
11 TraesCS3A01G536700 chr3D 97.826 46 1 0 2726 2771 614669910 614669955 2.820000e-11 80.5
12 TraesCS3A01G536700 chr3B 92.119 1510 112 2 919 2422 813311694 813313202 0.000000e+00 2122.0
13 TraesCS3A01G536700 chr3B 85.865 1613 204 17 1123 2726 816548863 816547266 0.000000e+00 1694.0
14 TraesCS3A01G536700 chr3B 90.050 995 80 8 1741 2733 825253366 825254343 0.000000e+00 1271.0
15 TraesCS3A01G536700 chr3B 92.453 265 19 1 925 1189 825272684 825272421 8.920000e-101 377.0
16 TraesCS3A01G536700 chr3B 87.342 79 10 0 3205 3283 825367733 825367811 1.300000e-14 91.6
17 TraesCS3A01G536700 chr6A 95.652 897 37 2 1 897 80791736 80792630 0.000000e+00 1439.0
18 TraesCS3A01G536700 chr6A 95.100 898 42 2 1 897 251805081 251804185 0.000000e+00 1413.0
19 TraesCS3A01G536700 chr6A 94.537 897 44 3 2 898 433955678 433956569 0.000000e+00 1380.0
20 TraesCS3A01G536700 chr5A 95.089 896 43 1 2 897 500951373 500952267 0.000000e+00 1410.0
21 TraesCS3A01G536700 chr5A 94.649 897 47 1 1 897 585381525 585380630 0.000000e+00 1389.0
22 TraesCS3A01G536700 chr5A 94.144 905 51 2 1 905 143476169 143477071 0.000000e+00 1376.0
23 TraesCS3A01G536700 chr1A 94.889 900 46 0 1 900 264119996 264119097 0.000000e+00 1408.0
24 TraesCS3A01G536700 chr2A 98.571 70 1 0 3329 3398 35998232 35998163 1.280000e-24 124.0
25 TraesCS3A01G536700 chrUn 85.965 114 9 1 3205 3311 41130896 41130783 7.720000e-22 115.0


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 TraesCS3A01G536700 chr3A 748233515 748236918 3403 False 6287.000000 6287 100.000000 1 3404 1 chr3A.!!$F2 3403
1 TraesCS3A01G536700 chr3A 750213195 750215666 2471 False 4263.000000 4263 97.709000 919 3404 1 chr3A.!!$F3 2485
2 TraesCS3A01G536700 chr3A 489602304 489603199 895 True 1389.000000 1389 94.655000 1 897 1 chr3A.!!$R1 896
3 TraesCS3A01G536700 chr3A 686233493 686234389 896 False 1386.000000 1386 94.549000 1 898 1 chr3A.!!$F1 897
4 TraesCS3A01G536700 chr3D 607079210 607080614 1404 True 1681.000000 1681 88.327000 1123 2521 1 chr3D.!!$R1 1398
5 TraesCS3A01G536700 chr3D 614667887 614670037 2150 False 788.833333 2130 95.634333 1223 2868 3 chr3D.!!$F2 1645
6 TraesCS3A01G536700 chr3D 608037185 608038393 1208 True 215.000000 215 70.770000 1155 2386 1 chr3D.!!$R2 1231
7 TraesCS3A01G536700 chr3B 813311694 813313202 1508 False 2122.000000 2122 92.119000 919 2422 1 chr3B.!!$F1 1503
8 TraesCS3A01G536700 chr3B 816547266 816548863 1597 True 1694.000000 1694 85.865000 1123 2726 1 chr3B.!!$R1 1603
9 TraesCS3A01G536700 chr3B 825253366 825254343 977 False 1271.000000 1271 90.050000 1741 2733 1 chr3B.!!$F2 992
10 TraesCS3A01G536700 chr6A 80791736 80792630 894 False 1439.000000 1439 95.652000 1 897 1 chr6A.!!$F1 896
11 TraesCS3A01G536700 chr6A 251804185 251805081 896 True 1413.000000 1413 95.100000 1 897 1 chr6A.!!$R1 896
12 TraesCS3A01G536700 chr6A 433955678 433956569 891 False 1380.000000 1380 94.537000 2 898 1 chr6A.!!$F2 896
13 TraesCS3A01G536700 chr5A 500951373 500952267 894 False 1410.000000 1410 95.089000 2 897 1 chr5A.!!$F2 895
14 TraesCS3A01G536700 chr5A 585380630 585381525 895 True 1389.000000 1389 94.649000 1 897 1 chr5A.!!$R1 896
15 TraesCS3A01G536700 chr5A 143476169 143477071 902 False 1376.000000 1376 94.144000 1 905 1 chr5A.!!$F1 904
16 TraesCS3A01G536700 chr1A 264119097 264119996 899 True 1408.000000 1408 94.889000 1 900 1 chr1A.!!$R1 899

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
534 540 0.398696 TGCGTGAATAACAGGGGTGT 59.601 50.0 0.00 0.0 35.28 4.16 F
1192 1202 0.032615 ACCTCCTGCTCGAGATCCTT 60.033 55.0 18.75 0.0 30.97 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1866 2.432456 GACTGCGCATCACCGTCA 60.432 61.111 12.24 0.0 0.0 4.35 R
2593 2628 1.168714 GTTGGAGATGTCTTGCCACC 58.831 55.000 0.00 0.0 0.0 4.61 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
271 272 2.035832 CCACCAAAACTCCGCAAGAAAT 59.964 45.455 0.00 0.00 43.02 2.17
459 465 0.543174 ACGAGTTCAGGCCCTTCTCT 60.543 55.000 0.00 0.00 0.00 3.10
517 523 1.069906 GGTCGATTGGATTATGCGTGC 60.070 52.381 0.00 0.00 0.00 5.34
534 540 0.398696 TGCGTGAATAACAGGGGTGT 59.601 50.000 0.00 0.00 35.28 4.16
660 668 3.263937 TGGTAACGCCCCTAATAAAGTGT 59.736 43.478 0.00 0.00 42.51 3.55
700 708 5.422145 ACTATTTAATAGCCGACCGTTTGT 58.578 37.500 11.50 0.00 36.30 2.83
724 732 2.943449 GGAGTGACTTTAGGTCTCCG 57.057 55.000 0.00 0.00 44.74 4.63
748 756 1.899814 AGTCGAGTGGTTGGCTTCATA 59.100 47.619 0.00 0.00 0.00 2.15
837 845 4.479786 AGGTGACTTCTTCTAAGGATGC 57.520 45.455 0.00 0.00 37.44 3.91
889 897 3.403394 TGCCCATACCCTAGGTACATAGA 59.597 47.826 15.94 0.00 41.31 1.98
905 913 3.960755 ACATAGATTCATCACTCGGTCCA 59.039 43.478 0.00 0.00 0.00 4.02
906 914 4.405680 ACATAGATTCATCACTCGGTCCAA 59.594 41.667 0.00 0.00 0.00 3.53
907 915 5.070981 ACATAGATTCATCACTCGGTCCAAT 59.929 40.000 0.00 0.00 0.00 3.16
908 916 6.267699 ACATAGATTCATCACTCGGTCCAATA 59.732 38.462 0.00 0.00 0.00 1.90
909 917 5.815233 AGATTCATCACTCGGTCCAATAT 57.185 39.130 0.00 0.00 0.00 1.28
910 918 6.918067 AGATTCATCACTCGGTCCAATATA 57.082 37.500 0.00 0.00 0.00 0.86
911 919 6.692486 AGATTCATCACTCGGTCCAATATAC 58.308 40.000 0.00 0.00 0.00 1.47
912 920 4.866508 TCATCACTCGGTCCAATATACC 57.133 45.455 0.00 0.00 0.00 2.73
913 921 4.480115 TCATCACTCGGTCCAATATACCT 58.520 43.478 0.00 0.00 34.66 3.08
914 922 4.523173 TCATCACTCGGTCCAATATACCTC 59.477 45.833 0.00 0.00 34.66 3.85
915 923 3.905968 TCACTCGGTCCAATATACCTCA 58.094 45.455 0.00 0.00 34.66 3.86
916 924 4.283337 TCACTCGGTCCAATATACCTCAA 58.717 43.478 0.00 0.00 34.66 3.02
917 925 4.098960 TCACTCGGTCCAATATACCTCAAC 59.901 45.833 0.00 0.00 34.66 3.18
1000 1008 1.200484 CCCAACATAAAACGAACCCCG 59.800 52.381 0.00 0.00 45.44 5.73
1004 1012 2.988570 ACATAAAACGAACCCCGCATA 58.011 42.857 0.00 0.00 43.32 3.14
1096 1106 4.331137 CCGAACGAAGTATACGACGTTAA 58.669 43.478 28.33 0.00 45.00 2.01
1099 1109 5.388004 CGAACGAAGTATACGACGTTAAGAG 59.612 44.000 28.33 20.26 45.00 2.85
1119 1129 3.380393 AGGCCAAATTAATAACACCCCC 58.620 45.455 5.01 0.00 0.00 5.40
1192 1202 0.032615 ACCTCCTGCTCGAGATCCTT 60.033 55.000 18.75 0.00 30.97 3.36
1840 1866 2.224784 GGACGAACGTACCAATTGCTTT 59.775 45.455 0.00 0.00 0.00 3.51
2593 2628 1.743321 GCGTCCCCTCTCATCTCCTG 61.743 65.000 0.00 0.00 0.00 3.86
2737 3299 8.514330 AAGGAGAAACAATGTACTGTTTTACA 57.486 30.769 12.83 0.00 46.84 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.677966 CGAGACTTCGGAGGTGGGA 60.678 63.158 0.00 0.00 43.05 4.37
459 465 1.822990 CGTAGGGCTGTTACTTCCTCA 59.177 52.381 0.00 0.00 0.00 3.86
517 523 2.465860 TCACACCCCTGTTATTCACG 57.534 50.000 0.00 0.00 0.00 4.35
700 708 1.544691 GACCTAAAGTCACTCCGCAGA 59.455 52.381 0.00 0.00 45.55 4.26
724 732 2.358737 CCAACCACTCGACTGCCC 60.359 66.667 0.00 0.00 0.00 5.36
748 756 3.093057 ACCAAGAAGCTATCACTCGACT 58.907 45.455 0.00 0.00 0.00 4.18
872 880 8.402683 AGTGATGAATCTATGTACCTAGGGTAT 58.597 37.037 14.81 6.81 40.54 2.73
889 897 5.544176 AGGTATATTGGACCGAGTGATGAAT 59.456 40.000 0.00 0.00 42.21 2.57
905 913 6.412362 AGCAGAGATTCGTTGAGGTATATT 57.588 37.500 0.00 0.00 0.00 1.28
906 914 6.040955 TCAAGCAGAGATTCGTTGAGGTATAT 59.959 38.462 0.00 0.00 0.00 0.86
907 915 5.359860 TCAAGCAGAGATTCGTTGAGGTATA 59.640 40.000 0.00 0.00 0.00 1.47
908 916 4.160439 TCAAGCAGAGATTCGTTGAGGTAT 59.840 41.667 0.00 0.00 0.00 2.73
909 917 3.509967 TCAAGCAGAGATTCGTTGAGGTA 59.490 43.478 0.00 0.00 0.00 3.08
910 918 2.300152 TCAAGCAGAGATTCGTTGAGGT 59.700 45.455 0.00 0.00 0.00 3.85
911 919 2.964740 TCAAGCAGAGATTCGTTGAGG 58.035 47.619 0.00 0.00 0.00 3.86
972 980 6.317893 GGTTCGTTTTATGTTGGGATCAGTAT 59.682 38.462 0.00 0.00 0.00 2.12
1000 1008 0.963355 TGGGTGGCTCCGTTTTATGC 60.963 55.000 0.00 0.00 37.00 3.14
1004 1012 1.106944 CACTTGGGTGGCTCCGTTTT 61.107 55.000 0.00 0.00 39.59 2.43
1096 1106 4.286707 GGGGTGTTATTAATTTGGCCTCT 58.713 43.478 3.32 0.00 0.00 3.69
1099 1109 2.101750 CGGGGGTGTTATTAATTTGGCC 59.898 50.000 0.00 0.00 0.00 5.36
1840 1866 2.432456 GACTGCGCATCACCGTCA 60.432 61.111 12.24 0.00 0.00 4.35
2477 2512 7.069085 CACCAGAGTTCATCAATCCCATAAAAT 59.931 37.037 0.00 0.00 0.00 1.82
2593 2628 1.168714 GTTGGAGATGTCTTGCCACC 58.831 55.000 0.00 0.00 0.00 4.61
3266 3828 3.302092 GCTGCGATGAAAATCAGAGTACG 60.302 47.826 0.00 0.00 0.00 3.67
3327 3889 3.313012 TTGGAACGTATCACAGTCCAG 57.687 47.619 3.32 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.