Multiple sequence alignment - TraesCS3A01G412400

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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 TraesCS3A01G412400 chr3A 100.000 2972 0 0 1 2972 655937616 655934645 0.000000e+00 5489.0
1 TraesCS3A01G412400 chr3A 96.396 2997 62 13 1 2972 658185864 658188839 0.000000e+00 4894.0
2 TraesCS3A01G412400 chr3A 92.586 1160 80 3 961 2120 655994968 655993815 0.000000e+00 1661.0
3 TraesCS3A01G412400 chr3B 93.442 2272 109 24 8 2261 685876169 685873920 0.000000e+00 3334.0
4 TraesCS3A01G412400 chr3B 95.330 1456 66 2 807 2261 685763763 685762309 0.000000e+00 2311.0
5 TraesCS3A01G412400 chr3B 88.809 1528 106 31 626 2120 685910500 685909005 0.000000e+00 1814.0
6 TraesCS3A01G412400 chr3B 86.591 1499 150 21 626 2091 685941996 685940516 0.000000e+00 1607.0
7 TraesCS3A01G412400 chr3B 86.479 1494 156 21 626 2092 685980452 685978978 0.000000e+00 1598.0
8 TraesCS3A01G412400 chr3B 93.213 722 41 6 2252 2972 480336686 480337400 0.000000e+00 1055.0
9 TraesCS3A01G412400 chr3B 91.787 621 40 7 1 615 685764413 685763798 0.000000e+00 854.0
10 TraesCS3A01G412400 chr3B 85.581 215 22 3 317 529 686045881 686045674 1.790000e-52 217.0
11 TraesCS3A01G412400 chr3D 95.257 1265 54 5 1000 2261 520641870 520640609 0.000000e+00 1999.0
12 TraesCS3A01G412400 chr3D 89.260 1527 102 28 626 2120 520678584 520677088 0.000000e+00 1855.0
13 TraesCS3A01G412400 chr3D 88.286 1400 133 13 712 2091 520684429 520683041 0.000000e+00 1648.0
14 TraesCS3A01G412400 chr3D 86.609 1501 143 24 626 2092 520703905 520702429 0.000000e+00 1605.0
15 TraesCS3A01G412400 chr3D 92.748 979 53 9 2 965 520642847 520641872 0.000000e+00 1399.0
16 TraesCS3A01G412400 chr3D 93.166 717 41 8 2256 2972 66239039 66238331 0.000000e+00 1046.0
17 TraesCS3A01G412400 chr3D 83.841 328 36 8 264 582 520704240 520703921 2.240000e-76 296.0
18 TraesCS3A01G412400 chr3D 86.897 145 17 1 819 961 520656991 520656847 8.530000e-36 161.0
19 TraesCS3A01G412400 chr3D 79.845 129 14 4 443 568 520676674 520676555 1.900000e-12 84.2
20 TraesCS3A01G412400 chr4A 93.584 717 38 5 2260 2972 477293326 477292614 0.000000e+00 1062.0
21 TraesCS3A01G412400 chr2A 93.251 726 40 6 2252 2972 721914706 721915427 0.000000e+00 1061.0
22 TraesCS3A01G412400 chr5D 93.566 715 32 10 2261 2972 8703241 8703944 0.000000e+00 1053.0
23 TraesCS3A01G412400 chr1D 93.427 715 35 10 2261 2972 278094244 278094949 0.000000e+00 1050.0
24 TraesCS3A01G412400 chr1D 90.323 62 6 0 17 78 382888606 382888667 6.830000e-12 82.4
25 TraesCS3A01G412400 chr7A 92.828 725 43 8 2251 2972 142489773 142489055 0.000000e+00 1042.0
26 TraesCS3A01G412400 chr7A 92.700 726 44 7 2251 2972 171763969 171763249 0.000000e+00 1038.0
27 TraesCS3A01G412400 chrUn 92.497 733 42 10 2248 2972 233048437 233049164 0.000000e+00 1037.0
28 TraesCS3A01G412400 chrUn 76.642 137 32 0 17 153 81057288 81057152 3.180000e-10 76.8
29 TraesCS3A01G412400 chr2B 78.836 189 34 6 9 195 568267662 568267846 4.020000e-24 122.0
30 TraesCS3A01G412400 chr4D 77.612 134 30 0 17 150 178515391 178515524 6.830000e-12 82.4
31 TraesCS3A01G412400 chr2D 81.553 103 14 5 18 118 218288379 218288280 2.460000e-11 80.5


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 TraesCS3A01G412400 chr3A 655934645 655937616 2971 True 5489.0 5489 100.0000 1 2972 1 chr3A.!!$R1 2971
1 TraesCS3A01G412400 chr3A 658185864 658188839 2975 False 4894.0 4894 96.3960 1 2972 1 chr3A.!!$F1 2971
2 TraesCS3A01G412400 chr3A 655993815 655994968 1153 True 1661.0 1661 92.5860 961 2120 1 chr3A.!!$R2 1159
3 TraesCS3A01G412400 chr3B 685873920 685876169 2249 True 3334.0 3334 93.4420 8 2261 1 chr3B.!!$R1 2253
4 TraesCS3A01G412400 chr3B 685909005 685910500 1495 True 1814.0 1814 88.8090 626 2120 1 chr3B.!!$R2 1494
5 TraesCS3A01G412400 chr3B 685940516 685941996 1480 True 1607.0 1607 86.5910 626 2091 1 chr3B.!!$R3 1465
6 TraesCS3A01G412400 chr3B 685978978 685980452 1474 True 1598.0 1598 86.4790 626 2092 1 chr3B.!!$R4 1466
7 TraesCS3A01G412400 chr3B 685762309 685764413 2104 True 1582.5 2311 93.5585 1 2261 2 chr3B.!!$R6 2260
8 TraesCS3A01G412400 chr3B 480336686 480337400 714 False 1055.0 1055 93.2130 2252 2972 1 chr3B.!!$F1 720
9 TraesCS3A01G412400 chr3D 520640609 520642847 2238 True 1699.0 1999 94.0025 2 2261 2 chr3D.!!$R4 2259
10 TraesCS3A01G412400 chr3D 520683041 520684429 1388 True 1648.0 1648 88.2860 712 2091 1 chr3D.!!$R3 1379
11 TraesCS3A01G412400 chr3D 66238331 66239039 708 True 1046.0 1046 93.1660 2256 2972 1 chr3D.!!$R1 716
12 TraesCS3A01G412400 chr3D 520676555 520678584 2029 True 969.6 1855 84.5525 443 2120 2 chr3D.!!$R5 1677
13 TraesCS3A01G412400 chr3D 520702429 520704240 1811 True 950.5 1605 85.2250 264 2092 2 chr3D.!!$R6 1828
14 TraesCS3A01G412400 chr4A 477292614 477293326 712 True 1062.0 1062 93.5840 2260 2972 1 chr4A.!!$R1 712
15 TraesCS3A01G412400 chr2A 721914706 721915427 721 False 1061.0 1061 93.2510 2252 2972 1 chr2A.!!$F1 720
16 TraesCS3A01G412400 chr5D 8703241 8703944 703 False 1053.0 1053 93.5660 2261 2972 1 chr5D.!!$F1 711
17 TraesCS3A01G412400 chr1D 278094244 278094949 705 False 1050.0 1050 93.4270 2261 2972 1 chr1D.!!$F1 711
18 TraesCS3A01G412400 chr7A 142489055 142489773 718 True 1042.0 1042 92.8280 2251 2972 1 chr7A.!!$R1 721
19 TraesCS3A01G412400 chr7A 171763249 171763969 720 True 1038.0 1038 92.7000 2251 2972 1 chr7A.!!$R2 721
20 TraesCS3A01G412400 chrUn 233048437 233049164 727 False 1037.0 1037 92.4970 2248 2972 1 chrUn.!!$F1 724

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
136 138 1.213013 CCGAACACTCTCTGACGGG 59.787 63.158 0.0 0.0 38.61 5.28 F
153 155 2.310647 ACGGGGTATCAGGGTTTCAAAT 59.689 45.455 0.0 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1684 0.550914 AAGGTGTGTGCTCCTTGGAA 59.449 50.00 0.83 0.00 44.28 3.53 R
2124 2200 9.430623 TGTTTATCGAAGACAAGTCATTTGATA 57.569 29.63 2.72 9.49 42.51 2.15 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
112 114 6.258287 TGAGAAAAATTGAATGCACTTTGTGG 59.742 34.615 0.00 0.00 33.64 4.17
136 138 1.213013 CCGAACACTCTCTGACGGG 59.787 63.158 0.00 0.00 38.61 5.28
153 155 2.310647 ACGGGGTATCAGGGTTTCAAAT 59.689 45.455 0.00 0.00 0.00 2.32
2019 2094 5.062934 TGTGAACTCGTTGTCTTTGTGTAAG 59.937 40.000 0.00 0.00 35.04 2.34
2106 2182 9.891828 GTGTAAATGTTCAGTATGTGATTTTCA 57.108 29.630 0.00 0.00 37.40 2.69
2491 2737 2.810870 TCCTAAGGCGTCTCTCTCTT 57.189 50.000 0.00 0.00 0.00 2.85
2501 2747 3.458189 CGTCTCTCTCTTCCTCTCTCTC 58.542 54.545 0.00 0.00 0.00 3.20
2502 2748 3.741388 CGTCTCTCTCTTCCTCTCTCTCC 60.741 56.522 0.00 0.00 0.00 3.71
2503 2749 3.199946 GTCTCTCTCTTCCTCTCTCTCCA 59.800 52.174 0.00 0.00 0.00 3.86
2504 2750 3.199946 TCTCTCTCTTCCTCTCTCTCCAC 59.800 52.174 0.00 0.00 0.00 4.02
2505 2751 2.241176 TCTCTCTTCCTCTCTCTCCACC 59.759 54.545 0.00 0.00 0.00 4.61
2507 2753 1.287739 CTCTTCCTCTCTCTCCACCCT 59.712 57.143 0.00 0.00 0.00 4.34
2513 2759 0.553862 TCTCTCTCCACCCTCTCCCT 60.554 60.000 0.00 0.00 0.00 4.20
2563 2841 0.735471 TTCTCTCACTCTCGCGATGG 59.265 55.000 10.36 8.18 0.00 3.51
2585 2863 3.895041 GGAAATCTGTTGTTTTCCCCTGA 59.105 43.478 3.56 0.00 42.18 3.86
2597 2875 5.423610 TGTTTTCCCCTGAGACATTTTTCAA 59.576 36.000 0.00 0.00 0.00 2.69
2665 2945 3.304829 AGTGGGGTGTTTATTTGCAGTT 58.695 40.909 0.00 0.00 0.00 3.16
2849 3209 9.970395 TCGAAGTTACAGTTTAAAAGACATAGA 57.030 29.630 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 6.258287 CCACAAAGTGCATTCAATTTTTCTCA 59.742 34.615 0.00 0.00 38.29 3.27
96 98 4.180057 GTTTGTCCACAAAGTGCATTCAA 58.820 39.130 5.09 0.00 45.36 2.69
97 99 3.430098 GGTTTGTCCACAAAGTGCATTCA 60.430 43.478 5.09 0.00 45.36 2.57
108 110 1.208535 AGAGTGTTCGGTTTGTCCACA 59.791 47.619 0.00 0.00 35.57 4.17
112 114 2.795470 GTCAGAGAGTGTTCGGTTTGTC 59.205 50.000 0.00 0.00 0.00 3.18
136 138 7.827729 ACACTTACTATTTGAAACCCTGATACC 59.172 37.037 0.00 0.00 0.00 2.73
215 221 8.911918 ACTTTGAGTGGTGTGTGTTAAATATA 57.088 30.769 0.00 0.00 0.00 0.86
602 623 6.374417 ACTCCAGCCGTTCCATAATATAAT 57.626 37.500 0.00 0.00 0.00 1.28
904 943 1.520120 CGCAGCGATGGATGTGAGT 60.520 57.895 9.98 0.00 42.46 3.41
1117 1192 2.422832 CGTAGAAGGACGAGCTTAACCT 59.577 50.000 0.00 0.00 45.82 3.50
1329 1404 4.662961 CCGCGTGCTGACCTGTCA 62.663 66.667 4.92 0.00 38.06 3.58
1609 1684 0.550914 AAGGTGTGTGCTCCTTGGAA 59.449 50.000 0.83 0.00 44.28 3.53
2019 2094 9.696917 ACAGTTGGAATGAATTAAAAGAATGAC 57.303 29.630 0.00 0.00 0.00 3.06
2080 2156 9.891828 TGAAAATCACATACTGAACATTTACAC 57.108 29.630 0.00 0.00 30.60 2.90
2124 2200 9.430623 TGTTTATCGAAGACAAGTCATTTGATA 57.569 29.630 2.72 9.49 42.51 2.15
2419 2665 0.107643 TGTGTGAACATCGAGGGCAA 59.892 50.000 0.69 0.00 0.00 4.52
2491 2737 0.923358 GAGAGGGTGGAGAGAGAGGA 59.077 60.000 0.00 0.00 0.00 3.71
2501 2747 0.106217 GAGAGAGAGGGAGAGGGTGG 60.106 65.000 0.00 0.00 0.00 4.61
2502 2748 0.926293 AGAGAGAGAGGGAGAGGGTG 59.074 60.000 0.00 0.00 0.00 4.61
2503 2749 1.222567 GAGAGAGAGAGGGAGAGGGT 58.777 60.000 0.00 0.00 0.00 4.34
2504 2750 1.421646 GAGAGAGAGAGAGGGAGAGGG 59.578 61.905 0.00 0.00 0.00 4.30
2505 2751 1.421646 GGAGAGAGAGAGAGGGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
2507 2753 1.010793 AGGGAGAGAGAGAGAGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
2513 2759 3.051803 AGAGAGAGAGGGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2585 2863 6.869913 CACATGCATACCTTTGAAAAATGTCT 59.130 34.615 0.00 0.00 0.00 3.41
2597 2875 6.156748 TCGATAACTACACATGCATACCTT 57.843 37.500 0.00 0.00 0.00 3.50
2855 3215 9.617523 ATTTGAGTCAAACCAAATGATTTTCTT 57.382 25.926 20.26 0.00 40.33 2.52


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

AutoCloner maintained by Alex Coulton.