Multiple sequence alignment - TraesCS5B01G051500

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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 TraesCS5B01G051500 chr5B 100.000 3716 0 0 1 3716 56333906 56337621 0 6863
1 TraesCS5B01G051500 chr5B 95.240 2836 104 13 104 2913 209178512 209175682 0 4460
2 TraesCS5B01G051500 chr7A 96.687 3713 118 3 1 3712 56071587 56075295 0 6170
3 TraesCS5B01G051500 chr2A 96.632 3622 112 7 96 3712 610787022 610790638 0 6004
4 TraesCS5B01G051500 chr1A 93.261 3754 158 48 21 3712 340068665 340072385 0 5443
5 TraesCS5B01G051500 chr3D 93.183 3726 163 41 21 3715 229430042 229426377 0 5389
6 TraesCS5B01G051500 chr6B 92.562 3630 206 33 104 3698 238424487 238420887 0 5149
7 TraesCS5B01G051500 chr6D 94.815 3240 129 14 26 3238 297173803 297170576 0 5016
8 TraesCS5B01G051500 chr6D 94.923 2482 100 14 769 3238 446365950 446363483 0 3862
9 TraesCS5B01G051500 chr4D 94.868 3176 144 5 557 3715 236674431 236671258 0 4944
10 TraesCS5B01G051500 chr1D 94.679 3176 146 6 557 3715 463795413 463792244 0 4907
11 TraesCS5B01G051500 chr3A 96.431 2914 100 3 1 2913 153247275 153244365 0 4802
12 TraesCS5B01G051500 chr3A 91.271 1707 68 16 21 1698 702235193 702236847 0 2252
13 TraesCS5B01G051500 chr3A 93.037 833 53 3 2861 3690 706571677 706570847 0 1212
14 TraesCS5B01G051500 chr7D 92.935 3199 162 22 557 3712 501762378 501765555 0 4597
15 TraesCS5B01G051500 chr7D 96.579 497 17 0 3216 3712 79227533 79228029 0 824
16 TraesCS5B01G051500 chr5A 95.165 2916 96 7 1 2913 596912105 596914978 0 4562
17 TraesCS5B01G051500 chr5A 92.691 2709 173 10 964 3653 235673729 235676431 0 3882
18 TraesCS5B01G051500 chr5D 94.131 2726 119 9 548 3238 384513915 384511196 0 4109
19 TraesCS5B01G051500 chr5D 94.974 2507 94 13 21 2501 140955183 140952683 0 3903
20 TraesCS5B01G051500 chr5D 96.579 497 17 0 3219 3715 384511181 384510685 0 824
21 TraesCS5B01G051500 chr4B 92.671 1378 58 14 9 1360 343792679 343794039 0 1945
22 TraesCS5B01G051500 chr4A 97.026 975 24 4 1 974 404405848 404404878 0 1635


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 TraesCS5B01G051500 chr5B 56333906 56337621 3715 False 6863.0 6863 100.000 1 3716 1 chr5B.!!$F1 3715
1 TraesCS5B01G051500 chr5B 209175682 209178512 2830 True 4460.0 4460 95.240 104 2913 1 chr5B.!!$R1 2809
2 TraesCS5B01G051500 chr7A 56071587 56075295 3708 False 6170.0 6170 96.687 1 3712 1 chr7A.!!$F1 3711
3 TraesCS5B01G051500 chr2A 610787022 610790638 3616 False 6004.0 6004 96.632 96 3712 1 chr2A.!!$F1 3616
4 TraesCS5B01G051500 chr1A 340068665 340072385 3720 False 5443.0 5443 93.261 21 3712 1 chr1A.!!$F1 3691
5 TraesCS5B01G051500 chr3D 229426377 229430042 3665 True 5389.0 5389 93.183 21 3715 1 chr3D.!!$R1 3694
6 TraesCS5B01G051500 chr6B 238420887 238424487 3600 True 5149.0 5149 92.562 104 3698 1 chr6B.!!$R1 3594
7 TraesCS5B01G051500 chr6D 297170576 297173803 3227 True 5016.0 5016 94.815 26 3238 1 chr6D.!!$R1 3212
8 TraesCS5B01G051500 chr6D 446363483 446365950 2467 True 3862.0 3862 94.923 769 3238 1 chr6D.!!$R2 2469
9 TraesCS5B01G051500 chr4D 236671258 236674431 3173 True 4944.0 4944 94.868 557 3715 1 chr4D.!!$R1 3158
10 TraesCS5B01G051500 chr1D 463792244 463795413 3169 True 4907.0 4907 94.679 557 3715 1 chr1D.!!$R1 3158
11 TraesCS5B01G051500 chr3A 153244365 153247275 2910 True 4802.0 4802 96.431 1 2913 1 chr3A.!!$R1 2912
12 TraesCS5B01G051500 chr3A 702235193 702236847 1654 False 2252.0 2252 91.271 21 1698 1 chr3A.!!$F1 1677
13 TraesCS5B01G051500 chr3A 706570847 706571677 830 True 1212.0 1212 93.037 2861 3690 1 chr3A.!!$R2 829
14 TraesCS5B01G051500 chr7D 501762378 501765555 3177 False 4597.0 4597 92.935 557 3712 1 chr7D.!!$F2 3155
15 TraesCS5B01G051500 chr5A 596912105 596914978 2873 False 4562.0 4562 95.165 1 2913 1 chr5A.!!$F2 2912
16 TraesCS5B01G051500 chr5A 235673729 235676431 2702 False 3882.0 3882 92.691 964 3653 1 chr5A.!!$F1 2689
17 TraesCS5B01G051500 chr5D 140952683 140955183 2500 True 3903.0 3903 94.974 21 2501 1 chr5D.!!$R1 2480
18 TraesCS5B01G051500 chr5D 384510685 384513915 3230 True 2466.5 4109 95.355 548 3715 2 chr5D.!!$R2 3167
19 TraesCS5B01G051500 chr4B 343792679 343794039 1360 False 1945.0 1945 92.671 9 1360 1 chr4B.!!$F1 1351
20 TraesCS5B01G051500 chr4A 404404878 404405848 970 True 1635.0 1635 97.026 1 974 1 chr4A.!!$R1 973

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
334 355 3.074538 AGGGTTTCCATCAGCAGTACTTT 59.925 43.478 0.00 0.0 34.83 2.66 F
1413 1519 0.846427 AGGAAGGGTGATGGCCTCAA 60.846 55.000 3.32 0.0 35.07 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1604 0.246635 CTTTCCTGATGGTCCGTCGT 59.753 55.000 6.60 0.0 34.23 4.34 R
2826 2935 1.962807 CAAACAGGGCATGGACAAAGA 59.037 47.619 3.46 0.0 0.00 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
67 68 8.880750 GTCTTAACTTGTGTGTCTTCTAGTTTT 58.119 33.333 0.00 0.00 33.45 2.43
90 92 4.098914 AGCCATTTTTGGTGTGTAGAGA 57.901 40.909 0.00 0.00 0.00 3.10
334 355 3.074538 AGGGTTTCCATCAGCAGTACTTT 59.925 43.478 0.00 0.00 34.83 2.66
487 532 6.236017 TGCTTGCTTGTTTAGTGTACATAC 57.764 37.500 0.00 0.00 0.00 2.39
593 638 7.130681 TGGTCCAAATGTTTTCCTTTATTGT 57.869 32.000 0.00 0.00 0.00 2.71
931 997 7.658525 TGCATTCCAAACATTCACCTAATAT 57.341 32.000 0.00 0.00 0.00 1.28
1056 1122 1.457303 GGTGCAATAGCGTCGATGATC 59.543 52.381 9.31 0.00 46.23 2.92
1131 1197 3.809832 GTGGAGTTATCAATGATGACCCG 59.190 47.826 13.53 0.00 38.69 5.28
1204 1300 4.127171 GACTGTTAAGGTGCAAACTCTGA 58.873 43.478 0.00 0.00 0.00 3.27
1410 1516 2.311854 CCAGGAAGGGTGATGGCCT 61.312 63.158 3.32 0.00 0.00 5.19
1413 1519 0.846427 AGGAAGGGTGATGGCCTCAA 60.846 55.000 3.32 0.00 35.07 3.02
1497 1604 3.002791 CAGAAAGCAAAGATGGCGACTA 58.997 45.455 0.00 0.00 36.08 2.59
1917 2025 4.597940 ACTAGACTTAGAAAGGGCAAAGGT 59.402 41.667 0.00 0.00 0.00 3.50
1939 2047 1.479709 AGAGAGGATCACCAAGTCGG 58.520 55.000 0.00 0.00 37.82 4.79
2048 2156 1.338200 ACTCGTCACAAGAAGCCATCC 60.338 52.381 0.00 0.00 0.00 3.51
2082 2191 7.435068 TCCTCACTTCAAGCTATACAAAAAC 57.565 36.000 0.00 0.00 0.00 2.43
2120 2229 5.163141 TGGAGAACTACATTGGGAAAGTTGA 60.163 40.000 0.00 0.00 32.51 3.18
2204 2313 9.262358 GATCACTAATATTGTTCCTACCTTGTC 57.738 37.037 0.00 0.00 0.00 3.18
2346 2455 2.285083 TGATACCATAGCCGCAAACAC 58.715 47.619 0.00 0.00 0.00 3.32
2404 2513 1.340017 GGTGAATGGCAAGCTCTGGTA 60.340 52.381 0.00 0.00 0.00 3.25
2447 2556 3.378427 ACACAAGGTTTGTCTCTGCTTTC 59.622 43.478 0.00 0.00 43.23 2.62
2687 2796 8.579006 TCTGATTCTTGCTGAATAACATTTTGT 58.421 29.630 5.70 0.00 44.70 2.83
2738 2847 1.471119 CGTAAGGGTGAGGAGCTGTA 58.529 55.000 0.00 0.00 0.00 2.74
2826 2935 6.836527 AGACTGCTATAGTAAGTCACTCCATT 59.163 38.462 26.31 11.24 42.28 3.16
2863 3001 3.243501 TGTTTGATTCACAGCCAGCTTTC 60.244 43.478 0.00 0.00 0.00 2.62
2899 3064 6.279123 TGCTTTGATGCTTTGATGTTGTTTA 58.721 32.000 0.00 0.00 0.00 2.01
3053 3218 3.877559 AGTTTGATGATCGGCTCAATCA 58.122 40.909 12.36 2.97 37.44 2.57
3198 3363 5.741388 TCTTCTTCTGTTTGAGTTTGAGC 57.259 39.130 0.00 0.00 0.00 4.26
3237 3446 2.175202 TGTGTGCTGGTTTGGTTTCTT 58.825 42.857 0.00 0.00 0.00 2.52
3261 3470 3.760684 TGCTTGGTTTGGTTTGCAAAATT 59.239 34.783 14.67 0.00 0.00 1.82
3471 3680 1.234821 CAAGTCCGGCAAAGCAACTA 58.765 50.000 0.00 0.00 0.00 2.24
3556 3765 5.072055 TGAAGTGATGCAAGAAGAATTGGA 58.928 37.500 0.00 0.00 34.85 3.53
3603 3812 0.461870 TGAAGCTGCACGTGACAAGT 60.462 50.000 22.23 0.00 0.00 3.16
3712 3921 5.518848 TGATTGTGCAGTTTGTCTTTGAT 57.481 34.783 0.00 0.00 0.00 2.57
3715 3924 2.290367 TGTGCAGTTTGTCTTTGATCCG 59.710 45.455 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 5.472137 GTCTCTACACACCAAAAATGGCTAA 59.528 40.000 0.00 0.00 0.00 3.09
152 154 3.243704 GCCACTGGTAAAGCATGAAACAA 60.244 43.478 0.00 0.00 0.00 2.83
153 155 2.295909 GCCACTGGTAAAGCATGAAACA 59.704 45.455 0.00 0.00 0.00 2.83
334 355 4.956075 TCTCCATGTGCTACTGATACAAGA 59.044 41.667 0.00 0.00 0.00 3.02
487 532 4.689071 AGCATGCATGTACAATGGAAATG 58.311 39.130 26.79 0.00 0.00 2.32
787 852 7.428020 CCAGCTTATTTAGATTGCAGCAATAA 58.572 34.615 20.90 12.03 33.90 1.40
1056 1122 6.142818 TCTTGTACACCATTTGTTTTCCTG 57.857 37.500 0.00 0.00 39.91 3.86
1131 1197 5.141182 TCTCCATCATTAGGACTGTACTCC 58.859 45.833 0.00 0.00 0.00 3.85
1204 1300 1.153756 CCCAACCCTCCAAGCAAGT 59.846 57.895 0.00 0.00 0.00 3.16
1497 1604 0.246635 CTTTCCTGATGGTCCGTCGT 59.753 55.000 6.60 0.00 34.23 4.34
1917 2025 3.546724 CGACTTGGTGATCCTCTCTAGA 58.453 50.000 0.00 0.00 34.23 2.43
1939 2047 2.158798 GGATAGGCACCTTCCTACCAAC 60.159 54.545 0.00 0.00 41.18 3.77
1947 2055 2.101415 GGCAATTTGGATAGGCACCTTC 59.899 50.000 0.00 0.00 0.00 3.46
2048 2156 1.618837 TGAAGTGAGGAAGAACCGGAG 59.381 52.381 9.46 0.00 44.74 4.63
2082 2191 7.492524 TGTAGTTCTCCAATAGACTAGCATTG 58.507 38.462 0.00 0.00 32.51 2.82
2161 2270 6.239217 AGTGATCATGCATAGGAGTAACAA 57.761 37.500 0.00 0.00 0.00 2.83
2204 2313 4.749245 AATTTGCCTACGAAGACAACAG 57.251 40.909 0.00 0.00 0.00 3.16
2346 2455 2.093973 ACCGGAGACTTAATGCTGACTG 60.094 50.000 9.46 0.00 0.00 3.51
2447 2556 5.463286 TGTGCAGAACATAAAGCATCAAAG 58.537 37.500 0.00 0.00 39.43 2.77
2713 2822 2.376109 CTCCTCACCCTTACGCTCTTA 58.624 52.381 0.00 0.00 0.00 2.10
2738 2847 3.119495 GGCCTTAAACAAGTCAATCGCAT 60.119 43.478 0.00 0.00 0.00 4.73
2826 2935 1.962807 CAAACAGGGCATGGACAAAGA 59.037 47.619 3.46 0.00 0.00 2.52
2863 3001 3.062099 GCATCAAAGCATCAAACAGCATG 59.938 43.478 0.00 0.00 46.00 4.06
2899 3064 3.817647 GTGTTCTTGACTGGCTCTGAATT 59.182 43.478 0.00 0.00 0.00 2.17
3053 3218 5.337652 GCGGTTCTATATAAGATGGCTTCCT 60.338 44.000 0.00 0.00 35.56 3.36
3237 3446 2.479566 TGCAAACCAAACCAAGCAAA 57.520 40.000 0.00 0.00 0.00 3.68
3261 3470 6.101734 AGGCATTAGTGGGAGATCTATTTCAA 59.898 38.462 0.00 0.00 0.00 2.69
3434 3643 4.421131 ACTTGTTCCTAGATGACTGGAGT 58.579 43.478 0.00 0.00 0.00 3.85
3471 3680 0.399454 ACATGAGCAGCCACTTCAGT 59.601 50.000 0.00 0.00 0.00 3.41
3556 3765 1.386533 CGCCTTCATCTTGATTGCCT 58.613 50.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.