Multiple sequence alignment - TraesCS5D01G058600

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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 TraesCS5D01G058600 chr5D 100.000 2264 0 0 1 2264 55375404 55377667 0.000000e+00 4181.0
1 TraesCS5D01G058600 chr5D 93.486 829 52 2 1 829 55384228 55385054 0.000000e+00 1230.0
2 TraesCS5D01G058600 chr5D 92.909 832 47 9 1 829 415363943 415363121 0.000000e+00 1199.0
3 TraesCS5D01G058600 chr5D 97.856 653 12 2 829 1479 299970705 299970053 0.000000e+00 1127.0
4 TraesCS5D01G058600 chr5D 91.440 771 47 15 1500 2264 257438454 257437697 0.000000e+00 1040.0
5 TraesCS5D01G058600 chr5D 92.061 718 37 16 1530 2241 236830292 236829589 0.000000e+00 992.0
6 TraesCS5D01G058600 chr5D 89.084 797 41 23 1480 2264 236838896 236838134 0.000000e+00 948.0
7 TraesCS5D01G058600 chr5D 92.857 616 30 12 1654 2264 415371136 415370530 0.000000e+00 881.0
8 TraesCS5D01G058600 chr1D 92.651 830 60 1 1 829 291030137 291030966 0.000000e+00 1194.0
9 TraesCS5D01G058600 chr1D 97.243 653 16 2 829 1479 254460686 254461338 0.000000e+00 1105.0
10 TraesCS5D01G058600 chr1D 92.105 722 38 12 1534 2242 286035381 286034666 0.000000e+00 1000.0
11 TraesCS5D01G058600 chr3D 92.575 835 52 9 1 829 142273611 142274441 0.000000e+00 1190.0
12 TraesCS5D01G058600 chr3D 90.780 564 31 14 1497 2053 503985625 503986174 0.000000e+00 734.0
13 TraesCS5D01G058600 chr3D 85.337 416 37 13 1854 2264 181835546 181835942 2.090000e-110 409.0
14 TraesCS5D01G058600 chr3D 97.674 43 0 1 2222 2264 361877004 361877045 3.120000e-09 73.1
15 TraesCS5D01G058600 chr6D 92.446 834 55 8 1 830 144334799 144333970 0.000000e+00 1184.0
16 TraesCS5D01G058600 chr6D 92.326 834 52 9 1 829 370558549 370559375 0.000000e+00 1175.0
17 TraesCS5D01G058600 chr6D 93.192 661 34 8 1607 2264 370559984 370560636 0.000000e+00 961.0
18 TraesCS5D01G058600 chr4D 92.512 828 53 8 1 825 375627373 375626552 0.000000e+00 1177.0
19 TraesCS5D01G058600 chr7D 92.206 834 57 8 1 830 588372362 588371533 0.000000e+00 1173.0
20 TraesCS5D01G058600 chr7D 97.674 43 1 0 2222 2264 259932281 259932323 8.670000e-10 75.0
21 TraesCS5D01G058600 chr2D 92.298 831 55 6 1 827 338379736 338378911 0.000000e+00 1171.0
22 TraesCS5D01G058600 chr2D 90.896 692 48 13 1557 2242 338378528 338377846 0.000000e+00 915.0
23 TraesCS5D01G058600 chr1A 97.856 653 12 2 829 1479 554483306 554483958 0.000000e+00 1127.0
24 TraesCS5D01G058600 chr1A 90.027 732 56 15 1517 2241 261024087 261023366 0.000000e+00 931.0
25 TraesCS5D01G058600 chr5A 97.856 653 11 3 829 1479 559030664 559030013 0.000000e+00 1125.0
26 TraesCS5D01G058600 chr5A 87.484 767 71 18 1505 2264 686379345 686380093 0.000000e+00 861.0
27 TraesCS5D01G058600 chrUn 97.550 653 14 2 829 1479 386224902 386225554 0.000000e+00 1116.0
28 TraesCS5D01G058600 chrUn 97.090 653 17 2 829 1479 261567408 261566756 0.000000e+00 1099.0
29 TraesCS5D01G058600 chr5B 97.397 653 15 2 829 1479 57513840 57513188 0.000000e+00 1110.0
30 TraesCS5D01G058600 chr2B 97.397 653 15 2 829 1479 683728726 683729378 0.000000e+00 1110.0
31 TraesCS5D01G058600 chr3A 97.243 653 16 2 829 1479 105555675 105555023 0.000000e+00 1105.0


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 TraesCS5D01G058600 chr5D 55375404 55377667 2263 False 4181 4181 100.000 1 2264 1 chr5D.!!$F1 2263
1 TraesCS5D01G058600 chr5D 55384228 55385054 826 False 1230 1230 93.486 1 829 1 chr5D.!!$F2 828
2 TraesCS5D01G058600 chr5D 415363121 415363943 822 True 1199 1199 92.909 1 829 1 chr5D.!!$R5 828
3 TraesCS5D01G058600 chr5D 299970053 299970705 652 True 1127 1127 97.856 829 1479 1 chr5D.!!$R4 650
4 TraesCS5D01G058600 chr5D 257437697 257438454 757 True 1040 1040 91.440 1500 2264 1 chr5D.!!$R3 764
5 TraesCS5D01G058600 chr5D 236829589 236830292 703 True 992 992 92.061 1530 2241 1 chr5D.!!$R1 711
6 TraesCS5D01G058600 chr5D 236838134 236838896 762 True 948 948 89.084 1480 2264 1 chr5D.!!$R2 784
7 TraesCS5D01G058600 chr5D 415370530 415371136 606 True 881 881 92.857 1654 2264 1 chr5D.!!$R6 610
8 TraesCS5D01G058600 chr1D 291030137 291030966 829 False 1194 1194 92.651 1 829 1 chr1D.!!$F2 828
9 TraesCS5D01G058600 chr1D 254460686 254461338 652 False 1105 1105 97.243 829 1479 1 chr1D.!!$F1 650
10 TraesCS5D01G058600 chr1D 286034666 286035381 715 True 1000 1000 92.105 1534 2242 1 chr1D.!!$R1 708
11 TraesCS5D01G058600 chr3D 142273611 142274441 830 False 1190 1190 92.575 1 829 1 chr3D.!!$F1 828
12 TraesCS5D01G058600 chr3D 503985625 503986174 549 False 734 734 90.780 1497 2053 1 chr3D.!!$F4 556
13 TraesCS5D01G058600 chr6D 144333970 144334799 829 True 1184 1184 92.446 1 830 1 chr6D.!!$R1 829
14 TraesCS5D01G058600 chr6D 370558549 370560636 2087 False 1068 1175 92.759 1 2264 2 chr6D.!!$F1 2263
15 TraesCS5D01G058600 chr4D 375626552 375627373 821 True 1177 1177 92.512 1 825 1 chr4D.!!$R1 824
16 TraesCS5D01G058600 chr7D 588371533 588372362 829 True 1173 1173 92.206 1 830 1 chr7D.!!$R1 829
17 TraesCS5D01G058600 chr2D 338377846 338379736 1890 True 1043 1171 91.597 1 2242 2 chr2D.!!$R1 2241
18 TraesCS5D01G058600 chr1A 554483306 554483958 652 False 1127 1127 97.856 829 1479 1 chr1A.!!$F1 650
19 TraesCS5D01G058600 chr1A 261023366 261024087 721 True 931 931 90.027 1517 2241 1 chr1A.!!$R1 724
20 TraesCS5D01G058600 chr5A 559030013 559030664 651 True 1125 1125 97.856 829 1479 1 chr5A.!!$R1 650
21 TraesCS5D01G058600 chr5A 686379345 686380093 748 False 861 861 87.484 1505 2264 1 chr5A.!!$F1 759
22 TraesCS5D01G058600 chrUn 386224902 386225554 652 False 1116 1116 97.550 829 1479 1 chrUn.!!$F1 650
23 TraesCS5D01G058600 chrUn 261566756 261567408 652 True 1099 1099 97.090 829 1479 1 chrUn.!!$R1 650
24 TraesCS5D01G058600 chr5B 57513188 57513840 652 True 1110 1110 97.397 829 1479 1 chr5B.!!$R1 650
25 TraesCS5D01G058600 chr2B 683728726 683729378 652 False 1110 1110 97.397 829 1479 1 chr2B.!!$F1 650
26 TraesCS5D01G058600 chr3A 105555023 105555675 652 True 1105 1105 97.243 829 1479 1 chr3A.!!$R1 650

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
656 662 0.526739 AACGGGCAAAAAGTGTTCGC 60.527 50.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 2192 0.687354 AAACTCTCACCGGACTGCAT 59.313 50.0 9.46 0.0 0.0 3.96 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
68 71 3.952323 TCTACCTCATCAACTACTTCCCG 59.048 47.826 0.00 0.00 0.00 5.14
92 96 6.350110 CGAACCCACAATTTAATCACATCCTT 60.350 38.462 0.00 0.00 0.00 3.36
114 118 6.543465 CCTTATCATGCAGTGTTTGAGGATTA 59.457 38.462 0.00 0.00 0.00 1.75
122 126 6.426937 TGCAGTGTTTGAGGATTAGAACTAAC 59.573 38.462 0.00 0.00 0.00 2.34
160 164 9.337396 GGGTATGAAAAGTGTATGATCAATGTA 57.663 33.333 0.00 0.00 0.00 2.29
209 213 2.442502 ACCTAGGGACTCGTAGTAGCAT 59.557 50.000 14.81 0.00 41.75 3.79
351 355 6.516718 TCCGGTTTGCAAAAAGAATCAAATA 58.483 32.000 14.67 0.00 32.07 1.40
355 359 9.662545 CGGTTTGCAAAAAGAATCAAATAAAAT 57.337 25.926 14.67 0.00 32.07 1.82
461 465 8.527567 TCTTGTTCAAGTTGGTTAAACAAAAG 57.472 30.769 7.69 6.39 41.61 2.27
602 608 5.191059 CACGAGAAAAGAAAAACTGACGAG 58.809 41.667 0.00 0.00 0.00 4.18
656 662 0.526739 AACGGGCAAAAAGTGTTCGC 60.527 50.000 0.00 0.00 0.00 4.70
695 701 4.914312 TGAACGTCCGCTAAATAAACAG 57.086 40.909 0.00 0.00 0.00 3.16
985 998 7.759465 TCGATTACAGAAAGTCGAACTAGAAT 58.241 34.615 0.00 0.00 39.80 2.40
1041 1054 9.399403 GAGATAGAACGAGAAAAAGCAAATTTT 57.601 29.630 0.00 0.00 43.04 1.82
1133 1146 1.302907 AGGGCAATGAATCAGGTCCT 58.697 50.000 5.19 5.19 0.00 3.85
1165 1179 0.250553 CCAACAGGCCGTACAAGGAA 60.251 55.000 0.00 0.00 0.00 3.36
1187 1201 8.337739 AGGAACTCTAGGAACTCTGAATAGTTA 58.662 37.037 0.00 0.00 39.78 2.24
1435 1449 8.734386 CAATATAATAGGAAAGCAGGGATTGAC 58.266 37.037 0.00 0.00 0.00 3.18
1453 1467 4.219143 TGACAATATAGGTCGCGTAGTG 57.781 45.455 5.77 2.49 38.10 2.74
1483 1497 2.280186 GGGATTGCTCGTAGCGGG 60.280 66.667 3.08 0.00 46.26 6.13
1485 1499 2.967615 GATTGCTCGTAGCGGGGC 60.968 66.667 3.08 0.00 46.26 5.80
1586 1857 2.286242 GGCGACGGCTTATAAAAAGAGC 60.286 50.000 15.00 0.00 39.81 4.09
1693 2154 3.385384 CTCTCCCGAGCCAGTGCA 61.385 66.667 0.00 0.00 41.13 4.57
1744 2205 2.350895 CCCAATGCAGTCCGGTGA 59.649 61.111 0.00 0.00 0.00 4.02
1750 2213 0.687354 ATGCAGTCCGGTGAGAGTTT 59.313 50.000 0.00 0.00 0.00 2.66
1874 2350 4.222810 GGGTGAACATTTTCTTGGCCTAAT 59.777 41.667 3.32 0.00 32.36 1.73
2126 2614 1.555533 GAAATCCCCAACTCTCTCCGT 59.444 52.381 0.00 0.00 0.00 4.69
2151 2640 5.243954 GGGTCCTTGAGTTGCTTAGAATTTT 59.756 40.000 0.00 0.00 0.00 1.82
2162 2651 3.846383 GCTTAGAATTTTGAGGATCGCGC 60.846 47.826 0.00 0.00 38.61 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 71 6.530019 AGGATGTGATTAAATTGTGGGTTC 57.470 37.500 0.00 0.00 0.00 3.62
92 96 6.888105 TCTAATCCTCAAACACTGCATGATA 58.112 36.000 0.00 0.00 0.00 2.15
114 118 5.067954 ACCCAGTTTTTATGCGTTAGTTCT 58.932 37.500 0.00 0.00 0.00 3.01
122 126 6.307800 CACTTTTCATACCCAGTTTTTATGCG 59.692 38.462 0.00 0.00 0.00 4.73
160 164 4.818546 CGGATCATCAGCAAGGAAAGTAAT 59.181 41.667 0.00 0.00 0.00 1.89
167 171 1.906995 TGCGGATCATCAGCAAGGA 59.093 52.632 10.33 0.00 44.13 3.36
321 325 4.200874 TCTTTTTGCAAACCGGAGTTCTA 58.799 39.130 12.39 0.00 34.19 2.10
351 355 4.647424 TTGAGTTTCGTTGCTCCATTTT 57.353 36.364 0.00 0.00 0.00 1.82
355 359 2.354510 CAGTTTGAGTTTCGTTGCTCCA 59.645 45.455 0.00 0.00 0.00 3.86
458 462 3.135895 TCTTTGTCTCGAAACCCTCCTTT 59.864 43.478 0.00 0.00 0.00 3.11
461 465 2.833631 TCTTTGTCTCGAAACCCTCC 57.166 50.000 0.00 0.00 0.00 4.30
580 585 4.260253 GCTCGTCAGTTTTTCTTTTCTCGT 60.260 41.667 0.00 0.00 0.00 4.18
602 608 2.442188 CGTTCGTCCGTTAGCCTGC 61.442 63.158 0.00 0.00 0.00 4.85
656 662 4.030977 CGTTCATCCCTACGTTCGTTTTAG 59.969 45.833 2.62 0.00 33.33 1.85
670 676 1.949465 ATTTAGCGGACGTTCATCCC 58.051 50.000 0.00 0.00 35.03 3.85
695 701 2.286595 GGTTCGTTGGTTTTCTCGGTTC 60.287 50.000 0.00 0.00 0.00 3.62
788 799 1.345176 CGGAGTTCGCAAATCTCGC 59.655 57.895 0.00 0.00 0.00 5.03
818 829 1.208358 GTTTACAACCGGAAGCCGC 59.792 57.895 9.46 0.00 46.86 6.53
985 998 4.522789 TCCATTCATTCGATACTCATCCGA 59.477 41.667 0.00 0.00 0.00 4.55
1133 1146 1.600023 CTGTTGGAAAACCCGCTGTA 58.400 50.000 0.00 0.00 37.93 2.74
1187 1201 5.650543 GGAAATGTAACTCGGCATTCAAAT 58.349 37.500 0.00 0.00 34.61 2.32
1195 1209 1.585214 CGTACGGAAATGTAACTCGGC 59.415 52.381 7.57 0.00 0.00 5.54
1307 1321 2.168313 AGCAAGGGGAAAAATAATGCCG 59.832 45.455 0.00 0.00 32.95 5.69
1425 1439 3.997021 GCGACCTATATTGTCAATCCCTG 59.003 47.826 0.07 0.00 32.91 4.45
1435 1449 3.007979 TGCACTACGCGACCTATATTG 57.992 47.619 15.93 0.00 46.97 1.90
1453 1467 1.044790 CAATCCCATCCCCCACTTGC 61.045 60.000 0.00 0.00 0.00 4.01
1561 1832 3.795499 TTATAAGCCGTCGCCCCGC 62.795 63.158 0.00 0.00 34.57 6.13
1567 1838 2.034001 CCGCTCTTTTTATAAGCCGTCG 60.034 50.000 0.00 0.00 32.31 5.12
1569 1840 3.195661 CTCCGCTCTTTTTATAAGCCGT 58.804 45.455 0.00 0.00 32.31 5.68
1731 2192 0.687354 AAACTCTCACCGGACTGCAT 59.313 50.000 9.46 0.00 0.00 3.96
1874 2350 7.507733 AAGGTGCATTTTTCAAAATTGCATA 57.492 28.000 26.81 9.71 40.67 3.14
2126 2614 2.334977 TCTAAGCAACTCAAGGACCCA 58.665 47.619 0.00 0.00 0.00 4.51
2162 2651 9.838163 CATATCATATTTTGTTGCATTTCGTTG 57.162 29.630 0.00 0.00 0.00 4.10
2215 2706 9.618890 TTGTAACATCCCAAATTTTCAATTTGA 57.381 25.926 19.15 0.00 40.42 2.69


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

AutoCloner maintained by Alex Coulton.