Multiple sequence alignment - TraesCS3D01G339800

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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 TraesCS3D01G339800 chr3D 100.000 3524 0 0 1 3524 453096353 453099876 0.000000e+00 6508
1 TraesCS3D01G339800 chr3A 94.770 3537 143 21 1 3524 595433928 595437435 0.000000e+00 5469
2 TraesCS3D01G339800 chr3B 95.669 2909 107 6 1 2893 595287586 595290491 0.000000e+00 4656
3 TraesCS3D01G339800 chr3B 88.176 296 21 5 3124 3419 595290736 595291017 1.210000e-89 340
4 TraesCS3D01G339800 chr3B 95.098 102 4 1 3423 3524 595291185 595291285 3.640000e-35 159
5 TraesCS3D01G339800 chr2A 92.257 762 55 3 351 1109 279048890 279048130 0.000000e+00 1077
6 TraesCS3D01G339800 chr6B 78.094 1406 288 18 989 2384 169318576 169317181 0.000000e+00 872


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 TraesCS3D01G339800 chr3D 453096353 453099876 3523 False 6508.000000 6508 100.000 1 3524 1 chr3D.!!$F1 3523
1 TraesCS3D01G339800 chr3A 595433928 595437435 3507 False 5469.000000 5469 94.770 1 3524 1 chr3A.!!$F1 3523
2 TraesCS3D01G339800 chr3B 595287586 595291285 3699 False 1718.333333 4656 92.981 1 3524 3 chr3B.!!$F1 3523
3 TraesCS3D01G339800 chr2A 279048130 279048890 760 True 1077.000000 1077 92.257 351 1109 1 chr2A.!!$R1 758
4 TraesCS3D01G339800 chr6B 169317181 169318576 1395 True 872.000000 872 78.094 989 2384 1 chr6B.!!$R1 1395

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
263 270 0.716108 CCGATCGATTTCTATGGCGC 59.284 55.0 18.66 0.00 0.0 6.53 F
1638 1653 0.111639 TTGTGGCTGGTTACCTTCCC 59.888 55.0 2.07 0.82 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 1944 0.611714 TCAGGTTCGGGAGGCTTAAC 59.388 55.0 0.0 0.0 0.0 2.01 R
2945 2977 0.539438 ATTCGCAGCCCACCTCAAAA 60.539 50.0 0.0 0.0 0.0 2.44 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
66 70 1.224069 CCGGGCTACAATCATCGCTG 61.224 60.000 0.00 0.00 0.00 5.18
183 190 1.757118 TCCCAGAATCTACCAAGAGCG 59.243 52.381 0.00 0.00 34.49 5.03
263 270 0.716108 CCGATCGATTTCTATGGCGC 59.284 55.000 18.66 0.00 0.00 6.53
429 436 7.120138 GGAATGGTCGGTTTTTGAGTTAGAATA 59.880 37.037 0.00 0.00 0.00 1.75
522 529 4.691175 TCTGATTGCTGTAGATGCTCTTC 58.309 43.478 0.00 0.00 0.00 2.87
533 540 5.698089 TGTAGATGCTCTTCTTTGTTCTGTG 59.302 40.000 0.00 0.00 0.00 3.66
566 573 4.380843 TGATAGACAACATTGGGGTGTT 57.619 40.909 0.00 0.00 42.75 3.32
607 616 3.569701 TGTCTTCAAAGGCCACTGAATTC 59.430 43.478 17.17 13.70 31.40 2.17
610 619 2.151202 TCAAAGGCCACTGAATTCGTC 58.849 47.619 5.01 0.00 0.00 4.20
655 665 4.202461 CCCACCCTGCATTACATGTATACT 60.202 45.833 6.36 0.00 0.00 2.12
695 705 2.309613 TCTTGCTGGCAGTTGTTGATT 58.690 42.857 17.16 0.00 0.00 2.57
703 713 3.703556 TGGCAGTTGTTGATTGGAAGAAA 59.296 39.130 0.00 0.00 0.00 2.52
725 735 4.038271 ACTTGGGAATGCAGAAAGATGA 57.962 40.909 0.00 0.00 0.00 2.92
839 849 2.104170 CTGGTACTGTTCCTCCTCTCC 58.896 57.143 5.04 0.00 0.00 3.71
919 929 3.931578 AGACAGTTAACATCTGCTCCAC 58.068 45.455 8.61 0.00 36.50 4.02
1094 1109 3.318017 CGAAGGTCTATTATGCCCGAAG 58.682 50.000 0.00 0.00 0.00 3.79
1149 1164 8.425577 AGATGATCAACAAAGATAAGGTTACG 57.574 34.615 0.00 0.00 0.00 3.18
1458 1473 7.421530 TGAGAATGAAAACCTAAAAGTCTCG 57.578 36.000 0.00 0.00 33.31 4.04
1638 1653 0.111639 TTGTGGCTGGTTACCTTCCC 59.888 55.000 2.07 0.82 0.00 3.97
1656 1671 3.624777 TCCCTTTCATGAGGCAAATCTC 58.375 45.455 0.00 0.00 35.37 2.75
1720 1735 2.618053 CTCGGTATTTTTCCGCTGAGT 58.382 47.619 0.00 0.00 46.49 3.41
1926 1944 1.555075 TCTGAGGGAAATCAAGGGTCG 59.445 52.381 0.00 0.00 0.00 4.79
1938 1956 2.186125 GGGTCGTTAAGCCTCCCG 59.814 66.667 0.00 0.00 42.62 5.14
2565 2583 3.814005 AAGTACCTCGTGTGTGTTTCT 57.186 42.857 0.00 0.00 0.00 2.52
2703 2735 8.041919 GCATACTATAGGGGGAAATAAACTCTC 58.958 40.741 4.43 0.00 0.00 3.20
2710 2742 4.384868 GGGGGAAATAAACTCTCGATTCCA 60.385 45.833 11.22 0.00 38.42 3.53
2716 2748 9.290483 GGAAATAAACTCTCGATTCCATTTTTC 57.710 33.333 5.50 2.77 37.02 2.29
2812 2844 2.420687 CCCAAGGAGAGTGAACCTATGC 60.421 54.545 0.00 0.00 35.25 3.14
2856 2888 3.982576 ATGGTCAAAGAACACGTTTCC 57.017 42.857 0.00 0.00 29.56 3.13
2877 2909 1.920351 GGGAGGATGGTTTGGAGGTAA 59.080 52.381 0.00 0.00 0.00 2.85
2923 2955 4.565022 GCCTCTATAATCTGACCTTCAGC 58.435 47.826 0.00 0.00 43.95 4.26
2957 2989 1.754226 TCAACTGTTTTTGAGGTGGGC 59.246 47.619 0.00 0.00 31.68 5.36
2960 2992 0.032540 CTGTTTTTGAGGTGGGCTGC 59.967 55.000 0.00 0.00 0.00 5.25
2972 3004 2.324860 GTGGGCTGCGAATGTTTAAAC 58.675 47.619 11.54 11.54 0.00 2.01
2979 3011 4.613031 GCTGCGAATGTTTAAACTTCAGAC 59.387 41.667 18.72 11.62 0.00 3.51
2983 3015 4.319190 CGAATGTTTAAACTTCAGACCGCA 60.319 41.667 18.72 0.00 0.00 5.69
3001 3033 0.035056 CAACTTGGTGGGGGAGCTAG 60.035 60.000 0.00 0.00 0.00 3.42
3069 3104 2.224892 GGGGGAAGAGGAGGATAAATGC 60.225 54.545 0.00 0.00 0.00 3.56
3083 3118 0.936600 AAATGCGTTTGCTTGGTTGC 59.063 45.000 2.32 0.00 43.34 4.17
3125 3270 0.542232 AGCAGACGTAGAGGTTGGGT 60.542 55.000 0.00 0.00 0.00 4.51
3141 3286 0.179081 GGGTGCGGATGTAGAAGGAC 60.179 60.000 0.00 0.00 0.00 3.85
3153 3298 0.314302 AGAAGGACCGACAAGACACG 59.686 55.000 0.00 0.00 0.00 4.49
3154 3299 1.282930 GAAGGACCGACAAGACACGC 61.283 60.000 0.00 0.00 0.00 5.34
3167 3312 0.598065 GACACGCCAGCAAAAAGGAT 59.402 50.000 0.00 0.00 0.00 3.24
3212 3357 2.030805 GCTCACGCCAAGATGAAAGTTT 60.031 45.455 0.00 0.00 0.00 2.66
3213 3358 3.550842 GCTCACGCCAAGATGAAAGTTTT 60.551 43.478 0.00 0.00 0.00 2.43
3222 3368 6.030228 CCAAGATGAAAGTTTTCCGATTAGC 58.970 40.000 2.41 0.00 36.36 3.09
3238 3384 5.345741 CCGATTAGCCTTGTTTTGATGTTTG 59.654 40.000 0.00 0.00 0.00 2.93
3275 3421 5.361285 ACTGTCTGGTAGTAATAAGCTCTGG 59.639 44.000 0.00 0.00 0.00 3.86
3276 3422 4.099573 TGTCTGGTAGTAATAAGCTCTGGC 59.900 45.833 0.00 0.00 39.06 4.85
3392 3538 0.179067 TTGTGGGTTCGTGACAGGAC 60.179 55.000 0.00 0.00 0.00 3.85
3434 3744 7.305418 GCTTGTCTGTTGTTTTATCAGTTTTCG 60.305 37.037 0.00 0.00 0.00 3.46
3457 3767 1.656818 ATGAAAACTGGGCGCGATGG 61.657 55.000 12.10 0.00 0.00 3.51
3458 3768 3.051392 GAAAACTGGGCGCGATGGG 62.051 63.158 12.10 0.00 0.00 4.00
3513 3823 8.625651 TCTAATCGGTTTTGACTTTTGATTCAA 58.374 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 70 5.589192 TCGGAATCTTCTAATTTCGGTCTC 58.411 41.667 0.00 0.00 38.04 3.36
153 160 1.216427 AGATTCTGGGATTTCTGGGCC 59.784 52.381 0.00 0.00 0.00 5.80
247 254 1.670087 CGGAGCGCCATAGAAATCGAT 60.670 52.381 7.44 0.00 0.00 3.59
315 322 5.450412 GCAAGTAGATCTCTTCCTGTCAGAG 60.450 48.000 0.00 0.00 39.45 3.35
360 367 0.532115 AAAATTCATGCCCAGGACGC 59.468 50.000 0.00 0.00 0.00 5.19
371 378 4.333372 GCATCCAAAATCGGCAAAATTCAT 59.667 37.500 0.00 0.00 0.00 2.57
438 445 6.035435 CCATCTCTTGAGTTCTACAAACGATG 59.965 42.308 0.00 0.00 35.82 3.84
446 453 5.275067 AGATGCCATCTCTTGAGTTCTAC 57.725 43.478 0.08 0.00 33.42 2.59
533 540 6.985188 TGTTGTCTATCAAACTTAGATGGC 57.015 37.500 0.00 0.00 37.81 4.40
566 573 5.826643 AGACATTAAGGCAAATCTTGGGTA 58.173 37.500 0.00 0.00 0.00 3.69
607 616 6.627690 TTACGAGCTCTAATGAAAAAGACG 57.372 37.500 12.85 0.00 0.00 4.18
610 619 6.538742 TGGGATTACGAGCTCTAATGAAAAAG 59.461 38.462 12.85 0.00 0.00 2.27
678 688 0.675083 CCAATCAACAACTGCCAGCA 59.325 50.000 0.00 0.00 0.00 4.41
695 705 3.303938 TGCATTCCCAAGTTTTCTTCCA 58.696 40.909 0.00 0.00 38.17 3.53
703 713 4.410099 TCATCTTTCTGCATTCCCAAGTT 58.590 39.130 0.00 0.00 0.00 2.66
919 929 9.161629 CAGTATCTAGACTGTATACCTCATGAG 57.838 40.741 16.24 16.24 41.67 2.90
1080 1095 3.466836 TGCAAGACTTCGGGCATAATAG 58.533 45.455 0.00 0.00 0.00 1.73
1094 1109 1.006922 GCTTGGCCAGTTGCAAGAC 60.007 57.895 18.48 0.00 43.89 3.01
1134 1149 5.935789 TCCAACCTTCGTAACCTTATCTTTG 59.064 40.000 0.00 0.00 0.00 2.77
1149 1164 3.055094 TCTGCTCCATAAGTCCAACCTTC 60.055 47.826 0.00 0.00 0.00 3.46
1392 1407 3.000322 GCTTCAGATCACGGTGATAAACG 60.000 47.826 22.70 11.74 37.20 3.60
1458 1473 1.970640 AGGGCACTCAAACCAAAATCC 59.029 47.619 0.00 0.00 0.00 3.01
1638 1653 7.662258 ATCTCTATGAGATTTGCCTCATGAAAG 59.338 37.037 14.56 9.71 45.86 2.62
1656 1671 9.473007 TTGGAGATCCTTCTATACATCTCTATG 57.527 37.037 7.52 0.00 40.74 2.23
1881 1896 0.622136 TGCATCCTGTTGAGCCTGAT 59.378 50.000 0.00 0.00 0.00 2.90
1926 1944 0.611714 TCAGGTTCGGGAGGCTTAAC 59.388 55.000 0.00 0.00 0.00 2.01
1938 1956 5.063180 TGATGTCAAATGCATTCAGGTTC 57.937 39.130 13.38 8.31 0.00 3.62
2012 2030 1.726853 AAATCGTTCTTCCCTGCGAG 58.273 50.000 0.00 0.00 36.79 5.03
2565 2583 7.661536 AAGAGTATGGAATTAGCAGTACAGA 57.338 36.000 0.00 0.00 0.00 3.41
2703 2735 7.475771 TCAAAAAGGTTGAAAAATGGAATCG 57.524 32.000 0.00 0.00 0.00 3.34
2738 2770 5.189736 AGAACTAGATGGTGCTGGTCAATAA 59.810 40.000 0.00 0.00 0.00 1.40
2779 2811 4.760204 ACTCTCCTTGGGAAACAAATTACG 59.240 41.667 0.00 0.00 38.91 3.18
2791 2823 2.420687 GCATAGGTTCACTCTCCTTGGG 60.421 54.545 0.00 0.00 35.51 4.12
2856 2888 1.224592 CCTCCAAACCATCCTCCCG 59.775 63.158 0.00 0.00 0.00 5.14
2945 2977 0.539438 ATTCGCAGCCCACCTCAAAA 60.539 50.000 0.00 0.00 0.00 2.44
2957 2989 5.147162 GGTCTGAAGTTTAAACATTCGCAG 58.853 41.667 20.06 16.62 0.00 5.18
2960 2992 4.148891 GCGGTCTGAAGTTTAAACATTCG 58.851 43.478 20.06 13.23 0.00 3.34
2972 3004 0.588252 CACCAAGTTGCGGTCTGAAG 59.412 55.000 0.00 0.00 33.25 3.02
2979 3011 4.278513 TCCCCCACCAAGTTGCGG 62.279 66.667 0.00 0.00 0.00 5.69
2983 3015 1.853250 GCTAGCTCCCCCACCAAGTT 61.853 60.000 7.70 0.00 0.00 2.66
3001 3033 4.199310 TGTAATTCCTGCCAGATAACAGC 58.801 43.478 0.00 0.00 32.37 4.40
3083 3118 2.367868 AAAAACCCAGCTGCCGCTTG 62.368 55.000 8.66 0.00 46.47 4.01
3115 3150 0.907704 TACATCCGCACCCAACCTCT 60.908 55.000 0.00 0.00 0.00 3.69
3125 3270 0.681887 TCGGTCCTTCTACATCCGCA 60.682 55.000 0.00 0.00 40.81 5.69
3141 3286 3.414700 GCTGGCGTGTCTTGTCGG 61.415 66.667 0.00 0.00 0.00 4.79
3153 3298 1.826720 TCCATCATCCTTTTTGCTGGC 59.173 47.619 0.00 0.00 31.83 4.85
3154 3299 4.540359 TTTCCATCATCCTTTTTGCTGG 57.460 40.909 0.00 0.00 32.80 4.85
3212 3357 4.764823 ACATCAAAACAAGGCTAATCGGAA 59.235 37.500 0.00 0.00 0.00 4.30
3213 3358 4.331968 ACATCAAAACAAGGCTAATCGGA 58.668 39.130 0.00 0.00 0.00 4.55
3222 3368 7.220683 CAGTAACTCACAAACATCAAAACAAGG 59.779 37.037 0.00 0.00 0.00 3.61
3238 3384 3.256136 ACCAGACAGTAGCAGTAACTCAC 59.744 47.826 0.00 0.00 0.00 3.51
3308 3454 1.466360 GGAACATAACGCAGCAGCAAG 60.466 52.381 0.82 0.00 42.27 4.01
3357 3503 2.802816 CCACAAGAAAACCAGTCTCGAG 59.197 50.000 5.93 5.93 0.00 4.04
3434 3744 1.803289 GCGCCCAGTTTTCATCTCC 59.197 57.895 0.00 0.00 0.00 3.71
3457 3767 1.208293 AGACTTCTCGGAATCAAGGCC 59.792 52.381 0.00 0.00 0.00 5.19
3458 3768 2.682155 AGACTTCTCGGAATCAAGGC 57.318 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.