Multiple sequence alignment - TraesCS7D01G296500

Loading Multiple Alignment...

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 TraesCS7D01G296500 chr7D 100.000 3828 0 0 1 3828 372906543 372902716 0.000000e+00 7070
1 TraesCS7D01G296500 chr7B 94.893 3818 119 30 1 3768 368157313 368153522 0.000000e+00 5901
2 TraesCS7D01G296500 chr7A 97.186 3269 65 12 253 3508 418115751 418112497 0.000000e+00 5502
3 TraesCS7D01G296500 chr7A 92.879 323 18 4 3511 3828 418106661 418106339 7.490000e-127 464
4 TraesCS7D01G296500 chr7A 91.353 266 11 9 1 262 418116113 418115856 1.690000e-93 353


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 TraesCS7D01G296500 chr7D 372902716 372906543 3827 True 7070.0 7070 100.0000 1 3828 1 chr7D.!!$R1 3827
1 TraesCS7D01G296500 chr7B 368153522 368157313 3791 True 5901.0 5901 94.8930 1 3768 1 chr7B.!!$R1 3767
2 TraesCS7D01G296500 chr7A 418112497 418116113 3616 True 2927.5 5502 94.2695 1 3508 2 chr7A.!!$R2 3507

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
431 563 0.035458 CGGGGATATTCAGGCCAGAC 59.965 60.0 5.01 0.0 0.00 3.51 F
447 579 0.118144 AGACCAGCCTTTCTCCTCCT 59.882 55.0 0.00 0.0 0.00 3.69 F
465 597 0.991920 CTACATCCACCACTTGGGGT 59.008 55.0 0.00 0.0 46.92 4.95 F
2372 2529 0.932123 CGGTCACATCTCTGATCGCG 60.932 60.0 0.00 0.0 37.93 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2331 1.109920 ACAGGCATCCGAGTCGCTAT 61.110 55.000 7.12 0.00 0.00 2.97 R
2228 2385 4.721776 AGGCCTATCAGGAATGAACACTTA 59.278 41.667 1.29 0.00 37.67 2.24 R
2632 2789 4.488136 AGCAATGGCCCGATCGCA 62.488 61.111 10.32 2.57 42.56 5.10 R
3700 3874 2.041115 GCGGGAGGAAGAGCCAAAC 61.041 63.158 0.00 0.00 40.02 2.93 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
41 42 2.432628 CGCGGAGGTGTGTTCTCC 60.433 66.667 0.00 0.00 45.46 3.71
128 129 2.896745 AGCTTTGTTCCCTTTGCTTG 57.103 45.000 0.00 0.00 0.00 4.01
143 144 1.794222 CTTGTTTGGATCGTCGGGC 59.206 57.895 0.00 0.00 0.00 6.13
212 213 3.322466 CGAGGGCAGGGAGTTGGT 61.322 66.667 0.00 0.00 0.00 3.67
227 228 5.353400 GGGAGTTGGTAAGGATTTTTAGTCG 59.647 44.000 0.00 0.00 0.00 4.18
426 558 3.713826 TTTATCCGGGGATATTCAGGC 57.286 47.619 8.19 0.00 37.02 4.85
431 563 0.035458 CGGGGATATTCAGGCCAGAC 59.965 60.000 5.01 0.00 0.00 3.51
444 576 1.846712 GCCAGACCAGCCTTTCTCCT 61.847 60.000 0.00 0.00 0.00 3.69
447 579 0.118144 AGACCAGCCTTTCTCCTCCT 59.882 55.000 0.00 0.00 0.00 3.69
448 580 1.362932 AGACCAGCCTTTCTCCTCCTA 59.637 52.381 0.00 0.00 0.00 2.94
449 581 1.483004 GACCAGCCTTTCTCCTCCTAC 59.517 57.143 0.00 0.00 0.00 3.18
450 582 1.203313 ACCAGCCTTTCTCCTCCTACA 60.203 52.381 0.00 0.00 0.00 2.74
451 583 2.122768 CCAGCCTTTCTCCTCCTACAT 58.877 52.381 0.00 0.00 0.00 2.29
452 584 2.103941 CCAGCCTTTCTCCTCCTACATC 59.896 54.545 0.00 0.00 0.00 3.06
453 585 2.103941 CAGCCTTTCTCCTCCTACATCC 59.896 54.545 0.00 0.00 0.00 3.51
454 586 2.119495 GCCTTTCTCCTCCTACATCCA 58.881 52.381 0.00 0.00 0.00 3.41
465 597 0.991920 CTACATCCACCACTTGGGGT 59.008 55.000 0.00 0.00 46.92 4.95
526 658 7.932335 AGATACTTGATACTTTAGAGTCACGG 58.068 38.462 0.00 0.00 37.33 4.94
809 966 4.641541 TGCTTTGGATCATTAGACATGTGG 59.358 41.667 1.15 0.00 0.00 4.17
1470 1627 6.108687 CACTTTGCTTGGTGAGATAGATGTA 58.891 40.000 0.00 0.00 35.69 2.29
1584 1741 1.097232 GCACTGCCATATTCACTGCA 58.903 50.000 0.00 0.00 0.00 4.41
1674 1831 4.795308 GCTGGCTTATTTCAATCATCTGGC 60.795 45.833 0.00 0.00 0.00 4.85
2174 2331 2.045561 TGTTTCCTTTGGTGCTTCGA 57.954 45.000 0.00 0.00 0.00 3.71
2228 2385 6.071391 CCTGTTATAACCTGAACCATGCTTTT 60.071 38.462 13.01 0.00 0.00 2.27
2372 2529 0.932123 CGGTCACATCTCTGATCGCG 60.932 60.000 0.00 0.00 37.93 5.87
2827 2984 6.892658 ACTACCTGCTCAGATCAAGTATAG 57.107 41.667 0.00 0.00 0.00 1.31
3046 3203 8.792830 TTATTTAGACAAGATGGAGGTGAAAG 57.207 34.615 0.00 0.00 0.00 2.62
3102 3259 9.959721 TTCTTTTCTCTAGTGCCTTGTAAATAT 57.040 29.630 0.00 0.00 0.00 1.28
3322 3487 4.640647 AGAGAAGTGTTGGTCCAAGAAAAC 59.359 41.667 3.96 1.75 0.00 2.43
3345 3510 7.615582 ACAAATGGTGTACTGATTATCTGTG 57.384 36.000 13.75 0.00 39.29 3.66
3370 3535 7.908082 TGCATATGCTTTCAGTTTCGTTATTAC 59.092 33.333 27.13 0.00 42.66 1.89
3371 3536 8.122952 GCATATGCTTTCAGTTTCGTTATTACT 58.877 33.333 20.64 0.00 38.21 2.24
3430 3595 6.207614 TGGAGTGATCTGATATACACTGCTAC 59.792 42.308 21.43 7.80 46.39 3.58
3431 3596 6.432783 GGAGTGATCTGATATACACTGCTACT 59.567 42.308 16.81 0.00 44.20 2.57
3432 3597 7.608376 GGAGTGATCTGATATACACTGCTACTA 59.392 40.741 16.81 0.00 44.20 1.82
3501 3671 7.225145 ACATGTCCTTTTGATGTTTCATTGTTG 59.775 33.333 0.00 0.00 0.00 3.33
3514 3684 7.424803 TGTTTCATTGTTGTATCTTTGTCCTG 58.575 34.615 0.00 0.00 0.00 3.86
3516 3686 8.299570 GTTTCATTGTTGTATCTTTGTCCTGAT 58.700 33.333 0.00 0.00 0.00 2.90
3547 3717 8.806146 ACCAAGTCTATAGAAAAACATGCAAAT 58.194 29.630 3.40 0.00 0.00 2.32
3558 3728 8.767085 AGAAAAACATGCAAATATCAACAACAG 58.233 29.630 0.00 0.00 0.00 3.16
3700 3874 9.912634 ATAAACATGTAGACAAATGAAAACAGG 57.087 29.630 0.00 0.00 0.00 4.00
3717 3891 1.377333 GGTTTGGCTCTTCCTCCCG 60.377 63.158 0.00 0.00 35.26 5.14
3718 3892 2.041115 GTTTGGCTCTTCCTCCCGC 61.041 63.158 0.00 0.00 35.26 6.13
3719 3893 2.525124 TTTGGCTCTTCCTCCCGCA 61.525 57.895 0.00 0.00 35.26 5.69
3720 3894 1.852157 TTTGGCTCTTCCTCCCGCAT 61.852 55.000 0.00 0.00 35.26 4.73
3721 3895 0.980754 TTGGCTCTTCCTCCCGCATA 60.981 55.000 0.00 0.00 35.26 3.14
3793 3970 9.877178 AAAACTTAAACATGTCAAAATACACCA 57.123 25.926 0.00 0.00 30.75 4.17
3802 3979 9.639563 ACATGTCAAAATACACCATATATTCCA 57.360 29.630 0.00 0.00 30.75 3.53
3810 3987 9.920946 AAATACACCATATATTCCAAACAGACT 57.079 29.630 0.00 0.00 0.00 3.24
3821 3998 5.693769 TCCAAACAGACTATAAAGAGGGG 57.306 43.478 0.00 0.00 0.00 4.79
3822 3999 5.347124 TCCAAACAGACTATAAAGAGGGGA 58.653 41.667 0.00 0.00 0.00 4.81
3823 4000 5.788533 TCCAAACAGACTATAAAGAGGGGAA 59.211 40.000 0.00 0.00 0.00 3.97
3824 4001 6.273730 TCCAAACAGACTATAAAGAGGGGAAA 59.726 38.462 0.00 0.00 0.00 3.13
3825 4002 6.946009 CCAAACAGACTATAAAGAGGGGAAAA 59.054 38.462 0.00 0.00 0.00 2.29
3826 4003 7.615757 CCAAACAGACTATAAAGAGGGGAAAAT 59.384 37.037 0.00 0.00 0.00 1.82
3827 4004 8.678199 CAAACAGACTATAAAGAGGGGAAAATC 58.322 37.037 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 0.953960 AACAGCCCGACGATCCAAAC 60.954 55.000 0.00 0.00 0.00 2.93
143 144 3.254014 CTCGCCGCCAAACCAACAG 62.254 63.158 0.00 0.00 0.00 3.16
212 213 8.098286 TGAATCCTGAACGACTAAAAATCCTTA 58.902 33.333 0.00 0.00 0.00 2.69
227 228 1.846439 TCTCCCCCATGAATCCTGAAC 59.154 52.381 0.00 0.00 0.00 3.18
426 558 0.251634 GAGGAGAAAGGCTGGTCTGG 59.748 60.000 5.74 0.00 0.00 3.86
431 563 1.573108 TGTAGGAGGAGAAAGGCTGG 58.427 55.000 0.00 0.00 0.00 4.85
453 585 3.069016 GGTAAAAAGAACCCCAAGTGGTG 59.931 47.826 0.00 0.00 39.05 4.17
454 586 3.052414 AGGTAAAAAGAACCCCAAGTGGT 60.052 43.478 0.00 0.00 41.55 4.16
465 597 2.891191 ATCGGGGCAGGTAAAAAGAA 57.109 45.000 0.00 0.00 0.00 2.52
526 658 3.309954 CCTTAGCAATCAACCGACTTAGC 59.690 47.826 0.00 0.00 0.00 3.09
803 960 5.163972 CGCAAACATGGTAAAAATCCACATG 60.164 40.000 0.00 0.00 43.29 3.21
804 961 4.928615 CGCAAACATGGTAAAAATCCACAT 59.071 37.500 0.00 0.00 37.81 3.21
809 966 5.898630 AACACGCAAACATGGTAAAAATC 57.101 34.783 0.00 0.00 0.00 2.17
987 1144 7.282224 GTGGTTAGTAACATCCATAAGCAATCA 59.718 37.037 14.81 0.00 37.37 2.57
1033 1190 9.427127 GAGCGATTCTCTGTTAAAATTGATAAC 57.573 33.333 7.22 7.22 38.78 1.89
1049 1206 0.665298 GGGCAAATGGAGCGATTCTC 59.335 55.000 0.00 0.00 41.15 2.87
1584 1741 3.624777 CCAATATCCAGCACCAAAGAGT 58.375 45.455 0.00 0.00 0.00 3.24
2174 2331 1.109920 ACAGGCATCCGAGTCGCTAT 61.110 55.000 7.12 0.00 0.00 2.97
2228 2385 4.721776 AGGCCTATCAGGAATGAACACTTA 59.278 41.667 1.29 0.00 37.67 2.24
2632 2789 4.488136 AGCAATGGCCCGATCGCA 62.488 61.111 10.32 2.57 42.56 5.10
2827 2984 4.051922 CGAGCAGACCATACTTACAATCC 58.948 47.826 0.00 0.00 0.00 3.01
3046 3203 1.269778 GGGCTCAGAAACTTTTGGTGC 60.270 52.381 0.00 0.00 0.00 5.01
3102 3259 3.307339 GCCCAAACTTATTGCCCAATTCA 60.307 43.478 0.00 0.00 32.50 2.57
3285 3443 4.782156 ACACTTCTCTGGGATCTCAATTCT 59.218 41.667 0.00 0.00 0.00 2.40
3301 3466 4.340617 TGTTTTCTTGGACCAACACTTCT 58.659 39.130 1.69 0.00 0.00 2.85
3322 3487 6.093909 TGCACAGATAATCAGTACACCATTTG 59.906 38.462 0.00 0.00 0.00 2.32
3341 3506 4.093514 CGAAACTGAAAGCATATGCACAG 58.906 43.478 29.78 29.78 45.16 3.66
3345 3510 8.122952 AGTAATAACGAAACTGAAAGCATATGC 58.877 33.333 20.36 20.36 37.60 3.14
3370 3535 7.411588 GCGTGTAAACCACAAGTTATCTTCTAG 60.412 40.741 0.00 0.00 44.78 2.43
3371 3536 6.366877 GCGTGTAAACCACAAGTTATCTTCTA 59.633 38.462 0.00 0.00 44.78 2.10
3372 3537 5.178809 GCGTGTAAACCACAAGTTATCTTCT 59.821 40.000 0.00 0.00 44.78 2.85
3479 3647 8.816640 ATACAACAATGAAACATCAAAAGGAC 57.183 30.769 0.00 0.00 0.00 3.85
3501 3671 6.716934 TGGTCTAGATCAGGACAAAGATAC 57.283 41.667 0.14 2.59 34.49 2.24
3626 3800 8.255206 AGAATATATCAACGTCTACAACACCAA 58.745 33.333 0.00 0.00 0.00 3.67
3670 3844 9.624697 TTTTCATTTGTCTACATGTTTATGAGC 57.375 29.630 2.30 0.00 37.73 4.26
3700 3874 2.041115 GCGGGAGGAAGAGCCAAAC 61.041 63.158 0.00 0.00 40.02 2.93
3776 3953 9.639563 TGGAATATATGGTGTATTTTGACATGT 57.360 29.630 0.00 0.00 0.00 3.21
3784 3961 9.920946 AGTCTGTTTGGAATATATGGTGTATTT 57.079 29.630 0.00 0.00 0.00 1.40
3795 3972 8.440771 CCCCTCTTTATAGTCTGTTTGGAATAT 58.559 37.037 0.00 0.00 32.44 1.28
3796 3973 7.626084 TCCCCTCTTTATAGTCTGTTTGGAATA 59.374 37.037 0.00 0.00 0.00 1.75
3797 3974 6.447084 TCCCCTCTTTATAGTCTGTTTGGAAT 59.553 38.462 0.00 0.00 0.00 3.01
3798 3975 5.788533 TCCCCTCTTTATAGTCTGTTTGGAA 59.211 40.000 0.00 0.00 0.00 3.53
3799 3976 5.347124 TCCCCTCTTTATAGTCTGTTTGGA 58.653 41.667 0.00 0.00 0.00 3.53
3800 3977 5.693769 TCCCCTCTTTATAGTCTGTTTGG 57.306 43.478 0.00 0.00 0.00 3.28
3801 3978 7.996098 TTTTCCCCTCTTTATAGTCTGTTTG 57.004 36.000 0.00 0.00 0.00 2.93
3802 3979 8.809468 GATTTTCCCCTCTTTATAGTCTGTTT 57.191 34.615 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.