Multiple sequence alignment - TraesCS6D01G265400

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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 TraesCS6D01G265400 chr6D 100.000 3974 0 0 1 3974 375014977 375018950 0.000000e+00 7339
1 TraesCS6D01G265400 chr6B 94.502 4056 106 50 1 3973 561691487 561695508 0.000000e+00 6146
2 TraesCS6D01G265400 chr6A 96.606 3477 72 22 1 3445 516407631 516411093 0.000000e+00 5725
3 TraesCS6D01G265400 chr6A 87.829 304 19 5 3687 3973 516411377 516411679 1.370000e-89 340
4 TraesCS6D01G265400 chr6A 87.027 185 6 7 3471 3640 516411088 516411269 4.050000e-45 193


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 TraesCS6D01G265400 chr6D 375014977 375018950 3973 False 7339 7339 100.000000 1 3974 1 chr6D.!!$F1 3973
1 TraesCS6D01G265400 chr6B 561691487 561695508 4021 False 6146 6146 94.502000 1 3973 1 chr6B.!!$F1 3972
2 TraesCS6D01G265400 chr6A 516407631 516411679 4048 False 2086 5725 90.487333 1 3973 3 chr6A.!!$F1 3972


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
211 212 0.744874 GCTGATCTAGGTGGCACGTA 59.255 55.000 18.03 18.03 0.0 3.57 F
428 429 6.983307 CCCAAATATGTTTGTTGTCTGTTTGA 59.017 34.615 13.13 0.00 42.5 2.69 F
1202 1224 1.120530 CCATACTGCCGTCCTAAGGT 58.879 55.000 0.00 0.00 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1040 1062 0.252479 AGCAGGAGCCATCACAAGAG 59.748 55.0 0.00 0.0 43.56 2.85 R
1902 1924 2.113860 TGCCAGCCAAGAACAGTATC 57.886 50.0 0.00 0.0 0.00 2.24 R
3171 3203 0.883153 AGAGCGCATTTGCATCAACA 59.117 45.0 11.47 0.0 42.21 3.33 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
26 27 1.743995 GTTTACCCGCTCGCATGGT 60.744 57.895 0.00 5.58 36.15 3.55
148 149 2.744768 AAGCAGCTCCAGTGCCACTC 62.745 60.000 0.00 0.00 42.24 3.51
211 212 0.744874 GCTGATCTAGGTGGCACGTA 59.255 55.000 18.03 18.03 0.00 3.57
428 429 6.983307 CCCAAATATGTTTGTTGTCTGTTTGA 59.017 34.615 13.13 0.00 42.50 2.69
475 479 9.673454 GTAAAAGAACGACTATGAATTGGTTTT 57.327 29.630 0.00 0.00 0.00 2.43
697 715 9.454859 CTTATTTTACTCTTTGATCCTCCTTGT 57.545 33.333 0.00 0.00 0.00 3.16
1040 1062 2.072298 CTCTGCTTTGCTAGTGGTGTC 58.928 52.381 0.00 0.00 0.00 3.67
1202 1224 1.120530 CCATACTGCCGTCCTAAGGT 58.879 55.000 0.00 0.00 0.00 3.50
1280 1302 2.118313 AATTCCCCTTACCGTTTCCG 57.882 50.000 0.00 0.00 0.00 4.30
1782 1804 2.103941 CAGGGAGAAGGAGCAGATTACC 59.896 54.545 0.00 0.00 0.00 2.85
1902 1924 6.313658 TCTCAATTATGAACTCGTTGATGGTG 59.686 38.462 0.00 0.00 34.49 4.17
2706 2728 3.182967 CGCTGAGGTATCTGTTGTTCTC 58.817 50.000 0.00 0.00 0.00 2.87
2809 2831 6.602406 TGTGTTCCTCTACTCTATCAACTACC 59.398 42.308 0.00 0.00 0.00 3.18
3136 3168 8.718102 TGTTCTAGTAGATGTGATTTTAAGCC 57.282 34.615 0.00 0.00 0.00 4.35
3171 3203 4.581824 TCTCTTCTCTTTGCTGCAACATTT 59.418 37.500 15.72 0.00 0.00 2.32
3192 3224 2.487372 TGTTGATGCAAATGCGCTCTTA 59.513 40.909 9.73 0.00 45.83 2.10
3199 3231 4.808558 TGCAAATGCGCTCTTAAAAATCT 58.191 34.783 9.73 0.00 45.83 2.40
3211 3243 7.229530 GCTCTTAAAAATCTTGAATTTTGCCG 58.770 34.615 6.65 0.00 32.23 5.69
3212 3244 7.095649 GCTCTTAAAAATCTTGAATTTTGCCGT 60.096 33.333 6.65 0.00 32.23 5.68
3215 3247 6.676237 AAAAATCTTGAATTTTGCCGTGTT 57.324 29.167 0.00 0.00 32.23 3.32
3216 3248 7.778470 AAAAATCTTGAATTTTGCCGTGTTA 57.222 28.000 0.00 0.00 32.23 2.41
3220 3252 5.837437 TCTTGAATTTTGCCGTGTTATTGT 58.163 33.333 0.00 0.00 0.00 2.71
3244 3276 1.774110 TGTGCAACTGTTGGTTCCAT 58.226 45.000 21.01 0.00 38.04 3.41
3275 3307 6.601332 TCTTTTCCAAGATAGGTTTGTCACT 58.399 36.000 0.00 0.00 33.80 3.41
3338 3398 3.186409 TGTGCTTTTCTGACTTGCGTATC 59.814 43.478 0.00 0.00 0.00 2.24
3410 3470 7.592938 TGGTAATTCATAAGTGAAGTGCTTTG 58.407 34.615 6.64 0.00 46.75 2.77
3517 3577 0.957888 GGTTTGCTCCTCTGTCCAGC 60.958 60.000 0.00 0.00 0.00 4.85
3518 3578 0.036022 GTTTGCTCCTCTGTCCAGCT 59.964 55.000 0.00 0.00 34.03 4.24
3577 3637 8.253810 TGTAAGAGACAGTTCCATTATTCTGAG 58.746 37.037 0.00 0.00 32.86 3.35
3578 3638 6.865834 AGAGACAGTTCCATTATTCTGAGT 57.134 37.500 0.00 0.00 0.00 3.41
3580 3640 7.327214 AGAGACAGTTCCATTATTCTGAGTTC 58.673 38.462 0.00 0.00 0.00 3.01
3610 3676 3.799035 CTTTCGCATATCGCACCATAAC 58.201 45.455 0.00 0.00 42.60 1.89
3630 3704 1.556911 CTTCTATGCCCATATCGCCCT 59.443 52.381 0.00 0.00 0.00 5.19
3635 3709 0.033601 TGCCCATATCGCCCTGTTTT 60.034 50.000 0.00 0.00 0.00 2.43
3662 3736 7.517614 TTTTTCTTTGCCTTTTGTTTTCCTT 57.482 28.000 0.00 0.00 0.00 3.36
3663 3737 7.517614 TTTTCTTTGCCTTTTGTTTTCCTTT 57.482 28.000 0.00 0.00 0.00 3.11
3676 3750 2.358322 TTCCTTTCCCTTTTCGCTGT 57.642 45.000 0.00 0.00 0.00 4.40
3693 3767 4.215185 TCGCTGTTGCATAATGTTCAAAGA 59.785 37.500 0.00 0.00 39.64 2.52
3697 3771 7.253422 GCTGTTGCATAATGTTCAAAGATAGT 58.747 34.615 0.00 0.00 39.41 2.12
3712 3869 7.603651 TCAAAGATAGTTCTGAGAACACTACC 58.396 38.462 25.45 10.61 30.72 3.18
3786 3955 3.554934 TCTCAGTGCAATCTTTGTTGGT 58.445 40.909 0.00 0.00 0.00 3.67
3854 4027 0.472471 ACCCGTGACAGTGAAATGGT 59.528 50.000 0.00 0.00 0.00 3.55
3866 4039 5.426509 ACAGTGAAATGGTGGATCTATCTCA 59.573 40.000 0.00 0.00 0.00 3.27
3890 4063 5.982465 TTTGCCTTACAAAAAGAACATGC 57.018 34.783 0.00 0.00 45.22 4.06
3901 4074 0.608130 AGAACATGCGAGGTGCTGTA 59.392 50.000 0.00 0.00 46.63 2.74
3967 4143 1.066143 GTGGCTCCAAGGAGATTTCGA 60.066 52.381 19.99 0.00 44.53 3.71
3973 4149 4.256920 CTCCAAGGAGATTTCGAACACAT 58.743 43.478 10.66 0.00 44.53 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.027314 CTCGGGCGAGCAGATCTG 59.973 66.667 18.84 18.84 35.31 2.90
148 149 6.835914 ACTAAATCAGCGACAAATCTTGAAG 58.164 36.000 0.00 0.00 0.00 3.02
211 212 4.164988 AGTTAGAAGCATGGATGGCTAAGT 59.835 41.667 0.00 0.00 41.66 2.24
475 479 7.836685 TGGCCAAAGGTGTTAGATGAAATAATA 59.163 33.333 0.61 0.00 0.00 0.98
489 493 1.145738 AGAATGTCTGGCCAAAGGTGT 59.854 47.619 7.01 0.00 0.00 4.16
697 715 0.474184 GCCCAGGATAAGCTAAGCCA 59.526 55.000 0.00 0.00 0.00 4.75
1040 1062 0.252479 AGCAGGAGCCATCACAAGAG 59.748 55.000 0.00 0.00 43.56 2.85
1202 1224 4.908601 TCAGCACTCTTCTTTATCCCAA 57.091 40.909 0.00 0.00 0.00 4.12
1280 1302 4.093998 AGAGCGATTCATTGACATTGACAC 59.906 41.667 0.00 0.00 0.00 3.67
1902 1924 2.113860 TGCCAGCCAAGAACAGTATC 57.886 50.000 0.00 0.00 0.00 2.24
2706 2728 1.325640 GCACAGAGATGCATGTACGTG 59.674 52.381 16.55 16.55 45.39 4.49
2809 2831 3.672808 AGCTTCTGAGATCAAACACCAG 58.327 45.455 0.00 0.00 0.00 4.00
3146 3178 3.947196 TGTTGCAGCAAAGAGAAGAGAAA 59.053 39.130 10.11 0.00 0.00 2.52
3171 3203 0.883153 AGAGCGCATTTGCATCAACA 59.117 45.000 11.47 0.00 42.21 3.33
3186 3218 7.095649 ACGGCAAAATTCAAGATTTTTAAGAGC 60.096 33.333 3.28 3.44 0.00 4.09
3192 3224 6.676237 AACACGGCAAAATTCAAGATTTTT 57.324 29.167 0.00 0.00 0.00 1.94
3199 3231 4.210120 GCACAATAACACGGCAAAATTCAA 59.790 37.500 0.00 0.00 0.00 2.69
3250 3282 7.013274 CAGTGACAAACCTATCTTGGAAAAGAA 59.987 37.037 0.00 0.00 31.77 2.52
3275 3307 9.851686 ACACTGCATAGATAAAATAAATCTCCA 57.148 29.630 0.00 0.00 35.36 3.86
3338 3398 3.877559 TGACATACAGAATCTTGGGCAG 58.122 45.455 0.00 0.00 0.00 4.85
3410 3470 8.094798 TGTCAGTCAACAAGGAATAATAACAC 57.905 34.615 0.00 0.00 0.00 3.32
3555 3615 6.865834 ACTCAGAATAATGGAACTGTCTCT 57.134 37.500 0.00 0.00 0.00 3.10
3556 3616 7.064016 GTGAACTCAGAATAATGGAACTGTCTC 59.936 40.741 0.00 0.00 0.00 3.36
3610 3676 1.556911 AGGGCGATATGGGCATAGAAG 59.443 52.381 13.23 0.00 0.00 2.85
3642 3716 5.182487 GGAAAGGAAAACAAAAGGCAAAGA 58.818 37.500 0.00 0.00 0.00 2.52
3643 3717 4.335315 GGGAAAGGAAAACAAAAGGCAAAG 59.665 41.667 0.00 0.00 0.00 2.77
3644 3718 4.018870 AGGGAAAGGAAAACAAAAGGCAAA 60.019 37.500 0.00 0.00 0.00 3.68
3645 3719 3.521531 AGGGAAAGGAAAACAAAAGGCAA 59.478 39.130 0.00 0.00 0.00 4.52
3646 3720 3.111484 AGGGAAAGGAAAACAAAAGGCA 58.889 40.909 0.00 0.00 0.00 4.75
3647 3721 3.838244 AGGGAAAGGAAAACAAAAGGC 57.162 42.857 0.00 0.00 0.00 4.35
3648 3722 5.293324 CGAAAAGGGAAAGGAAAACAAAAGG 59.707 40.000 0.00 0.00 0.00 3.11
3649 3723 5.220586 GCGAAAAGGGAAAGGAAAACAAAAG 60.221 40.000 0.00 0.00 0.00 2.27
3650 3724 4.632251 GCGAAAAGGGAAAGGAAAACAAAA 59.368 37.500 0.00 0.00 0.00 2.44
3651 3725 4.081365 AGCGAAAAGGGAAAGGAAAACAAA 60.081 37.500 0.00 0.00 0.00 2.83
3652 3726 3.449377 AGCGAAAAGGGAAAGGAAAACAA 59.551 39.130 0.00 0.00 0.00 2.83
3653 3727 3.028130 AGCGAAAAGGGAAAGGAAAACA 58.972 40.909 0.00 0.00 0.00 2.83
3654 3728 3.181479 ACAGCGAAAAGGGAAAGGAAAAC 60.181 43.478 0.00 0.00 0.00 2.43
3655 3729 3.028130 ACAGCGAAAAGGGAAAGGAAAA 58.972 40.909 0.00 0.00 0.00 2.29
3656 3730 2.661718 ACAGCGAAAAGGGAAAGGAAA 58.338 42.857 0.00 0.00 0.00 3.13
3657 3731 2.358322 ACAGCGAAAAGGGAAAGGAA 57.642 45.000 0.00 0.00 0.00 3.36
3658 3732 1.953686 CAACAGCGAAAAGGGAAAGGA 59.046 47.619 0.00 0.00 0.00 3.36
3659 3733 1.602920 GCAACAGCGAAAAGGGAAAGG 60.603 52.381 0.00 0.00 0.00 3.11
3660 3734 1.066908 TGCAACAGCGAAAAGGGAAAG 59.933 47.619 0.00 0.00 0.00 2.62
3661 3735 1.107114 TGCAACAGCGAAAAGGGAAA 58.893 45.000 0.00 0.00 0.00 3.13
3662 3736 1.327303 ATGCAACAGCGAAAAGGGAA 58.673 45.000 0.00 0.00 0.00 3.97
3663 3737 2.192664 TATGCAACAGCGAAAAGGGA 57.807 45.000 0.00 0.00 0.00 4.20
3676 3750 9.230122 TCAGAACTATCTTTGAACATTATGCAA 57.770 29.630 0.00 0.00 32.03 4.08
3693 3767 5.334421 ACTGGGTAGTGTTCTCAGAACTAT 58.666 41.667 18.49 9.34 35.34 2.12
3697 3771 3.830755 GGTACTGGGTAGTGTTCTCAGAA 59.169 47.826 0.00 0.00 37.78 3.02
3712 3869 5.527214 TCAGATTTCATTAATGCGGTACTGG 59.473 40.000 10.76 0.00 0.00 4.00
3807 3976 7.817962 AGCACAAATGGTTTACTAGTACTACTG 59.182 37.037 0.91 1.86 30.39 2.74
3811 3980 7.605309 GGTAAGCACAAATGGTTTACTAGTACT 59.395 37.037 0.91 0.00 44.10 2.73
3854 4027 6.899089 TGTAAGGCAAAATGAGATAGATCCA 58.101 36.000 0.00 0.00 0.00 3.41
3909 4082 8.146053 TCCCTCTATCTCAAAATGTAAAGACA 57.854 34.615 0.00 0.00 40.72 3.41



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

AutoCloner maintained by Alex Coulton.