Multiple sequence alignment - TraesCS3A01G221800

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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 TraesCS3A01G221800 chr3A 100.000 5250 0 0 1 5250 413677824 413683073 0.000000e+00 9696
1 TraesCS3A01G221800 chr3D 97.367 3038 61 5 2227 5250 316169610 316166578 0.000000e+00 5149
2 TraesCS3A01G221800 chr3D 96.066 2237 68 9 9 2230 316171895 316169664 0.000000e+00 3626
3 TraesCS3A01G221800 chr3B 97.270 3040 61 7 2227 5249 403906589 403909623 0.000000e+00 5134
4 TraesCS3A01G221800 chr3B 94.284 2257 96 13 1 2230 403904283 403906533 0.000000e+00 3422
5 TraesCS3A01G221800 chr1A 80.538 632 88 26 1256 1877 581832371 581831765 2.230000e-123 453
6 TraesCS3A01G221800 chr1D 80.063 632 94 24 1256 1877 484419147 484418538 1.740000e-119 440
7 TraesCS3A01G221800 chr1B 79.873 631 85 32 1256 1877 674671206 674670609 1.750000e-114 424


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 TraesCS3A01G221800 chr3A 413677824 413683073 5249 False 9696.0 9696 100.0000 1 5250 1 chr3A.!!$F1 5249
1 TraesCS3A01G221800 chr3D 316166578 316171895 5317 True 4387.5 5149 96.7165 9 5250 2 chr3D.!!$R1 5241
2 TraesCS3A01G221800 chr3B 403904283 403909623 5340 False 4278.0 5134 95.7770 1 5249 2 chr3B.!!$F1 5248
3 TraesCS3A01G221800 chr1A 581831765 581832371 606 True 453.0 453 80.5380 1256 1877 1 chr1A.!!$R1 621
4 TraesCS3A01G221800 chr1D 484418538 484419147 609 True 440.0 440 80.0630 1256 1877 1 chr1D.!!$R1 621
5 TraesCS3A01G221800 chr1B 674670609 674671206 597 True 424.0 424 79.8730 1256 1877 1 chr1B.!!$R1 621

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
637 664 0.032515 TTGCCCCCTGAGATACTCGA 60.033 55.0 0.00 0.00 32.35 4.04 F
1098 1130 1.225376 CCAAGGCTAACGTGTTCGCA 61.225 55.0 10.78 0.00 41.18 5.10 F
2385 2480 0.596082 AATTCTGTTCAAACGGGGCG 59.404 50.0 2.04 0.00 35.96 6.13 F
2989 3084 1.016627 TGGGAAGGTACGTACGATCG 58.983 55.0 24.41 14.88 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2480 1.217779 GCTCTCAGGTCAGGACAGC 59.782 63.158 1.41 0.0 0.00 4.40 R
2787 2882 1.302033 CTCAAGGCACGAAGCTGGT 60.302 57.895 0.00 0.0 44.79 4.00 R
3307 3402 0.536460 TCAACGGCTTTCTCCCAACC 60.536 55.000 0.00 0.0 0.00 3.77 R
4630 4729 1.331447 GTAACGAAAACCGCAACCAGT 59.669 47.619 0.00 0.0 43.32 4.00 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
84 87 9.784531 ATCTGATAGATAATGTTCAATTCCGTT 57.215 29.630 0.00 0.00 32.12 4.44
118 121 7.013178 TGTTGTCACCGCATCATCAATATTTAT 59.987 33.333 0.00 0.00 0.00 1.40
125 128 8.400947 ACCGCATCATCAATATTTATCTTATGC 58.599 33.333 0.00 0.00 34.21 3.14
307 310 7.334421 TGTCTAGATTGTATTGCCTCTTGAAAC 59.666 37.037 0.00 0.00 0.00 2.78
344 348 7.690952 AAAATTGCTATAACTCACCCGTAAA 57.309 32.000 0.00 0.00 0.00 2.01
637 664 0.032515 TTGCCCCCTGAGATACTCGA 60.033 55.000 0.00 0.00 32.35 4.04
815 846 1.302511 ACACGCGCTTTTCCTCCAT 60.303 52.632 5.73 0.00 0.00 3.41
860 892 3.253955 CAGTACTGCGCAACCACC 58.746 61.111 13.05 0.00 0.00 4.61
1098 1130 1.225376 CCAAGGCTAACGTGTTCGCA 61.225 55.000 10.78 0.00 41.18 5.10
1585 1620 1.734465 CCTTTCTCGGACACTCAATGC 59.266 52.381 0.00 0.00 0.00 3.56
1815 1850 3.827898 GACTCCGAGGAGGCCGTG 61.828 72.222 21.79 0.00 44.22 4.94
1965 2000 2.768253 TCCAGTTCGATGTGCAGATT 57.232 45.000 0.00 0.00 0.00 2.40
2058 2093 1.611491 CTTGCCAGCTTTTCCCGTTAA 59.389 47.619 0.00 0.00 0.00 2.01
2070 2105 2.574450 TCCCGTTAACAAAGTCCAACC 58.426 47.619 6.39 0.00 0.00 3.77
2153 2188 5.450412 CGATTTGATTGGGGATTGTTACTGG 60.450 44.000 0.00 0.00 0.00 4.00
2156 2191 2.891191 TTGGGGATTGTTACTGGTCC 57.109 50.000 0.00 0.00 0.00 4.46
2174 2209 1.414550 TCCGTGTGGTCTGTTTGATCA 59.585 47.619 0.00 0.00 36.30 2.92
2249 2344 1.875963 GGCGTTTCCCATCACACAG 59.124 57.895 0.00 0.00 0.00 3.66
2343 2438 3.890756 TGAATTCAGACCACACAATGCTT 59.109 39.130 3.38 0.00 0.00 3.91
2385 2480 0.596082 AATTCTGTTCAAACGGGGCG 59.404 50.000 2.04 0.00 35.96 6.13
2687 2782 4.090066 CGACTCGTCTCAGTTGGTAAATTG 59.910 45.833 0.00 0.00 0.00 2.32
2736 2831 7.123355 TCTTTCAAGTGTTGGAAAATGGAAT 57.877 32.000 0.00 0.00 33.05 3.01
2921 3016 1.675641 GCCAAACTCTCGGGCATGT 60.676 57.895 0.00 0.00 46.92 3.21
2989 3084 1.016627 TGGGAAGGTACGTACGATCG 58.983 55.000 24.41 14.88 0.00 3.69
3010 3105 2.890945 GTCCAACCCTGTAACAATGCTT 59.109 45.455 0.00 0.00 0.00 3.91
3047 3142 3.190744 CAGCAAAAGCAGATCATCACTGT 59.809 43.478 0.00 0.00 37.64 3.55
3126 3221 2.705658 ACTTATCGATCCTGGGAATGCA 59.294 45.455 0.00 0.00 0.00 3.96
3186 3281 2.436824 GCTCGAGCCCAAGGGAAC 60.437 66.667 27.22 0.56 37.50 3.62
3307 3402 0.037326 TTGCTGGTGGAAGCTAGACG 60.037 55.000 0.00 0.00 43.90 4.18
3408 3503 4.036852 GCAATGTCCTATTCCAAGGTAAGC 59.963 45.833 0.00 0.00 37.91 3.09
3428 3523 1.017387 GACCGGGCATTCTCATGTTC 58.983 55.000 0.00 0.00 32.28 3.18
3444 3539 4.018141 TCATGTTCTTGACATCCCATTCCT 60.018 41.667 0.00 0.00 45.88 3.36
3485 3580 7.283329 ACCTCTTCCATTTTTATTAGCTCGAT 58.717 34.615 0.00 0.00 0.00 3.59
3517 3612 0.463654 TGTGTGCGGGATTATGAGGC 60.464 55.000 0.00 0.00 0.00 4.70
3554 3649 0.176680 CTGCCGATACTGAGGTTGCT 59.823 55.000 0.00 0.00 0.00 3.91
3760 3855 4.058124 TCAGTTCTTGTGTGTATCTGTGC 58.942 43.478 0.00 0.00 0.00 4.57
4019 4116 7.672983 TTTCTGAAGGTAAAGCTACTTGATG 57.327 36.000 0.00 0.00 0.00 3.07
4334 4432 3.693578 CCCAAATTTGCAAAAACACCAGT 59.306 39.130 17.19 0.00 0.00 4.00
4431 4529 3.914771 CTTTCCACCCATCATTACCCAT 58.085 45.455 0.00 0.00 0.00 4.00
4432 4530 3.593442 TTCCACCCATCATTACCCATC 57.407 47.619 0.00 0.00 0.00 3.51
4433 4531 1.780309 TCCACCCATCATTACCCATCC 59.220 52.381 0.00 0.00 0.00 3.51
4434 4532 1.203050 CCACCCATCATTACCCATCCC 60.203 57.143 0.00 0.00 0.00 3.85
4435 4533 0.771127 ACCCATCATTACCCATCCCG 59.229 55.000 0.00 0.00 0.00 5.14
4630 4729 2.654204 GGGAGAGGGGAGGGGGTTA 61.654 68.421 0.00 0.00 0.00 2.85
4662 4761 5.173131 CGGTTTTCGTTACGTGTATATACCC 59.827 44.000 10.38 0.00 0.00 3.69
4804 4904 3.269592 TTGGTGTAGAGAGGGGAAAGA 57.730 47.619 0.00 0.00 0.00 2.52
4937 5041 9.073475 TGTATTTTACTCTGCTGTTGGTTATTT 57.927 29.630 0.00 0.00 0.00 1.40
5078 5192 1.451028 GCATGGCCTGTGAGAGTCC 60.451 63.158 3.32 0.00 0.00 3.85
5128 5242 0.607489 CTGGTCCTCTGGTTTGGCTG 60.607 60.000 0.00 0.00 0.00 4.85
5186 5300 1.909376 AGTAGTAACACAGCGCATCG 58.091 50.000 11.47 0.00 0.00 3.84
5213 5327 2.640332 TGTATGTGCTTAGGGGTGTGAA 59.360 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.089551 GTGGCATACAAGATACATACATCGTC 59.910 42.308 0.00 0.00 0.00 4.20
81 84 2.781101 CGGTGACAACATTTCAACAACG 59.219 45.455 0.00 0.00 29.22 4.10
84 87 1.745653 TGCGGTGACAACATTTCAACA 59.254 42.857 0.00 0.00 29.22 3.33
118 121 6.755141 GGAACGTCACTATACTTTGCATAAGA 59.245 38.462 13.35 1.51 0.00 2.10
125 128 8.697846 TTTAGATGGAACGTCACTATACTTTG 57.302 34.615 0.00 0.00 0.00 2.77
174 177 5.467399 TGATATATTTTTGTTCTACGGCGGG 59.533 40.000 13.24 3.49 0.00 6.13
204 207 4.215613 AGTGGATTTAGAAACGAACTTGGC 59.784 41.667 0.00 0.00 0.00 4.52
259 262 8.103305 AGACATAAGATGTGTTTTGACTGGTAT 58.897 33.333 0.00 0.00 45.03 2.73
325 329 7.690952 AAAAATTTACGGGTGAGTTATAGCA 57.309 32.000 0.00 0.00 0.00 3.49
351 355 4.846779 AAAATCTACCTTTTTGCAGCGA 57.153 36.364 0.00 0.00 0.00 4.93
465 491 8.198778 GGGTTAGAGAGTTATCGAGATTTCTTT 58.801 37.037 0.00 0.00 0.00 2.52
637 664 3.692406 GGTGACCCCGAGACGCTT 61.692 66.667 0.00 0.00 0.00 4.68
667 694 1.855360 GGAAGAAATAGACTCTGCGCG 59.145 52.381 0.00 0.00 0.00 6.86
673 700 3.738590 GCGTCAGGGGAAGAAATAGACTC 60.739 52.174 0.00 0.00 0.00 3.36
762 793 1.542108 GCGGGGAAATGGAGAGAGATG 60.542 57.143 0.00 0.00 0.00 2.90
815 846 5.127031 GGCAAGAACCCTGAGCAATAAATTA 59.873 40.000 0.00 0.00 0.00 1.40
969 1001 3.680490 TCACCGCAAAATCTCACCAATA 58.320 40.909 0.00 0.00 0.00 1.90
1585 1620 2.279784 GGAGCTTGCCGGAGATCG 60.280 66.667 5.05 0.00 32.97 3.69
1877 1912 3.125316 CCCAAAGATACGAGCACAAGAAC 59.875 47.826 0.00 0.00 0.00 3.01
1930 1965 2.939103 ACTGGAATCTAATGCGTTCTGC 59.061 45.455 0.00 0.00 46.70 4.26
1965 2000 4.471025 TGAGAGCAATGGAATCAAGTAGGA 59.529 41.667 0.00 0.00 0.00 2.94
2058 2093 4.437682 TCATCTTCAGGTTGGACTTTGT 57.562 40.909 0.00 0.00 0.00 2.83
2070 2105 6.387465 ACAATCATGTTGCTTTCATCTTCAG 58.613 36.000 7.62 0.00 35.91 3.02
2153 2188 1.798813 GATCAAACAGACCACACGGAC 59.201 52.381 0.00 0.00 35.59 4.79
2156 2191 2.416547 GGATGATCAAACAGACCACACG 59.583 50.000 0.00 0.00 0.00 4.49
2196 2232 8.306761 GTGATAATTCTGTCACCAAAATTCCTT 58.693 33.333 7.10 0.00 37.64 3.36
2249 2344 2.035066 AGCAACACCTTTCATTCAGCAC 59.965 45.455 0.00 0.00 0.00 4.40
2371 2466 3.283684 CAGCGCCCCGTTTGAACA 61.284 61.111 2.29 0.00 0.00 3.18
2385 2480 1.217779 GCTCTCAGGTCAGGACAGC 59.782 63.158 1.41 0.00 0.00 4.40
2687 2782 2.467826 GCACAAGCGAGGGATGAGC 61.468 63.158 0.00 0.00 0.00 4.26
2736 2831 8.918202 ACCAAGAATCTACAATGTAAAACTGA 57.082 30.769 0.00 0.00 0.00 3.41
2787 2882 1.302033 CTCAAGGCACGAAGCTGGT 60.302 57.895 0.00 0.00 44.79 4.00
2834 2929 2.552315 GAGTCGAATCAGCCTCCTCTAG 59.448 54.545 8.21 0.00 0.00 2.43
2989 3084 2.514803 AGCATTGTTACAGGGTTGGAC 58.485 47.619 0.00 0.00 0.00 4.02
3010 3105 5.163683 GCTTTTGCTGCAATCTAGAGAATCA 60.164 40.000 16.77 0.00 43.35 2.57
3047 3142 4.263905 ACCTGCAGAAATGAATCCCAACTA 60.264 41.667 17.39 0.00 0.00 2.24
3126 3221 9.927081 ACATTATTTAGAATCATCCCAACTTCT 57.073 29.630 0.00 0.00 0.00 2.85
3186 3281 0.603707 TGGCAGCCTTGAAGAGTTCG 60.604 55.000 14.15 0.00 0.00 3.95
3240 3335 4.811557 GGATTTGAAGGATCGTACTTGAGG 59.188 45.833 0.00 0.00 0.00 3.86
3307 3402 0.536460 TCAACGGCTTTCTCCCAACC 60.536 55.000 0.00 0.00 0.00 3.77
3408 3503 0.744414 AACATGAGAATGCCCGGTCG 60.744 55.000 0.00 0.00 0.00 4.79
3428 3523 2.686915 GCAAGAGGAATGGGATGTCAAG 59.313 50.000 0.00 0.00 0.00 3.02
3444 3539 3.620488 AGAGGTCAACAAAACAGCAAGA 58.380 40.909 0.00 0.00 0.00 3.02
3485 3580 1.514678 GCACACAATCAGCCCAACGA 61.515 55.000 0.00 0.00 0.00 3.85
3554 3649 2.516906 TGAGCATGGAACAATGCTTCA 58.483 42.857 16.38 12.78 46.94 3.02
3760 3855 6.417327 GCAGTTCTCGTTCTTCATGATAATG 58.583 40.000 0.00 0.16 0.00 1.90
4334 4432 1.883638 GCTGGTGAAATGCTGTGGAGA 60.884 52.381 0.00 0.00 0.00 3.71
4431 4529 3.407967 GCAAGGGATGGGACGGGA 61.408 66.667 0.00 0.00 0.00 5.14
4432 4530 4.506255 GGCAAGGGATGGGACGGG 62.506 72.222 0.00 0.00 0.00 5.28
4433 4531 4.856801 CGGCAAGGGATGGGACGG 62.857 72.222 0.00 0.00 0.00 4.79
4434 4532 3.622060 AACGGCAAGGGATGGGACG 62.622 63.158 0.00 0.00 0.00 4.79
4435 4533 2.046285 CAACGGCAAGGGATGGGAC 61.046 63.158 0.00 0.00 0.00 4.46
4630 4729 1.331447 GTAACGAAAACCGCAACCAGT 59.669 47.619 0.00 0.00 43.32 4.00
4804 4904 3.197549 GGCATCCAATTAACACCACCAAT 59.802 43.478 0.00 0.00 0.00 3.16
4937 5041 6.798427 ATACTCCAGCTCATTACAGAAAGA 57.202 37.500 0.00 0.00 0.00 2.52
5078 5192 2.702478 TGCCATCATCTCTACTCCCAAG 59.298 50.000 0.00 0.00 0.00 3.61
5128 5242 2.480610 CCAGCCACCACACACACAC 61.481 63.158 0.00 0.00 0.00 3.82
5213 5327 7.394641 ACAAGTGAGGAAAAAGTCTCTTCTTTT 59.605 33.333 0.00 0.00 45.66 2.27


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

AutoCloner maintained by Alex Coulton.