Multiple sequence alignment - TraesCS3A01G205700

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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 TraesCS3A01G205700 chr3A 100.000 4703 0 0 1 4703 361991599 361996301 0.000000e+00 8685
1 TraesCS3A01G205700 chr3D 96.735 3492 64 17 1 3479 277542054 277538600 0.000000e+00 5771
2 TraesCS3A01G205700 chr3D 96.095 1050 34 3 3476 4523 277538509 277537465 0.000000e+00 1705
3 TraesCS3A01G205700 chr3D 92.513 187 12 1 4517 4703 277537432 277537248 2.790000e-67 267
4 TraesCS3A01G205700 chr3B 95.528 3421 87 31 1 3400 372838932 372842307 0.000000e+00 5409
5 TraesCS3A01G205700 chr3B 92.363 1257 49 9 3473 4703 372842301 372843536 0.000000e+00 1746


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 TraesCS3A01G205700 chr3A 361991599 361996301 4702 False 8685.0 8685 100.000000 1 4703 1 chr3A.!!$F1 4702
1 TraesCS3A01G205700 chr3D 277537248 277542054 4806 True 2581.0 5771 95.114333 1 4703 3 chr3D.!!$R1 4702
2 TraesCS3A01G205700 chr3B 372838932 372843536 4604 False 3577.5 5409 93.945500 1 4703 2 chr3B.!!$F1 4702

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
667 674 0.371989 TGCGTCAACATAATTCGCCG 59.628 50.000 0.0 0.0 45.06 6.46 F
950 963 1.444383 GACCCGTAAACCGACCGAC 60.444 63.158 0.0 0.0 39.56 4.79 F
2268 2286 1.204704 TCACTGATAGGTGAACAGCGG 59.795 52.381 0.0 0.0 42.35 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 1671 1.129437 GGCTCGCTGAGTTCATTCAAC 59.871 52.381 7.27 0.0 34.86 3.18 R
2894 2920 0.385974 CAAGCTTGGAAAACCGCTCG 60.386 55.000 19.14 0.0 31.30 5.03 R
3900 4024 0.874390 GTGGCACGCTGATTCTTTCA 59.126 50.000 0.00 0.0 35.02 2.69 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
336 342 2.834549 CAGGGTGAAGAAAGCTCCTCTA 59.165 50.000 0.00 0.00 0.00 2.43
549 556 5.939883 TGCAAATGAGTTAGTTACAGATGCT 59.060 36.000 0.00 0.00 33.45 3.79
667 674 0.371989 TGCGTCAACATAATTCGCCG 59.628 50.000 0.00 0.00 45.06 6.46
796 809 6.000840 TGCACACATTAATTACTGGACAAGA 58.999 36.000 7.63 0.00 0.00 3.02
797 810 6.658816 TGCACACATTAATTACTGGACAAGAT 59.341 34.615 7.63 0.00 0.00 2.40
949 962 2.961768 GACCCGTAAACCGACCGA 59.038 61.111 0.00 0.00 39.56 4.69
950 963 1.444383 GACCCGTAAACCGACCGAC 60.444 63.158 0.00 0.00 39.56 4.79
951 964 2.125952 CCCGTAAACCGACCGACC 60.126 66.667 0.00 0.00 39.56 4.79
952 965 2.504681 CCGTAAACCGACCGACCG 60.505 66.667 0.00 0.00 39.56 4.79
953 966 2.560861 CGTAAACCGACCGACCGA 59.439 61.111 0.00 0.00 39.56 4.69
954 967 1.797537 CGTAAACCGACCGACCGAC 60.798 63.158 0.00 0.00 39.56 4.79
955 968 1.444383 GTAAACCGACCGACCGACC 60.444 63.158 0.00 0.00 0.00 4.79
956 969 2.976840 TAAACCGACCGACCGACCG 61.977 63.158 0.00 0.00 0.00 4.79
1518 1531 1.760086 CCTCGATCAGGCCAGGTCT 60.760 63.158 5.01 0.00 34.56 3.85
1557 1570 1.830883 GCCAGGGAGATGGAGCTCTAT 60.831 57.143 13.04 13.04 43.57 1.98
1644 1657 1.613437 ACAACTCTTCCCCGCATTTTG 59.387 47.619 0.00 0.00 0.00 2.44
1658 1671 3.360956 CGCATTTTGTTCTTCTTTGCACG 60.361 43.478 0.00 0.00 0.00 5.34
1659 1672 3.551485 GCATTTTGTTCTTCTTTGCACGT 59.449 39.130 0.00 0.00 0.00 4.49
1748 1764 6.889198 ACTTACTAGCTAATGATTTGCAGGA 58.111 36.000 13.60 3.71 0.00 3.86
1850 1866 8.827177 TCAATAAAACTGAGTTTCACGAGTAT 57.173 30.769 11.44 1.76 34.43 2.12
2025 2041 1.378531 TTCCGCAATCCTGATTTCCG 58.621 50.000 0.00 0.00 0.00 4.30
2106 2124 6.644347 ACGACTAGTACTTGGTACTTAGCTA 58.356 40.000 14.27 0.00 45.68 3.32
2201 2219 7.451281 AGAGTACATGAATTTACATCGTTCG 57.549 36.000 0.00 0.00 0.00 3.95
2266 2284 3.257393 CAGTCACTGATAGGTGAACAGC 58.743 50.000 0.00 0.00 46.00 4.40
2268 2286 1.204704 TCACTGATAGGTGAACAGCGG 59.795 52.381 0.00 0.00 42.35 5.52
2465 2486 8.227791 TCTAAATTAAGTGCAAAAGAAGCTACG 58.772 33.333 0.00 0.00 0.00 3.51
2779 2805 2.768527 TGTCCAGGCAGAGAGATAAAGG 59.231 50.000 0.00 0.00 0.00 3.11
2793 2819 4.273318 AGATAAAGGTGGTGATGGAAAGC 58.727 43.478 0.00 0.00 0.00 3.51
2801 2827 4.082733 GGTGGTGATGGAAAGCTAAACTTC 60.083 45.833 0.00 0.00 37.75 3.01
2894 2920 3.726607 TGGGAACATGACAATTGCAAAC 58.273 40.909 1.71 0.00 33.40 2.93
3261 3289 0.462047 AGGTACGTTAGCATGCTGCC 60.462 55.000 30.42 16.20 46.52 4.85
3294 3322 6.656314 ATGTGCATAATGAAAATGTTGCTG 57.344 33.333 0.00 0.00 0.00 4.41
3333 3361 9.959749 TTCTTCGAAATGCTAATTTGTTAGTTT 57.040 25.926 0.00 0.00 36.10 2.66
3382 3410 8.404000 AGCAGCTATTTGTTTTCTCATATCTTG 58.596 33.333 0.00 0.00 0.00 3.02
3448 3476 7.496920 TCATCAATCTCATTTGGCTAGTAACTG 59.503 37.037 0.00 0.00 0.00 3.16
3511 3633 3.066380 CAAGCAAAAGGGCAATTGTACC 58.934 45.455 7.40 10.02 35.83 3.34
3520 3642 2.945668 GGGCAATTGTACCTCAGCTTAG 59.054 50.000 7.40 0.00 0.00 2.18
3669 3792 3.645884 TGGTAGTGTTTACTTCAGCGAC 58.354 45.455 0.00 0.00 38.36 5.19
3816 3940 5.763204 TCTTTTCTTTTTGCAGATCGTAGGT 59.237 36.000 0.00 0.00 0.00 3.08
3818 3942 7.442969 TCTTTTCTTTTTGCAGATCGTAGGTAA 59.557 33.333 0.00 0.00 0.00 2.85
3887 4011 9.858247 CAAATGCATCATTACTAATCAAAATGC 57.142 29.630 0.00 0.00 38.90 3.56
3900 4024 8.796475 ACTAATCAAAATGCTGTGTGAATACTT 58.204 29.630 0.00 0.00 0.00 2.24
3902 4026 6.631971 TCAAAATGCTGTGTGAATACTTGA 57.368 33.333 0.00 0.00 0.00 3.02
4333 4475 6.182039 TCTTGCTGTGTCTATTAATGCAAC 57.818 37.500 0.00 0.00 35.52 4.17
4381 4529 7.535738 TCTATGATATAGGACAGGTGAAGGAA 58.464 38.462 0.00 0.00 0.00 3.36
4383 4531 4.901849 TGATATAGGACAGGTGAAGGAAGG 59.098 45.833 0.00 0.00 0.00 3.46
4386 4534 2.136026 AGGACAGGTGAAGGAAGGTTT 58.864 47.619 0.00 0.00 0.00 3.27
4516 4664 7.495135 ACTTTTGCAAGGGAAATTTTATGTG 57.505 32.000 0.00 0.00 33.82 3.21
4605 4793 1.916181 TCATCCTCTTTCCCACCCTTC 59.084 52.381 0.00 0.00 0.00 3.46
4617 4805 2.000701 ACCCTTCCCGATGATGGCA 61.001 57.895 0.00 0.00 37.05 4.92
4643 4831 0.981183 TCCACCCAATTGTAGAGCGT 59.019 50.000 4.43 0.00 0.00 5.07
4645 4833 1.066143 CCACCCAATTGTAGAGCGTCT 60.066 52.381 4.43 0.00 0.00 4.18
4675 4863 1.829222 CAATCCCAAGGCAATGAGCTT 59.171 47.619 0.00 0.00 44.79 3.74
4694 4882 1.812507 GGCCACCGAACGACATACC 60.813 63.158 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 244 5.948162 CCTCCTCTTTTTCCTGAATCAATCA 59.052 40.000 0.00 0.00 36.38 2.57
336 342 1.811558 CGGCGATGGGATCATGTCTTT 60.812 52.381 0.00 0.00 32.98 2.52
549 556 6.579666 AACACAGTACGATAACAAGAGGTA 57.420 37.500 0.00 0.00 0.00 3.08
667 674 3.942829 TGACAAATCTGACATCCAGGAC 58.057 45.455 0.00 0.00 43.12 3.85
721 728 7.990886 AGCTGTAGAATCCATTAATTAACGGAA 59.009 33.333 16.38 0.00 0.00 4.30
796 809 3.503748 GTGAGCACTTGAGCCAGTTTTAT 59.496 43.478 0.00 0.00 34.23 1.40
797 810 2.878406 GTGAGCACTTGAGCCAGTTTTA 59.122 45.455 0.00 0.00 34.23 1.52
1206 1219 0.901114 TTCCTCCGGAATCGTGGACA 60.901 55.000 5.23 0.00 36.71 4.02
1370 1383 3.481559 TGATGAAGTCCTCTTCCTCCT 57.518 47.619 5.68 0.00 46.66 3.69
1516 1529 2.895680 GCGATGGAGCTGGTCAGA 59.104 61.111 9.30 0.00 0.00 3.27
1557 1570 1.890041 CCCGTTGCCGTTCTTGTCA 60.890 57.895 0.00 0.00 0.00 3.58
1644 1657 4.597079 TCATTCAACGTGCAAAGAAGAAC 58.403 39.130 0.00 0.00 0.00 3.01
1658 1671 1.129437 GGCTCGCTGAGTTCATTCAAC 59.871 52.381 7.27 0.00 34.86 3.18
1659 1672 1.270785 TGGCTCGCTGAGTTCATTCAA 60.271 47.619 7.27 0.00 31.39 2.69
1748 1764 1.136329 ACCCCAGTGAGTTGCCATCT 61.136 55.000 0.00 0.00 0.00 2.90
1850 1866 7.036996 TCTTTTGTACACTGAAATGAATGCA 57.963 32.000 0.00 0.00 0.00 3.96
2025 2041 4.756084 ACTTGTCTGCTTTAATCTGCAC 57.244 40.909 0.00 0.00 35.20 4.57
2106 2124 4.615513 ACTAGCAGGAAATCAGGACTACT 58.384 43.478 0.00 0.00 0.00 2.57
2188 2206 4.258543 ACCATCCAACGAACGATGTAAAT 58.741 39.130 0.14 0.00 35.17 1.40
2201 2219 7.552687 TCATATTGAACTGTTAGACCATCCAAC 59.447 37.037 0.00 0.00 0.00 3.77
2266 2284 1.266178 AGAAAATTTTGGGGAGGCCG 58.734 50.000 8.47 0.00 0.00 6.13
2268 2286 3.169908 TGGTAGAAAATTTTGGGGAGGC 58.830 45.455 8.47 0.00 0.00 4.70
2465 2486 4.868734 GGTGTGTGCTTATAGGTCTACAAC 59.131 45.833 0.00 0.00 0.00 3.32
2779 2805 4.378459 CGAAGTTTAGCTTTCCATCACCAC 60.378 45.833 0.00 0.00 37.59 4.16
2793 2819 8.391106 CCCATGAAAGTATTCTTCGAAGTTTAG 58.609 37.037 23.85 10.15 36.48 1.85
2801 2827 5.116180 TGTAGCCCATGAAAGTATTCTTCG 58.884 41.667 0.00 0.00 36.48 3.79
2894 2920 0.385974 CAAGCTTGGAAAACCGCTCG 60.386 55.000 19.14 0.00 31.30 5.03
3261 3289 9.882996 ATTTTCATTATGCACATAGACATAACG 57.117 29.630 0.00 0.00 40.51 3.18
3289 3317 2.439507 AGAACTTCAGTCCCTTCAGCAA 59.560 45.455 0.00 0.00 0.00 3.91
3294 3322 3.662247 TCGAAGAACTTCAGTCCCTTC 57.338 47.619 13.72 10.04 39.46 3.46
3448 3476 6.487689 AAGTAAGTTCAAATAGCTGCAGTC 57.512 37.500 16.64 7.83 0.00 3.51
3511 3633 2.163010 CACATGTTTGCCCTAAGCTGAG 59.837 50.000 0.00 0.00 44.23 3.35
3520 3642 1.815817 GACCCCACACATGTTTGCCC 61.816 60.000 6.47 0.00 0.00 5.36
3788 3911 9.825972 CTACGATCTGCAAAAAGAAAAGATAAA 57.174 29.630 0.00 0.00 0.00 1.40
3803 3927 3.382546 GGTTAGGTTACCTACGATCTGCA 59.617 47.826 11.13 0.00 35.63 4.41
3811 3935 7.065443 GTCACATTTCATGGTTAGGTTACCTAC 59.935 40.741 11.13 6.55 39.04 3.18
3816 3940 5.943416 CCTGTCACATTTCATGGTTAGGTTA 59.057 40.000 0.00 0.00 33.60 2.85
3818 3942 4.335416 CCTGTCACATTTCATGGTTAGGT 58.665 43.478 0.00 0.00 33.60 3.08
3862 3986 9.826574 AGCATTTTGATTAGTAATGATGCATTT 57.173 25.926 20.60 0.00 40.65 2.32
3887 4011 7.020010 GCTGATTCTTTCAAGTATTCACACAG 58.980 38.462 0.00 0.00 32.78 3.66
3900 4024 0.874390 GTGGCACGCTGATTCTTTCA 59.126 50.000 0.00 0.00 35.02 2.69
3902 4026 1.577328 CCGTGGCACGCTGATTCTTT 61.577 55.000 33.15 0.00 40.91 2.52
4381 4529 1.140312 TCTCAGGAAGTGCCAAACCT 58.860 50.000 0.00 0.00 40.02 3.50
4383 4531 2.508526 ACATCTCAGGAAGTGCCAAAC 58.491 47.619 0.00 0.00 40.02 2.93
4386 4534 1.699083 TGAACATCTCAGGAAGTGCCA 59.301 47.619 0.00 0.00 40.02 4.92
4489 4637 7.877612 ACATAAAATTTCCCTTGCAAAAGTAGG 59.122 33.333 0.00 0.00 0.00 3.18
4516 4664 1.732259 CACGGACATGTTTGCTAGTCC 59.268 52.381 0.00 0.00 45.46 3.85
4605 4793 0.677731 ACAACACTGCCATCATCGGG 60.678 55.000 0.00 0.00 0.00 5.14
4643 4831 1.079405 GGGATTGACCGCGTTCAGA 60.079 57.895 6.42 0.00 40.11 3.27
4645 4833 0.953471 CTTGGGATTGACCGCGTTCA 60.953 55.000 0.74 0.74 40.11 3.18
4675 4863 1.079681 GTATGTCGTTCGGTGGCCA 60.080 57.895 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.