Multiple sequence alignment - TraesCS1A01G172600

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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 TraesCS1A01G172600 chr1A 100.000 3161 0 0 1 3161 308569001 308572161 0.000000e+00 5838.0
1 TraesCS1A01G172600 chr1D 96.726 2230 59 3 413 2633 237143182 237145406 0.000000e+00 3701.0
2 TraesCS1A01G172600 chr1D 91.498 494 28 8 2673 3161 237145770 237146254 0.000000e+00 667.0
3 TraesCS1A01G172600 chr1D 96.000 175 7 0 127 301 237142498 237142672 5.160000e-73 285.0
4 TraesCS1A01G172600 chr1D 87.121 132 2 5 298 429 237143050 237143166 5.500000e-28 135.0
5 TraesCS1A01G172600 chr1D 96.250 80 3 0 1 80 237142416 237142495 7.110000e-27 132.0
6 TraesCS1A01G172600 chr1B 95.189 2224 61 8 412 2622 342650111 342647921 0.000000e+00 3472.0
7 TraesCS1A01G172600 chr1B 92.629 502 31 4 2665 3161 342647915 342647415 0.000000e+00 717.0
8 TraesCS1A01G172600 chr1B 95.984 249 8 2 56 304 342650508 342650262 1.370000e-108 403.0
9 TraesCS1A01G172600 chr1B 100.000 61 0 0 366 426 342650185 342650125 2.580000e-21 113.0
10 TraesCS1A01G172600 chr1B 100.000 45 0 0 303 347 342650216 342650172 2.020000e-12 84.2
11 TraesCS1A01G172600 chr5A 76.946 681 93 38 2470 3110 551483569 551482913 2.350000e-86 329.0
12 TraesCS1A01G172600 chr5A 79.108 493 60 26 2470 2942 707723993 707724462 1.840000e-77 300.0
13 TraesCS1A01G172600 chr6A 78.261 115 25 0 1419 1533 123372118 123372004 1.220000e-09 75.0


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 TraesCS1A01G172600 chr1A 308569001 308572161 3160 False 5838.00 5838 100.0000 1 3161 1 chr1A.!!$F1 3160
1 TraesCS1A01G172600 chr1D 237142416 237146254 3838 False 984.00 3701 93.5190 1 3161 5 chr1D.!!$F1 3160
2 TraesCS1A01G172600 chr1B 342647415 342650508 3093 True 957.84 3472 96.7604 56 3161 5 chr1B.!!$R1 3105
3 TraesCS1A01G172600 chr5A 551482913 551483569 656 True 329.00 329 76.9460 2470 3110 1 chr5A.!!$R1 640

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
513 982 0.038343 CTTCCAAAATGGTGTGCGGG 60.038 55.0 0.0 0.0 39.03 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2803 1.066605 CACGCGCACCCTAGTATAACT 59.933 52.381 5.73 0.0 0.0 2.24 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
35 36 1.606601 AGTGGCTGACAGGCTCGTA 60.607 57.895 27.23 6.62 41.96 3.43
92 93 7.121382 TCCTAATCTAGACCTTTTCCTTACGA 58.879 38.462 0.00 0.00 0.00 3.43
115 116 8.926710 ACGAAAAGATTGACTGATACTAAACTG 58.073 33.333 0.00 0.00 0.00 3.16
135 136 0.884704 GGAAAACAGCTGAGCGGTGA 60.885 55.000 23.35 0.00 43.75 4.02
263 264 2.871427 GCTATCTTTCCACGCCGCG 61.871 63.158 12.14 12.14 0.00 6.46
341 770 7.305474 GTTTTCTTCACTGTCAAGTTCAAGAA 58.695 34.615 0.00 5.98 32.98 2.52
343 772 7.447374 TTCTTCACTGTCAAGTTCAAGAAAA 57.553 32.000 7.06 0.00 32.98 2.29
344 773 7.076842 TCTTCACTGTCAAGTTCAAGAAAAG 57.923 36.000 0.00 0.00 32.98 2.27
345 774 6.655003 TCTTCACTGTCAAGTTCAAGAAAAGT 59.345 34.615 0.00 0.00 32.98 2.66
346 775 6.817765 TCACTGTCAAGTTCAAGAAAAGTT 57.182 33.333 0.00 0.00 32.98 2.66
347 776 6.842163 TCACTGTCAAGTTCAAGAAAAGTTC 58.158 36.000 0.00 0.00 32.98 3.01
348 777 6.429692 TCACTGTCAAGTTCAAGAAAAGTTCA 59.570 34.615 0.00 0.00 32.98 3.18
349 778 7.121168 TCACTGTCAAGTTCAAGAAAAGTTCAT 59.879 33.333 0.00 0.00 32.98 2.57
350 779 7.756722 CACTGTCAAGTTCAAGAAAAGTTCATT 59.243 33.333 0.00 0.00 32.98 2.57
351 780 8.306761 ACTGTCAAGTTCAAGAAAAGTTCATTT 58.693 29.630 0.00 0.00 30.14 2.32
352 781 8.687824 TGTCAAGTTCAAGAAAAGTTCATTTC 57.312 30.769 0.00 0.00 39.16 2.17
353 782 8.303156 TGTCAAGTTCAAGAAAAGTTCATTTCA 58.697 29.630 2.99 0.00 40.89 2.69
354 783 9.139174 GTCAAGTTCAAGAAAAGTTCATTTCAA 57.861 29.630 2.99 0.00 40.89 2.69
355 784 9.703892 TCAAGTTCAAGAAAAGTTCATTTCAAA 57.296 25.926 2.99 0.00 40.89 2.69
356 785 9.962759 CAAGTTCAAGAAAAGTTCATTTCAAAG 57.037 29.630 2.99 0.00 40.89 2.77
465 925 4.409218 CGCAAAGCCGCACATGCT 62.409 61.111 11.62 0.00 41.89 3.79
513 982 0.038343 CTTCCAAAATGGTGTGCGGG 60.038 55.000 0.00 0.00 39.03 6.13
590 1059 2.607750 AAAGCGAGCCTCCCAGGA 60.608 61.111 0.00 0.00 37.67 3.86
755 1224 3.499737 CACGCATGGAGAACCGGC 61.500 66.667 0.00 0.00 39.42 6.13
908 1377 1.271934 CGCAGATCGATCTCCATTCCT 59.728 52.381 25.00 0.00 41.67 3.36
1006 1475 2.124860 TCGTCGAGAGGATGGCGA 60.125 61.111 0.00 0.00 32.24 5.54
1468 1937 1.745264 GCCAAGGAGATCGAGGAGG 59.255 63.158 0.00 0.00 0.00 4.30
1548 2017 0.535328 CGGAGGAGGCAGACGATCTA 60.535 60.000 0.00 0.00 0.00 1.98
1740 2212 0.687757 AGGCCAACTCGCTCATCCTA 60.688 55.000 5.01 0.00 0.00 2.94
1835 2309 1.311859 TGATTCTCATGCATTCCGCC 58.688 50.000 0.00 0.00 41.33 6.13
1848 2322 2.046023 CCGCCAAGATGCACCTGA 60.046 61.111 0.00 0.00 0.00 3.86
1905 2379 1.088340 TCTCGATCGACCTCGGTGAC 61.088 60.000 15.15 0.00 39.13 3.67
1938 2412 2.346803 GAGGACTATTTCAAGCGTGCA 58.653 47.619 0.00 0.00 0.00 4.57
2038 2512 2.100631 GCGGAGGACATGTTCACCG 61.101 63.158 31.72 31.72 43.84 4.94
2137 2611 1.934220 GACCTGCGTCATCGACTCCA 61.934 60.000 0.00 0.00 38.99 3.86
2146 2620 1.069978 TCATCGACTCCAGCAACAACA 59.930 47.619 0.00 0.00 0.00 3.33
2154 2628 0.732571 CCAGCAACAACAACGACACT 59.267 50.000 0.00 0.00 0.00 3.55
2165 2639 1.872952 CAACGACACTGAATGAAGCCA 59.127 47.619 0.00 0.00 0.00 4.75
2559 3033 9.941325 ACAATATGAAATGCATAAGGTTTTTCA 57.059 25.926 10.78 10.78 42.45 2.69
2651 3196 7.041098 GCTTGTACATACATATTTTCAGAGGGG 60.041 40.741 0.00 0.00 35.89 4.79
2962 3796 1.218047 GGCACGGTCTATCACTGCA 59.782 57.895 0.00 0.00 34.19 4.41
3033 3867 9.212641 TCTTTATGTTCATAATCTAGCATGCTC 57.787 33.333 26.57 6.09 0.00 4.26
3035 3869 5.200368 TGTTCATAATCTAGCATGCTCGA 57.800 39.130 26.57 24.31 0.00 4.04
3036 3870 5.787380 TGTTCATAATCTAGCATGCTCGAT 58.213 37.500 26.57 25.52 31.04 3.59
3052 3886 4.842029 GCTCGATGCAAAGATCTAAAAGG 58.158 43.478 0.00 0.00 42.31 3.11
3053 3887 4.333926 GCTCGATGCAAAGATCTAAAAGGT 59.666 41.667 0.00 0.00 42.31 3.50
3054 3888 5.163713 GCTCGATGCAAAGATCTAAAAGGTT 60.164 40.000 0.00 0.00 42.31 3.50
3059 3898 6.317789 TGCAAAGATCTAAAAGGTTCAGTG 57.682 37.500 0.00 0.00 0.00 3.66
3071 3910 1.338020 GGTTCAGTGTTTGGGAGCAAG 59.662 52.381 0.00 0.00 0.00 4.01
3117 3956 2.035832 ACACAAGCATTTTACACCCTGC 59.964 45.455 0.00 0.00 34.85 4.85
3121 3960 3.004752 AGCATTTTACACCCTGCCTAG 57.995 47.619 0.00 0.00 35.21 3.02
3122 3961 2.308866 AGCATTTTACACCCTGCCTAGT 59.691 45.455 0.00 0.00 35.21 2.57
3137 3976 3.319689 TGCCTAGTATACGCAATGTAGCA 59.680 43.478 1.93 0.32 36.25 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.568504 TTCCTCCATTACGAGCCTGT 58.431 50.000 0.00 0.00 0.00 4.00
29 30 4.494199 CGTTGATTTTCCTCCATTACGAGC 60.494 45.833 0.00 0.00 0.00 5.03
35 36 2.524306 TGGCGTTGATTTTCCTCCATT 58.476 42.857 0.00 0.00 0.00 3.16
92 93 8.383175 TCCCAGTTTAGTATCAGTCAATCTTTT 58.617 33.333 0.00 0.00 0.00 2.27
99 100 6.833041 TGTTTTCCCAGTTTAGTATCAGTCA 58.167 36.000 0.00 0.00 0.00 3.41
115 116 1.600916 ACCGCTCAGCTGTTTTCCC 60.601 57.895 14.67 0.00 0.00 3.97
135 136 4.270834 TCTGTCAGAAGCTATAAGGTCGT 58.729 43.478 0.00 0.00 0.00 4.34
234 235 6.046593 CGTGGAAAGATAGCATACCAAACTA 58.953 40.000 0.00 0.00 0.00 2.24
263 264 2.635714 CGGAGGGTTTTGGGTACATAC 58.364 52.381 0.00 0.00 0.00 2.39
465 925 2.096819 GGAGCGTTTGTTGTTCTGTTGA 59.903 45.455 0.00 0.00 0.00 3.18
683 1152 1.625508 GGGGAGAGGAAAGGGCTCTAA 60.626 57.143 0.00 0.00 0.00 2.10
685 1154 1.307430 GGGGAGAGGAAAGGGCTCT 60.307 63.158 0.00 0.00 0.00 4.09
1503 1972 2.774951 GCCGTTGTCATCGTCGTCG 61.775 63.158 0.00 0.00 38.55 5.12
1548 2017 1.077501 CATCCCCACCAGCATCGTT 60.078 57.895 0.00 0.00 0.00 3.85
1740 2212 1.519455 GAGCTGCGCGTAGTTGGAT 60.519 57.895 25.02 6.87 0.00 3.41
1835 2309 6.688385 CGTACAAATTAATCAGGTGCATCTTG 59.312 38.462 0.00 0.00 0.00 3.02
1848 2322 6.591062 ACCATGACACGTACGTACAAATTAAT 59.409 34.615 22.34 8.42 0.00 1.40
1986 2460 2.747855 CGGGCTTGCCAGAGGAAC 60.748 66.667 14.04 0.00 0.00 3.62
2038 2512 4.933064 CTCCTCGTCGATGGCGCC 62.933 72.222 22.73 22.73 37.46 6.53
2137 2611 1.732941 TCAGTGTCGTTGTTGTTGCT 58.267 45.000 0.00 0.00 0.00 3.91
2146 2620 2.254546 TGGCTTCATTCAGTGTCGTT 57.745 45.000 0.00 0.00 0.00 3.85
2154 2628 1.375853 CCGGCGATTGGCTTCATTCA 61.376 55.000 9.30 0.00 42.94 2.57
2305 2779 1.524621 CCTACAAGGGCCGATGCTG 60.525 63.158 11.63 5.54 37.74 4.41
2329 2803 1.066605 CACGCGCACCCTAGTATAACT 59.933 52.381 5.73 0.00 0.00 2.24
2555 3029 6.183360 GCAAACACAACTTACAGCAAATGAAA 60.183 34.615 0.00 0.00 0.00 2.69
2559 3033 4.566360 GTGCAAACACAACTTACAGCAAAT 59.434 37.500 0.00 0.00 46.61 2.32
2624 3106 7.716998 CCCTCTGAAAATATGTATGTACAAGCT 59.283 37.037 0.00 0.00 39.99 3.74
2656 3201 1.379044 CAGCAGGATGACAACCCCC 60.379 63.158 0.00 0.00 39.69 5.40
2657 3202 1.379044 CCAGCAGGATGACAACCCC 60.379 63.158 0.00 0.00 39.69 4.95
2758 3564 0.182061 GATTGGAGCTGGGATGCAGA 59.818 55.000 0.00 0.00 34.99 4.26
2962 3796 1.148310 CAGGCACGAACTTCACGAAT 58.852 50.000 0.00 0.00 34.70 3.34
3033 3867 6.128172 ACTGAACCTTTTAGATCTTTGCATCG 60.128 38.462 0.00 0.00 0.00 3.84
3035 3869 6.491403 ACACTGAACCTTTTAGATCTTTGCAT 59.509 34.615 0.00 0.00 0.00 3.96
3036 3870 5.827797 ACACTGAACCTTTTAGATCTTTGCA 59.172 36.000 0.00 0.00 0.00 4.08
3043 3877 5.701224 TCCCAAACACTGAACCTTTTAGAT 58.299 37.500 0.00 0.00 0.00 1.98
3045 3879 4.261614 GCTCCCAAACACTGAACCTTTTAG 60.262 45.833 0.00 0.00 0.00 1.85
3048 3882 2.031870 GCTCCCAAACACTGAACCTTT 58.968 47.619 0.00 0.00 0.00 3.11
3049 3883 1.064017 TGCTCCCAAACACTGAACCTT 60.064 47.619 0.00 0.00 0.00 3.50
3050 3884 0.550914 TGCTCCCAAACACTGAACCT 59.449 50.000 0.00 0.00 0.00 3.50
3052 3886 2.024414 ACTTGCTCCCAAACACTGAAC 58.976 47.619 0.00 0.00 0.00 3.18
3053 3887 2.023673 CACTTGCTCCCAAACACTGAA 58.976 47.619 0.00 0.00 0.00 3.02
3054 3888 1.679139 CACTTGCTCCCAAACACTGA 58.321 50.000 0.00 0.00 0.00 3.41
3059 3898 0.459489 TGTTGCACTTGCTCCCAAAC 59.541 50.000 2.33 0.00 42.66 2.93
3071 3910 1.355210 CCACACCGAGTTGTTGCAC 59.645 57.895 0.00 0.00 0.00 4.57
3117 3956 6.156519 TCATTGCTACATTGCGTATACTAGG 58.843 40.000 0.56 0.00 35.36 3.02
3121 3960 6.466308 TGATCATTGCTACATTGCGTATAC 57.534 37.500 0.00 0.00 35.36 1.47
3122 3961 7.520686 CATTGATCATTGCTACATTGCGTATA 58.479 34.615 4.75 0.00 35.36 1.47


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

AutoCloner maintained by Alex Coulton.