Multiple sequence alignment - TraesCS1D01G206800

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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 TraesCS1D01G206800 chr1D 100.000 3222 0 0 1 3222 293290000 293293221 0.000000e+00 5951.0
1 TraesCS1D01G206800 chr1B 93.468 2526 87 26 721 3222 394115829 394118300 0.000000e+00 3679.0
2 TraesCS1D01G206800 chr1B 93.188 690 28 8 5 676 394115127 394115815 0.000000e+00 996.0
3 TraesCS1D01G206800 chr1A 91.839 1936 81 30 933 2846 364935454 364937334 0.000000e+00 2628.0
4 TraesCS1D01G206800 chr1A 87.102 597 48 14 17 590 364934214 364934804 0.000000e+00 649.0
5 TraesCS1D01G206800 chr1A 93.573 389 14 4 2845 3222 364937486 364937874 1.300000e-158 569.0
6 TraesCS1D01G206800 chr1A 85.356 239 20 10 634 871 364934816 364935040 1.930000e-57 233.0
7 TraesCS1D01G206800 chr4D 87.500 160 19 1 1860 2018 485164405 485164564 1.970000e-42 183.0
8 TraesCS1D01G206800 chr4B 86.875 160 20 1 1860 2018 618348094 618348253 9.190000e-41 178.0
9 TraesCS1D01G206800 chr5A 85.897 156 22 0 1863 2018 666204956 666205111 1.990000e-37 167.0
10 TraesCS1D01G206800 chr7A 85.149 101 14 1 1340 1440 51239428 51239527 5.690000e-18 102.0
11 TraesCS1D01G206800 chr7A 84.158 101 16 0 1340 1440 51055420 51055520 7.360000e-17 99.0
12 TraesCS1D01G206800 chr7A 84.158 101 15 1 1340 1440 51102686 51102785 2.650000e-16 97.1
13 TraesCS1D01G206800 chr7A 83.168 101 17 0 1340 1440 51175446 51175546 3.420000e-15 93.5


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 TraesCS1D01G206800 chr1D 293290000 293293221 3221 False 5951.00 5951 100.0000 1 3222 1 chr1D.!!$F1 3221
1 TraesCS1D01G206800 chr1B 394115127 394118300 3173 False 2337.50 3679 93.3280 5 3222 2 chr1B.!!$F1 3217
2 TraesCS1D01G206800 chr1A 364934214 364937874 3660 False 1019.75 2628 89.4675 17 3222 4 chr1A.!!$F1 3205

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
368 379 0.459237 CAGCTTACTCACTCCCTGCG 60.459 60.0 0.00 0.0 0.0 5.18 F
489 515 0.533951 TCTGAGAGCGCACATGACAT 59.466 50.0 11.47 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 2268 0.931662 CGAACGAGAACGACACGGTT 60.932 55.0 0.00 0.0 42.66 4.44 R
2436 2868 0.879765 GCATGCATATGAGGCAGACC 59.120 55.0 14.21 0.0 45.68 3.85 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
31 32 4.452455 AGACAAGAATGCTAAAACACTCCG 59.548 41.667 0.00 0.00 0.00 4.63
35 36 3.008049 AGAATGCTAAAACACTCCGGAGT 59.992 43.478 31.69 31.69 43.61 3.85
36 37 4.222145 AGAATGCTAAAACACTCCGGAGTA 59.778 41.667 35.80 19.62 40.20 2.59
157 160 3.002965 CGGCGGGGTAAATGTAAATCTTC 59.997 47.826 0.00 0.00 0.00 2.87
172 178 8.348285 TGTAAATCTTCATTTTTACAGAGGGG 57.652 34.615 4.59 0.00 41.14 4.79
189 195 1.405121 GGGGGTAGTACACAAGAAGCG 60.405 57.143 4.63 0.00 0.00 4.68
196 202 1.394917 GTACACAAGAAGCGATGCCAG 59.605 52.381 0.00 0.00 0.00 4.85
215 221 3.181425 CCAGCCTATCCCCTCAAAATCAT 60.181 47.826 0.00 0.00 0.00 2.45
217 223 4.522022 CAGCCTATCCCCTCAAAATCATTC 59.478 45.833 0.00 0.00 0.00 2.67
234 240 5.560966 TCATTCTAAGCCCGTTTTCATTC 57.439 39.130 0.00 0.00 0.00 2.67
240 246 3.643159 AGCCCGTTTTCATTCTTTGAC 57.357 42.857 0.00 0.00 32.84 3.18
242 248 4.394729 AGCCCGTTTTCATTCTTTGACTA 58.605 39.130 0.00 0.00 32.84 2.59
243 249 5.010282 AGCCCGTTTTCATTCTTTGACTAT 58.990 37.500 0.00 0.00 32.84 2.12
244 250 5.095490 GCCCGTTTTCATTCTTTGACTATG 58.905 41.667 0.00 0.00 32.84 2.23
352 363 7.819900 AGCTGCCAAATACTAGTATAATACAGC 59.180 37.037 30.37 30.37 38.48 4.40
368 379 0.459237 CAGCTTACTCACTCCCTGCG 60.459 60.000 0.00 0.00 0.00 5.18
489 515 0.533951 TCTGAGAGCGCACATGACAT 59.466 50.000 11.47 0.00 0.00 3.06
642 669 3.160777 CATCAAAAGATGCTCCAAGCC 57.839 47.619 0.00 0.00 41.51 4.35
643 670 2.592102 TCAAAAGATGCTCCAAGCCT 57.408 45.000 0.00 0.00 41.51 4.58
645 672 1.131883 CAAAAGATGCTCCAAGCCTCG 59.868 52.381 0.00 0.00 41.51 4.63
646 673 1.028868 AAAGATGCTCCAAGCCTCGC 61.029 55.000 0.00 0.00 41.51 5.03
647 674 2.883267 AAGATGCTCCAAGCCTCGCC 62.883 60.000 0.00 0.00 41.51 5.54
648 675 4.845580 ATGCTCCAAGCCTCGCCG 62.846 66.667 0.00 0.00 41.51 6.46
676 711 3.501062 GGTTACTTTTCGTTGCTTAGCCT 59.499 43.478 0.29 0.00 0.00 4.58
678 713 2.846193 ACTTTTCGTTGCTTAGCCTCA 58.154 42.857 0.29 0.00 0.00 3.86
694 729 8.346300 GCTTAGCCTCATATAGTTTCCTTTTTC 58.654 37.037 0.00 0.00 0.00 2.29
695 730 9.620259 CTTAGCCTCATATAGTTTCCTTTTTCT 57.380 33.333 0.00 0.00 0.00 2.52
700 743 7.445707 CCTCATATAGTTTCCTTTTTCTAGCCC 59.554 40.741 0.00 0.00 0.00 5.19
721 764 2.821366 CCCTGGCTTAGCGCACAG 60.821 66.667 11.47 5.72 41.67 3.66
722 765 2.821366 CCTGGCTTAGCGCACAGG 60.821 66.667 11.47 14.86 44.77 4.00
723 766 3.503363 CTGGCTTAGCGCACAGGC 61.503 66.667 21.26 21.26 41.67 4.85
724 767 3.965539 CTGGCTTAGCGCACAGGCT 62.966 63.158 25.96 2.06 46.88 4.58
725 768 2.186903 GGCTTAGCGCACAGGCTA 59.813 61.111 20.92 0.00 44.29 3.93
729 772 2.186903 TAGCGCACAGGCTAAGGC 59.813 61.111 11.47 0.00 42.26 4.35
842 899 3.159984 GCAACCGACTCTTGCTCG 58.840 61.111 0.00 0.00 40.79 5.03
1012 1424 2.433838 CCAGCAGCACACCGAGAG 60.434 66.667 0.00 0.00 0.00 3.20
1013 1425 2.653115 CAGCAGCACACCGAGAGA 59.347 61.111 0.00 0.00 0.00 3.10
1049 1465 0.953471 TCCAAGGATCAAACGCCACG 60.953 55.000 0.00 0.00 0.00 4.94
1111 1536 4.740822 ATGGCAGTGGGGTTCCGC 62.741 66.667 0.00 0.00 43.69 5.54
1720 2145 1.617018 CCATCTTCTCCGGCCTGTCA 61.617 60.000 0.00 0.00 0.00 3.58
1831 2256 2.584391 GCTGGTGACGGACCTCCTT 61.584 63.158 7.34 0.00 46.32 3.36
2047 2472 1.993370 CGATCAGTTCTTTCCCGTGTC 59.007 52.381 0.00 0.00 0.00 3.67
2132 2557 3.550437 AGTGCTAGCGATTCCATTTCT 57.450 42.857 10.77 0.00 0.00 2.52
2191 2616 4.612264 ACTCTTGCTTGCAATGGAAAAT 57.388 36.364 8.55 0.00 0.00 1.82
2192 2617 5.726980 ACTCTTGCTTGCAATGGAAAATA 57.273 34.783 8.55 0.00 0.00 1.40
2251 2678 2.160721 TACTCGCCAATCTCCTCCTT 57.839 50.000 0.00 0.00 0.00 3.36
2252 2679 0.827368 ACTCGCCAATCTCCTCCTTC 59.173 55.000 0.00 0.00 0.00 3.46
2253 2680 0.249238 CTCGCCAATCTCCTCCTTCG 60.249 60.000 0.00 0.00 0.00 3.79
2264 2691 4.710324 TCTCCTCCTTCGAATACTCTCTC 58.290 47.826 0.00 0.00 0.00 3.20
2265 2692 3.818773 CTCCTCCTTCGAATACTCTCTCC 59.181 52.174 0.00 0.00 0.00 3.71
2266 2693 3.202373 TCCTCCTTCGAATACTCTCTCCA 59.798 47.826 0.00 0.00 0.00 3.86
2267 2694 4.141135 TCCTCCTTCGAATACTCTCTCCAT 60.141 45.833 0.00 0.00 0.00 3.41
2269 2696 5.508825 CCTCCTTCGAATACTCTCTCCATTG 60.509 48.000 0.00 0.00 0.00 2.82
2270 2697 4.342378 TCCTTCGAATACTCTCTCCATTGG 59.658 45.833 0.00 0.00 0.00 3.16
2271 2698 4.100189 CCTTCGAATACTCTCTCCATTGGT 59.900 45.833 0.00 0.00 0.00 3.67
2272 2699 4.655762 TCGAATACTCTCTCCATTGGTG 57.344 45.455 1.86 0.00 0.00 4.17
2292 2723 3.058432 GTGCTAATGTGCTATGCATCCTG 60.058 47.826 0.19 0.00 41.91 3.86
2388 2820 4.464008 TCCTTGTTCTTGAGCAAGTGAAT 58.536 39.130 20.20 0.00 40.13 2.57
2394 2826 7.977789 TGTTCTTGAGCAAGTGAATATTGTA 57.022 32.000 9.79 0.00 39.38 2.41
2415 2847 3.641437 TTCTTTCCATTTCAACTGCCG 57.359 42.857 0.00 0.00 0.00 5.69
2436 2868 0.469070 CAATCAGGGAGGGAGAGCTG 59.531 60.000 0.00 0.00 0.00 4.24
2441 2873 2.063378 GGGAGGGAGAGCTGGTCTG 61.063 68.421 14.96 0.00 34.71 3.51
2447 2879 1.336632 GGAGAGCTGGTCTGCCTCAT 61.337 60.000 14.96 0.00 37.67 2.90
2448 2880 1.407936 GAGAGCTGGTCTGCCTCATA 58.592 55.000 14.96 0.00 34.71 2.15
2492 2924 2.177531 GCACATTGCCGTCAGCTG 59.822 61.111 7.63 7.63 44.23 4.24
2493 2925 2.177531 CACATTGCCGTCAGCTGC 59.822 61.111 9.47 3.23 44.23 5.25
2494 2926 2.281692 ACATTGCCGTCAGCTGCA 60.282 55.556 9.47 0.00 44.23 4.41
2639 3071 2.743636 TCAGTGACCAAACTCGATCC 57.256 50.000 0.00 0.00 0.00 3.36
2700 3132 0.103026 CATCCACACGCAGCTAGCTA 59.897 55.000 18.86 0.00 42.61 3.32
2701 3133 0.387202 ATCCACACGCAGCTAGCTAG 59.613 55.000 18.86 16.84 42.61 3.42
2931 3522 1.658596 TGCGAAAGATGGACGAAATCG 59.341 47.619 0.48 0.48 46.33 3.34
2975 3567 2.521547 AGGTTACCGTACACCTAGCT 57.478 50.000 0.84 0.00 41.97 3.32
3046 3638 3.702330 ACGCCAACTTAACAAGAAAAGC 58.298 40.909 0.00 0.00 0.00 3.51
3187 3786 3.119884 TGTCCACATGAACGAATCAATGC 60.120 43.478 0.00 0.00 42.54 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.818136 TTAGCATTCTTGTCTAATGGCAC 57.182 39.130 0.00 0.00 35.34 5.01
15 16 3.418684 ACTCCGGAGTGTTTTAGCATT 57.581 42.857 35.89 6.65 40.75 3.56
31 32 6.532988 AACTCAACCTATCAAGAGTACTCC 57.467 41.667 19.38 1.81 40.22 3.85
157 160 5.878669 GTGTACTACCCCCTCTGTAAAAATG 59.121 44.000 0.00 0.00 0.00 2.32
166 172 3.442076 CTTCTTGTGTACTACCCCCTCT 58.558 50.000 0.00 0.00 0.00 3.69
172 178 2.603560 GCATCGCTTCTTGTGTACTACC 59.396 50.000 0.00 0.00 0.00 3.18
189 195 1.130054 TGAGGGGATAGGCTGGCATC 61.130 60.000 3.38 4.71 0.00 3.91
196 202 4.734266 AGAATGATTTTGAGGGGATAGGC 58.266 43.478 0.00 0.00 0.00 3.93
215 221 5.533154 TCAAAGAATGAAAACGGGCTTAGAA 59.467 36.000 0.00 0.00 34.30 2.10
217 223 5.048713 AGTCAAAGAATGAAAACGGGCTTAG 60.049 40.000 0.00 0.00 40.50 2.18
234 240 4.500837 CCAGTTCGATCGTCATAGTCAAAG 59.499 45.833 15.94 0.00 0.00 2.77
240 246 2.619177 ACCTCCAGTTCGATCGTCATAG 59.381 50.000 15.94 6.50 0.00 2.23
242 248 1.475403 ACCTCCAGTTCGATCGTCAT 58.525 50.000 15.94 0.00 0.00 3.06
243 249 2.118313 TACCTCCAGTTCGATCGTCA 57.882 50.000 15.94 0.00 0.00 4.35
244 250 2.879646 AGATACCTCCAGTTCGATCGTC 59.120 50.000 15.94 9.76 0.00 4.20
368 379 4.927425 TGTCGGCTTGTCTTGTTTATACTC 59.073 41.667 0.00 0.00 0.00 2.59
489 515 0.740868 GCGTATGCAAGTCTGGCTCA 60.741 55.000 0.89 0.00 42.15 4.26
610 637 0.958091 TTTTGATGCAAGACGGGGTG 59.042 50.000 0.00 0.00 0.00 4.61
647 674 1.134226 ACGAAAAGTAACCGTCTGCG 58.866 50.000 0.00 0.00 37.95 5.18
648 675 2.899977 CAACGAAAAGTAACCGTCTGC 58.100 47.619 0.00 0.00 35.28 4.26
657 692 3.997762 TGAGGCTAAGCAACGAAAAGTA 58.002 40.909 0.00 0.00 0.00 2.24
676 711 6.990349 CGGGCTAGAAAAAGGAAACTATATGA 59.010 38.462 0.00 0.00 42.68 2.15
678 713 6.296803 CCGGGCTAGAAAAAGGAAACTATAT 58.703 40.000 0.00 0.00 42.68 0.86
712 755 2.186903 GCCTTAGCCTGTGCGCTA 59.813 61.111 9.73 0.00 44.33 4.26
716 759 3.804193 GCACGCCTTAGCCTGTGC 61.804 66.667 0.06 0.06 45.05 4.57
717 760 2.358615 TGCACGCCTTAGCCTGTG 60.359 61.111 0.00 0.00 34.54 3.66
718 761 2.046892 CTGCACGCCTTAGCCTGT 60.047 61.111 0.00 0.00 34.57 4.00
719 762 3.503363 GCTGCACGCCTTAGCCTG 61.503 66.667 0.00 0.00 34.57 4.85
720 763 3.259633 AAGCTGCACGCCTTAGCCT 62.260 57.895 1.02 0.00 40.39 4.58
721 764 2.747855 AAGCTGCACGCCTTAGCC 60.748 61.111 1.02 0.00 40.39 3.93
722 765 1.700600 GAGAAGCTGCACGCCTTAGC 61.701 60.000 1.02 0.00 40.39 3.09
723 766 1.086634 GGAGAAGCTGCACGCCTTAG 61.087 60.000 1.02 0.00 40.39 2.18
724 767 1.079127 GGAGAAGCTGCACGCCTTA 60.079 57.895 1.02 0.00 40.39 2.69
725 768 2.359230 GGAGAAGCTGCACGCCTT 60.359 61.111 1.02 0.00 40.39 4.35
726 769 4.400961 GGGAGAAGCTGCACGCCT 62.401 66.667 15.69 2.18 40.39 5.52
727 770 4.704833 TGGGAGAAGCTGCACGCC 62.705 66.667 1.02 6.75 40.39 5.68
728 771 3.426568 GTGGGAGAAGCTGCACGC 61.427 66.667 1.02 0.00 39.57 5.34
729 772 1.572085 CTTGTGGGAGAAGCTGCACG 61.572 60.000 1.02 0.00 0.00 5.34
730 773 1.860484 GCTTGTGGGAGAAGCTGCAC 61.860 60.000 1.02 0.00 42.21 4.57
818 867 1.996191 CAAGAGTCGGTTGCTAGCTTC 59.004 52.381 17.23 8.63 0.00 3.86
842 899 1.368850 GGAACACGTTTGACTGCGC 60.369 57.895 0.00 0.00 0.00 6.09
1012 1424 1.886542 GGATTTGGTGGTGACTTGGTC 59.113 52.381 0.00 0.00 0.00 4.02
1013 1425 1.216678 TGGATTTGGTGGTGACTTGGT 59.783 47.619 0.00 0.00 0.00 3.67
1049 1465 0.671781 TGCTCGCTGGAGAAAGCTTC 60.672 55.000 0.00 0.00 43.27 3.86
1090 1515 3.628646 GAACCCCACTGCCATCGCT 62.629 63.158 0.00 0.00 35.36 4.93
1091 1516 3.134127 GAACCCCACTGCCATCGC 61.134 66.667 0.00 0.00 0.00 4.58
1092 1517 2.438434 GGAACCCCACTGCCATCG 60.438 66.667 0.00 0.00 0.00 3.84
1093 1518 2.438434 CGGAACCCCACTGCCATC 60.438 66.667 0.00 0.00 0.00 3.51
1174 1599 3.812019 CGCGCGTAGGAGGACAGT 61.812 66.667 24.19 0.00 0.00 3.55
1843 2268 0.931662 CGAACGAGAACGACACGGTT 60.932 55.000 0.00 0.00 42.66 4.44
2132 2557 4.509970 CACACAGGAGTCAACAAACGAATA 59.490 41.667 0.00 0.00 0.00 1.75
2207 2632 6.469782 ACAATTCATCACAAGGTTTTCTGT 57.530 33.333 0.00 0.00 0.00 3.41
2251 2678 3.181475 GCACCAATGGAGAGAGTATTCGA 60.181 47.826 6.16 0.00 0.00 3.71
2252 2679 3.126831 GCACCAATGGAGAGAGTATTCG 58.873 50.000 6.16 0.00 0.00 3.34
2253 2680 4.414337 AGCACCAATGGAGAGAGTATTC 57.586 45.455 6.16 0.00 0.00 1.75
2264 2691 3.551454 GCATAGCACATTAGCACCAATGG 60.551 47.826 0.00 0.00 39.71 3.16
2265 2692 3.067040 TGCATAGCACATTAGCACCAATG 59.933 43.478 4.66 4.66 40.93 2.82
2266 2693 3.289836 TGCATAGCACATTAGCACCAAT 58.710 40.909 0.00 0.00 36.85 3.16
2267 2694 2.720915 TGCATAGCACATTAGCACCAA 58.279 42.857 0.00 0.00 36.85 3.67
2269 2696 2.227388 GGATGCATAGCACATTAGCACC 59.773 50.000 0.00 0.00 43.04 5.01
2270 2697 3.058432 CAGGATGCATAGCACATTAGCAC 60.058 47.826 0.00 0.00 43.04 4.40
2271 2698 3.143728 CAGGATGCATAGCACATTAGCA 58.856 45.455 0.00 0.00 43.04 3.49
2272 2699 3.144506 ACAGGATGCATAGCACATTAGC 58.855 45.455 0.00 0.00 43.04 3.09
2292 2723 0.964358 AAGCAATGCAGGCAGAGGAC 60.964 55.000 8.35 0.00 0.00 3.85
2354 2786 6.987386 TCAAGAACAAGGAAGAAAACAAACA 58.013 32.000 0.00 0.00 0.00 2.83
2388 2820 8.250332 GGCAGTTGAAATGGAAAGAATACAATA 58.750 33.333 0.00 0.00 0.00 1.90
2394 2826 3.056607 CCGGCAGTTGAAATGGAAAGAAT 60.057 43.478 0.00 0.00 0.00 2.40
2415 2847 1.835693 CTCTCCCTCCCTGATTGCC 59.164 63.158 0.00 0.00 0.00 4.52
2436 2868 0.879765 GCATGCATATGAGGCAGACC 59.120 55.000 14.21 0.00 45.68 3.85
2504 2936 5.649395 AGAAAGATTTCTCGGCAATGAATGA 59.351 36.000 1.94 0.00 43.72 2.57
2639 3071 1.523258 CAGGGAGAAGCTGGCGATG 60.523 63.158 0.00 0.00 0.00 3.84
2700 3132 4.816984 GGAGCATGCAGGGCAGCT 62.817 66.667 21.98 12.61 43.65 4.24
2931 3522 1.580639 GCGTACGACTCGAGCTGAC 60.581 63.158 21.65 4.84 0.00 3.51
2975 3567 1.659794 GGCTGCTTTCGCCTTTTGA 59.340 52.632 0.00 0.00 44.17 2.69
3064 3656 2.582978 GTTGGCCGGAGACCCTAC 59.417 66.667 5.05 0.00 0.00 3.18
3187 3786 5.445964 AGGTACCCAATTATTTGTAGGCTG 58.554 41.667 8.74 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.