Multiple sequence alignment - TraesCS1B01G322600

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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 TraesCS1B01G322600 chr1B 100.000 2870 0 0 1 2870 547579365 547576496 0.000000e+00 5301
1 TraesCS1B01G322600 chr1D 91.632 1936 72 31 1 1889 407210111 407208219 0.000000e+00 2595
2 TraesCS1B01G322600 chr1D 86.756 521 30 12 2234 2719 407175649 407175133 6.990000e-151 544
3 TraesCS1B01G322600 chr1D 91.322 242 18 3 1884 2122 407206413 407206172 7.670000e-86 327
4 TraesCS1B01G322600 chr1D 91.045 134 11 1 2731 2863 407174914 407174781 2.270000e-41 180
5 TraesCS1B01G322600 chr1A 91.074 1210 45 13 1049 2236 502824424 502823256 0.000000e+00 1578
6 TraesCS1B01G322600 chr1A 90.681 955 59 10 15 961 502825553 502824621 0.000000e+00 1243
7 TraesCS1B01G322600 chr1A 82.738 336 49 7 2234 2560 502823196 502822861 1.010000e-74 291
8 TraesCS1B01G322600 chr1A 84.314 153 7 5 2728 2863 502822407 502822255 1.790000e-27 134
9 TraesCS1B01G322600 chr4A 85.965 741 90 7 1049 1782 625686007 625685274 0.000000e+00 780
10 TraesCS1B01G322600 chr3B 79.625 746 102 30 1059 1770 572790154 572790883 9.240000e-135 490
11 TraesCS1B01G322600 chr3A 79.073 755 102 35 1059 1770 575612973 575613714 4.330000e-128 468
12 TraesCS1B01G322600 chr3D 78.656 759 98 39 1059 1770 437669766 437670507 2.030000e-121 446


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 TraesCS1B01G322600 chr1B 547576496 547579365 2869 True 5301.0 5301 100.00000 1 2870 1 chr1B.!!$R1 2869
1 TraesCS1B01G322600 chr1D 407206172 407210111 3939 True 1461.0 2595 91.47700 1 2122 2 chr1D.!!$R2 2121
2 TraesCS1B01G322600 chr1D 407174781 407175649 868 True 362.0 544 88.90050 2234 2863 2 chr1D.!!$R1 629
3 TraesCS1B01G322600 chr1A 502822255 502825553 3298 True 811.5 1578 87.20175 15 2863 4 chr1A.!!$R1 2848
4 TraesCS1B01G322600 chr4A 625685274 625686007 733 True 780.0 780 85.96500 1049 1782 1 chr4A.!!$R1 733
5 TraesCS1B01G322600 chr3B 572790154 572790883 729 False 490.0 490 79.62500 1059 1770 1 chr3B.!!$F1 711
6 TraesCS1B01G322600 chr3A 575612973 575613714 741 False 468.0 468 79.07300 1059 1770 1 chr3A.!!$F1 711
7 TraesCS1B01G322600 chr3D 437669766 437670507 741 False 446.0 446 78.65600 1059 1770 1 chr3D.!!$F1 711

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
736 753 2.222819 GCTTTTCTGATCGCAACCGTAG 60.223 50.0 0.0 0.0 35.54 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 3959 0.10339 AACAAACGGGAAAAAGCCGG 59.897 50.0 0.0 0.0 0.0 6.13 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
65 66 4.760715 CAGGATTGATGATTGGTGGATCTC 59.239 45.833 0.00 0.00 0.00 2.75
67 68 4.446745 GGATTGATGATTGGTGGATCTCCA 60.447 45.833 6.17 6.17 45.30 3.86
459 462 4.524328 TCGCATGATACATGATCCAGTACT 59.476 41.667 14.65 0.00 33.07 2.73
460 463 5.710099 TCGCATGATACATGATCCAGTACTA 59.290 40.000 14.65 0.00 33.07 1.82
461 464 5.802451 CGCATGATACATGATCCAGTACTAC 59.198 44.000 14.65 0.00 33.07 2.73
465 468 6.296803 TGATACATGATCCAGTACTACGTCT 58.703 40.000 0.00 0.00 33.07 4.18
627 637 3.111536 CCAAGAATGGCGCTGTTTG 57.888 52.632 7.64 5.58 40.58 2.93
736 753 2.222819 GCTTTTCTGATCGCAACCGTAG 60.223 50.000 0.00 0.00 35.54 3.51
1818 2033 0.536687 AGGACACCGACTCTGACGAA 60.537 55.000 0.00 0.00 0.00 3.85
1902 3937 5.565439 GCTTGTCTTAGCCACATGAAAATGT 60.565 40.000 0.00 0.00 35.06 2.71
1924 3959 7.762588 TGTAGTAGAGTAGAAGCATATTCCC 57.237 40.000 0.00 0.00 0.00 3.97
1955 3991 3.194968 TCCCGTTTGTTTTGTTGGCTTTA 59.805 39.130 0.00 0.00 0.00 1.85
1976 4012 7.577046 GCTTTATATAATCTCGTGGCTCCTGTA 60.577 40.741 0.00 0.00 0.00 2.74
1993 4029 2.557924 CTGTAGCCTTGTTGCAATCCAA 59.442 45.455 0.59 2.00 0.00 3.53
2027 4063 3.241741 CGCACAGCTGTTTGTTTCTTTTG 60.242 43.478 18.94 2.09 0.00 2.44
2040 4077 2.341846 TCTTTTGGCGGTTCAGAAGT 57.658 45.000 0.00 0.00 32.66 3.01
2107 4150 2.664851 TCTCGCGGCCACAACTTG 60.665 61.111 6.13 0.00 0.00 3.16
2124 4167 7.425606 CACAACTTGCCTGAAATAAACTACTT 58.574 34.615 0.00 0.00 0.00 2.24
2126 4169 6.819397 ACTTGCCTGAAATAAACTACTTCC 57.181 37.500 0.00 0.00 0.00 3.46
2141 4184 1.887198 ACTTCCATAGTAGGATCGGCG 59.113 52.381 0.00 0.00 37.56 6.46
2142 4185 2.160205 CTTCCATAGTAGGATCGGCGA 58.840 52.381 13.87 13.87 37.56 5.54
2145 4188 0.179187 CATAGTAGGATCGGCGAGCG 60.179 60.000 19.61 0.00 0.00 5.03
2146 4189 1.924320 ATAGTAGGATCGGCGAGCGC 61.924 60.000 19.61 12.01 41.06 5.92
2173 4232 6.738453 GCGCCATGGATTAATTGATTACCTTT 60.738 38.462 18.40 0.00 0.00 3.11
2203 4262 0.105593 GAGGCGATCTCATGGCTGAA 59.894 55.000 0.00 0.00 41.57 3.02
2212 4271 4.767578 TCTCATGGCTGAATTTCTAGCT 57.232 40.909 15.58 0.00 39.80 3.32
2232 4291 0.038983 TCGGCGTCGATTTGTTCTCA 60.039 50.000 8.66 0.00 40.88 3.27
2283 4404 2.116533 CCATGGCAAGCGCATCTGA 61.117 57.895 11.47 0.00 41.24 3.27
2294 4415 0.580578 CGCATCTGACATGCACTAGC 59.419 55.000 7.32 0.00 44.75 3.42
2327 4448 2.289592 AGGTAGAACCACTGTCGTCT 57.710 50.000 0.00 0.00 41.95 4.18
2339 4460 1.795872 CTGTCGTCTAGCTCGATCGAT 59.204 52.381 19.78 7.42 39.45 3.59
2342 4463 3.995048 TGTCGTCTAGCTCGATCGATTAT 59.005 43.478 19.78 9.99 39.45 1.28
2352 4473 4.517453 GCTCGATCGATTATCTAGGCCTAT 59.483 45.833 19.78 2.53 29.96 2.57
2355 4476 6.589135 TCGATCGATTATCTAGGCCTATGTA 58.411 40.000 15.15 6.55 31.87 2.29
2431 4557 1.499056 CACTGCAGCGTCACATTCC 59.501 57.895 15.27 0.00 0.00 3.01
2457 4607 7.479916 CGAATTCAGAGTTTCAGATAAAAGTGC 59.520 37.037 6.22 0.00 0.00 4.40
2664 4820 4.074970 AGAAGGTTGTGGTTGCTTCATAG 58.925 43.478 0.00 0.00 0.00 2.23
2665 4821 3.508845 AGGTTGTGGTTGCTTCATAGT 57.491 42.857 0.00 0.00 0.00 2.12
2668 4824 5.186198 AGGTTGTGGTTGCTTCATAGTATC 58.814 41.667 0.00 0.00 0.00 2.24
2669 4825 4.941263 GGTTGTGGTTGCTTCATAGTATCA 59.059 41.667 0.00 0.00 0.00 2.15
2670 4826 5.590259 GGTTGTGGTTGCTTCATAGTATCAT 59.410 40.000 0.00 0.00 0.00 2.45
2671 4827 6.765989 GGTTGTGGTTGCTTCATAGTATCATA 59.234 38.462 0.00 0.00 0.00 2.15
2672 4828 7.445402 GGTTGTGGTTGCTTCATAGTATCATAT 59.555 37.037 0.00 0.00 0.00 1.78
2698 4854 8.534954 TGCTCTCTAAGTTACAGTTATATGGT 57.465 34.615 0.00 0.00 0.00 3.55
2719 4875 2.649312 TGATCCATTGGTCCTTCAAGGT 59.351 45.455 2.50 0.00 36.53 3.50
2721 4877 3.713826 TCCATTGGTCCTTCAAGGTAC 57.286 47.619 2.50 0.34 36.53 3.34
2724 4880 3.610911 CATTGGTCCTTCAAGGTACTCC 58.389 50.000 2.50 3.35 38.49 3.85
2726 4882 0.910338 GGTCCTTCAAGGTACTCCCC 59.090 60.000 2.50 0.00 38.49 4.81
2727 4883 0.910338 GTCCTTCAAGGTACTCCCCC 59.090 60.000 2.50 0.00 38.49 5.40
2768 5272 5.589855 TGAATCCACAAATATCGTTGCTCAT 59.410 36.000 0.00 0.00 31.29 2.90
2805 5326 7.381678 GTGGTATATCTGAATTCAGTAACGTCC 59.618 40.741 29.80 24.00 44.12 4.79
2812 5333 0.971386 TTCAGTAACGTCCCTCCACC 59.029 55.000 0.00 0.00 0.00 4.61
2852 5373 3.985925 GCGCATTGGTGTATAGTACTACC 59.014 47.826 4.31 5.11 33.39 3.18
2855 5376 5.295152 GCATTGGTGTATAGTACTACCACC 58.705 45.833 29.88 29.88 38.58 4.61
2863 5384 7.442666 GGTGTATAGTACTACCACCACTACTAC 59.557 44.444 30.76 16.83 33.17 2.73
2864 5385 8.207545 GTGTATAGTACTACCACCACTACTACT 58.792 40.741 17.78 0.00 0.00 2.57
2865 5386 9.434275 TGTATAGTACTACCACCACTACTACTA 57.566 37.037 4.31 0.00 0.00 1.82
2868 5389 7.264294 AGTACTACCACCACTACTACTAACT 57.736 40.000 0.00 0.00 0.00 2.24
2869 5390 8.380742 AGTACTACCACCACTACTACTAACTA 57.619 38.462 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 4.503007 CGTACGTACTGGATGAAGAATTGG 59.497 45.833 22.55 0.00 0.00 3.16
67 68 5.320549 ACGTACGTACTGGATGAAGAATT 57.679 39.130 21.41 0.00 0.00 2.17
68 69 4.978083 ACGTACGTACTGGATGAAGAAT 57.022 40.909 21.41 0.00 0.00 2.40
69 70 4.201851 GCTACGTACGTACTGGATGAAGAA 60.202 45.833 23.60 1.22 0.00 2.52
70 71 3.310774 GCTACGTACGTACTGGATGAAGA 59.689 47.826 23.60 1.43 0.00 2.87
71 72 3.615614 GCTACGTACGTACTGGATGAAG 58.384 50.000 23.60 13.57 0.00 3.02
72 73 2.030823 CGCTACGTACGTACTGGATGAA 59.969 50.000 23.60 2.74 0.00 2.57
73 74 1.594397 CGCTACGTACGTACTGGATGA 59.406 52.381 23.60 3.50 0.00 2.92
74 75 1.333524 CCGCTACGTACGTACTGGATG 60.334 57.143 26.09 16.85 0.00 3.51
247 249 1.452108 CAGGATTCCGTTGGCTCCC 60.452 63.158 0.00 0.00 0.00 4.30
257 259 2.297597 CACCGGATAGTCTCAGGATTCC 59.702 54.545 9.46 0.00 41.38 3.01
396 399 2.224719 ACGTACTCTATCTATGGCGGGT 60.225 50.000 0.00 0.00 0.00 5.28
459 462 6.377996 TGCCCATCTTAGTTTACTTAGACGTA 59.622 38.462 1.11 0.00 34.89 3.57
460 463 5.186409 TGCCCATCTTAGTTTACTTAGACGT 59.814 40.000 1.11 0.00 34.89 4.34
461 464 5.657474 TGCCCATCTTAGTTTACTTAGACG 58.343 41.667 1.11 0.00 34.89 4.18
465 468 6.170506 CACACTGCCCATCTTAGTTTACTTA 58.829 40.000 0.00 0.00 0.00 2.24
597 607 1.841302 ATTCTTGGACCGGAGCAGCA 61.841 55.000 9.46 0.00 0.00 4.41
620 630 3.056328 GCCCTCCGTCCAAACAGC 61.056 66.667 0.00 0.00 0.00 4.40
646 662 1.282157 ACGCTAATCCCTCTTGCCTTT 59.718 47.619 0.00 0.00 0.00 3.11
788 805 2.047844 CACACCTGCTCCTCGTGG 60.048 66.667 0.00 0.00 0.00 4.94
907 924 1.738099 GAGCGTGACTGCGATTGGT 60.738 57.895 0.00 0.00 40.67 3.67
909 926 0.733909 TCTGAGCGTGACTGCGATTG 60.734 55.000 0.00 0.00 40.67 2.67
1818 2033 2.426023 GTGGCAGTGAACCCGTCT 59.574 61.111 0.00 0.00 0.00 4.18
1845 2069 4.429212 TCCATGTGCCGGTCGTCG 62.429 66.667 1.90 0.00 38.88 5.12
1846 2070 2.509336 CTCCATGTGCCGGTCGTC 60.509 66.667 1.90 0.00 0.00 4.20
1847 2071 4.760047 GCTCCATGTGCCGGTCGT 62.760 66.667 1.90 0.00 0.00 4.34
1848 2072 4.457496 AGCTCCATGTGCCGGTCG 62.457 66.667 1.90 0.00 0.00 4.79
1849 2073 2.821366 CAGCTCCATGTGCCGGTC 60.821 66.667 1.90 0.00 0.00 4.79
1850 2074 3.640407 ACAGCTCCATGTGCCGGT 61.640 61.111 1.90 1.85 30.46 5.28
1851 2075 3.129502 CACAGCTCCATGTGCCGG 61.130 66.667 0.00 0.00 43.69 6.13
1902 3937 5.944599 CGGGGAATATGCTTCTACTCTACTA 59.055 44.000 0.00 0.00 0.00 1.82
1924 3959 0.103390 AACAAACGGGAAAAAGCCGG 59.897 50.000 0.00 0.00 0.00 6.13
1955 3991 4.158764 GCTACAGGAGCCACGAGATTATAT 59.841 45.833 0.00 0.00 46.41 0.86
1976 4012 3.775261 AAATTGGATTGCAACAAGGCT 57.225 38.095 0.00 0.00 34.04 4.58
2027 4063 1.300697 ACGTCACTTCTGAACCGCC 60.301 57.895 0.00 0.00 0.00 6.13
2100 4143 7.255486 GGAAGTAGTTTATTTCAGGCAAGTTGT 60.255 37.037 4.48 0.00 0.00 3.32
2124 4167 1.822506 CTCGCCGATCCTACTATGGA 58.177 55.000 0.00 0.00 40.82 3.41
2126 4169 0.179187 CGCTCGCCGATCCTACTATG 60.179 60.000 0.00 0.00 40.02 2.23
2145 4188 0.664166 CAATTAATCCATGGCGCCGC 60.664 55.000 23.90 0.00 0.00 6.53
2146 4189 0.950836 TCAATTAATCCATGGCGCCG 59.049 50.000 23.90 8.36 0.00 6.46
2147 4190 3.665745 AATCAATTAATCCATGGCGCC 57.334 42.857 22.73 22.73 0.00 6.53
2148 4191 4.218417 AGGTAATCAATTAATCCATGGCGC 59.782 41.667 6.96 0.00 0.00 6.53
2149 4192 5.964958 AGGTAATCAATTAATCCATGGCG 57.035 39.130 6.96 0.00 0.00 5.69
2150 4193 7.500141 ACAAAGGTAATCAATTAATCCATGGC 58.500 34.615 6.96 0.00 0.00 4.40
2151 4194 9.889128 AAACAAAGGTAATCAATTAATCCATGG 57.111 29.630 4.97 4.97 0.00 3.66
2173 4232 3.009723 GAGATCGCCTCAAATGGAAACA 58.990 45.455 0.64 0.00 43.00 2.83
2203 4262 0.454600 TCGACGCCGAAGCTAGAAAT 59.545 50.000 0.00 0.00 42.51 2.17
2212 4271 4.410375 ATTGAGAACAAATCGACGCCGAA 61.410 43.478 0.00 0.00 41.86 4.30
2232 4291 5.132502 TCTGTTGTCCATTTGTCTGTCATT 58.867 37.500 0.00 0.00 0.00 2.57
2283 4404 1.466856 CAATGGTGGCTAGTGCATGT 58.533 50.000 0.00 0.00 41.91 3.21
2294 4415 3.071874 TCTACCTTTGAGCAATGGTGG 57.928 47.619 23.38 21.21 45.11 4.61
2327 4448 3.878103 GGCCTAGATAATCGATCGAGCTA 59.122 47.826 23.84 16.68 39.80 3.32
2339 4460 6.327781 TCACCCATTACATAGGCCTAGATAA 58.672 40.000 19.33 17.86 0.00 1.75
2342 4463 4.207698 TCACCCATTACATAGGCCTAGA 57.792 45.455 19.33 3.03 0.00 2.43
2352 4473 1.404748 CGCAATGCATCACCCATTACA 59.595 47.619 5.91 0.00 32.03 2.41
2355 4476 1.817881 CCGCAATGCATCACCCATT 59.182 52.632 5.91 0.00 33.41 3.16
2421 4547 3.254060 ACTCTGAATTCGGAATGTGACG 58.746 45.455 17.54 7.09 0.00 4.35
2427 4553 8.792830 TTTATCTGAAACTCTGAATTCGGAAT 57.207 30.769 17.54 5.35 42.48 3.01
2431 4557 7.479916 GCACTTTTATCTGAAACTCTGAATTCG 59.520 37.037 0.04 0.00 0.00 3.34
2494 4644 4.561959 TCGAATCGAACATTCAGTTTCG 57.438 40.909 1.57 15.51 41.51 3.46
2608 4758 2.361610 AGGCAATGGCTTCCCGTG 60.362 61.111 2.53 0.00 40.87 4.94
2611 4761 1.780503 ATTACAGGCAATGGCTTCCC 58.219 50.000 6.58 0.00 40.87 3.97
2671 4827 9.988815 CCATATAACTGTAACTTAGAGAGCAAT 57.011 33.333 0.06 0.00 0.00 3.56
2672 4828 8.978472 ACCATATAACTGTAACTTAGAGAGCAA 58.022 33.333 0.06 0.00 0.00 3.91
2698 4854 2.649312 ACCTTGAAGGACCAATGGATCA 59.351 45.455 19.83 1.97 37.67 2.92
2724 4880 2.171448 CAGAGACAATCTACCAAGGGGG 59.829 54.545 0.00 0.00 38.50 5.40
2726 4882 4.826274 TTCAGAGACAATCTACCAAGGG 57.174 45.455 0.00 0.00 36.10 3.95
2727 4883 5.104776 TGGATTCAGAGACAATCTACCAAGG 60.105 44.000 0.00 0.00 36.10 3.61
2728 4884 5.814705 GTGGATTCAGAGACAATCTACCAAG 59.185 44.000 0.00 0.00 36.32 3.61
2729 4885 5.248248 TGTGGATTCAGAGACAATCTACCAA 59.752 40.000 6.49 0.00 39.68 3.67
2768 5272 3.832490 CAGATATACCACCATCTTCCGGA 59.168 47.826 0.00 0.00 28.88 5.14
2805 5326 1.910580 AATGCGGTACTGGGTGGAGG 61.911 60.000 3.34 0.00 0.00 4.30
2812 5333 1.006832 GCACTGTAATGCGGTACTGG 58.993 55.000 3.34 0.00 35.50 4.00


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

AutoCloner maintained by Alex Coulton.