Multiple sequence alignment - TraesCS1D01G131500

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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 TraesCS1D01G131500 chr1D 100.000 7711 0 0 1 7711 153769095 153776805 0.000000e+00 14240.0
1 TraesCS1D01G131500 chr1D 95.041 121 6 0 3981 4101 308456418 308456538 2.840000e-44 191.0
2 TraesCS1D01G131500 chr1A 97.768 3943 59 7 3771 7711 208212860 208208945 0.000000e+00 6767.0
3 TraesCS1D01G131500 chr1A 97.473 3799 54 14 1 3770 208216734 208212949 0.000000e+00 6445.0
4 TraesCS1D01G131500 chr1A 96.842 855 27 0 5129 5983 207986861 207986007 0.000000e+00 1430.0
5 TraesCS1D01G131500 chr1A 95.672 439 18 1 5982 6419 207957766 207957328 0.000000e+00 704.0
6 TraesCS1D01G131500 chr1B 96.909 3624 84 8 4097 7711 230946287 230949891 0.000000e+00 6047.0
7 TraesCS1D01G131500 chr1B 94.923 2659 80 21 1 2626 230942109 230944745 0.000000e+00 4111.0
8 TraesCS1D01G131500 chr1B 94.678 1165 29 11 2628 3770 230944835 230945988 0.000000e+00 1777.0
9 TraesCS1D01G131500 chr1B 94.860 214 11 0 3771 3984 230946077 230946290 1.240000e-87 335.0
10 TraesCS1D01G131500 chr4B 86.736 2503 302 25 4229 6713 203850380 203847890 0.000000e+00 2756.0
11 TraesCS1D01G131500 chr4B 79.798 693 114 22 2838 3515 203851762 203851081 1.500000e-131 481.0
12 TraesCS1D01G131500 chr4D 86.685 2501 303 25 4231 6713 172023461 172025949 0.000000e+00 2747.0
13 TraesCS1D01G131500 chr4D 79.568 695 112 25 2838 3515 172022074 172022755 3.260000e-128 470.0
14 TraesCS1D01G131500 chr4D 93.130 131 7 2 3973 4103 55352565 55352437 2.840000e-44 191.0
15 TraesCS1D01G131500 chr4A 86.520 2500 309 24 4231 6713 415680871 415683359 0.000000e+00 2724.0
16 TraesCS1D01G131500 chr4A 79.190 716 121 24 2838 3537 415679487 415680190 9.060000e-129 472.0
17 TraesCS1D01G131500 chr4A 89.431 123 13 0 1459 1581 514233821 514233943 1.040000e-33 156.0
18 TraesCS1D01G131500 chrUn 100.000 391 0 0 1603 1993 479833821 479833431 0.000000e+00 723.0
19 TraesCS1D01G131500 chr5D 82.660 421 57 12 4521 4939 55548073 55547667 7.360000e-95 359.0
20 TraesCS1D01G131500 chr5D 84.836 244 29 7 2813 3053 55548837 55548599 1.000000e-58 239.0
21 TraesCS1D01G131500 chr5D 83.673 245 27 12 2813 3051 55545060 55544823 1.300000e-52 219.0
22 TraesCS1D01G131500 chr6A 84.585 253 25 8 1 242 235923058 235923307 1.000000e-58 239.0
23 TraesCS1D01G131500 chr6A 92.593 81 6 0 1505 1585 20530069 20530149 4.890000e-22 117.0
24 TraesCS1D01G131500 chr6A 90.141 71 7 0 11 81 379034967 379034897 8.240000e-15 93.5
25 TraesCS1D01G131500 chr6A 90.141 71 7 0 11 81 379044012 379043942 8.240000e-15 93.5
26 TraesCS1D01G131500 chr6D 84.524 252 25 8 1 241 179955344 179955592 3.600000e-58 237.0
27 TraesCS1D01G131500 chr6B 84.524 252 25 8 1 241 293101647 293101399 3.600000e-58 237.0
28 TraesCS1D01G131500 chr6B 95.082 122 6 0 3980 4101 21137137 21137258 7.900000e-45 193.0
29 TraesCS1D01G131500 chr6B 93.701 127 8 0 1459 1585 538999208 538999334 2.840000e-44 191.0
30 TraesCS1D01G131500 chr6B 92.683 82 4 2 1505 1585 69881564 69881644 4.890000e-22 117.0
31 TraesCS1D01G131500 chr6B 92.593 81 6 0 1505 1585 317011227 317011307 4.890000e-22 117.0
32 TraesCS1D01G131500 chr5B 84.298 242 30 7 2813 3051 57977297 57977061 6.020000e-56 230.0
33 TraesCS1D01G131500 chr5B 81.224 245 40 4 1 241 227123547 227123789 7.900000e-45 193.0
34 TraesCS1D01G131500 chr5B 97.500 40 0 1 1 40 331377380 331377418 4.990000e-07 67.6
35 TraesCS1D01G131500 chr5A 83.137 255 28 12 2787 3037 44287295 44287052 1.300000e-52 219.0
36 TraesCS1D01G131500 chr5A 93.023 129 8 1 3981 4109 446022573 446022446 3.670000e-43 187.0
37 TraesCS1D01G131500 chr5A 91.339 127 10 1 1459 1585 452465229 452465104 1.030000e-38 172.0
38 TraesCS1D01G131500 chr2A 95.082 122 6 0 3981 4102 78845572 78845693 7.900000e-45 193.0
39 TraesCS1D01G131500 chr3D 93.023 129 9 0 3973 4101 94848713 94848841 1.020000e-43 189.0
40 TraesCS1D01G131500 chr2D 93.600 125 8 0 3974 4098 599946106 599946230 3.670000e-43 187.0
41 TraesCS1D01G131500 chr2D 92.969 128 8 1 3968 4094 120988216 120988343 1.320000e-42 185.0
42 TraesCS1D01G131500 chr2D 82.550 149 20 5 96 240 229582548 229582694 8.120000e-25 126.0
43 TraesCS1D01G131500 chr7A 92.913 127 9 0 1459 1585 145456771 145456645 1.320000e-42 185.0
44 TraesCS1D01G131500 chr3B 82.692 156 18 7 90 241 288736784 288736934 6.280000e-26 130.0
45 TraesCS1D01G131500 chr7B 82.667 150 20 5 96 241 97138943 97139090 2.260000e-25 128.0


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 TraesCS1D01G131500 chr1D 153769095 153776805 7710 False 14240.000000 14240 100.0000 1 7711 1 chr1D.!!$F1 7710
1 TraesCS1D01G131500 chr1A 208208945 208216734 7789 True 6606.000000 6767 97.6205 1 7711 2 chr1A.!!$R3 7710
2 TraesCS1D01G131500 chr1A 207986007 207986861 854 True 1430.000000 1430 96.8420 5129 5983 1 chr1A.!!$R2 854
3 TraesCS1D01G131500 chr1B 230942109 230949891 7782 False 3067.500000 6047 95.3425 1 7711 4 chr1B.!!$F1 7710
4 TraesCS1D01G131500 chr4B 203847890 203851762 3872 True 1618.500000 2756 83.2670 2838 6713 2 chr4B.!!$R1 3875
5 TraesCS1D01G131500 chr4D 172022074 172025949 3875 False 1608.500000 2747 83.1265 2838 6713 2 chr4D.!!$F1 3875
6 TraesCS1D01G131500 chr4A 415679487 415683359 3872 False 1598.000000 2724 82.8550 2838 6713 2 chr4A.!!$F2 3875
7 TraesCS1D01G131500 chr5D 55544823 55548837 4014 True 272.333333 359 83.7230 2813 4939 3 chr5D.!!$R1 2126

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
225 230 0.844661 TGCCCCTGTACAAGGTGGAT 60.845 55.000 9.67 0.0 45.78 3.41 F
1357 1415 1.380380 GGGCCCTCCAATCAGGTTG 60.380 63.158 17.04 0.0 39.02 3.77 F
2182 2240 1.891150 CCAAGCAGTTCAAAGGCAGAT 59.109 47.619 0.00 0.0 0.00 2.90 F
2488 2547 2.443887 ATGCGCTTGTGAAATTTGCT 57.556 40.000 9.73 0.0 0.00 3.91 F
3994 4463 1.000019 CACCTACTCCCTCCGTCCA 60.000 63.158 0.00 0.0 0.00 4.02 F
4621 5122 0.242017 GCACAAGCAATGGAGTGGTC 59.758 55.000 0.00 0.0 41.58 4.02 F
5359 5864 0.395173 AAAGCAGGTTCCGTGTTGGT 60.395 50.000 0.00 0.0 39.52 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2240 1.076187 TGCTCTCTGGGAAGAGACTGA 59.924 52.381 5.13 0.00 44.67 3.41 R
2977 3149 1.875576 GCATCCCTTGATACAGCCTCG 60.876 57.143 0.00 0.00 0.00 4.63 R
3976 4445 0.613853 TTGGACGGAGGGAGTAGGTG 60.614 60.000 0.00 0.00 0.00 4.00 R
4046 4515 5.634859 CCAAACTTGTTACTCAAATGGATGC 59.365 40.000 0.00 0.00 36.92 3.91 R
4975 5480 2.268298 CGGTAAACCTTCATCTCACCG 58.732 52.381 0.00 0.00 41.12 4.94 R
6260 6765 7.441760 AGCATTTGTTCATAGCATGTTTTGAAA 59.558 29.630 14.99 3.33 30.51 2.69 R
7134 9795 3.823304 TGCCCATGCGCATGTATTTATAA 59.177 39.130 39.70 18.83 41.78 0.98 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
137 142 3.244422 ACCTAGCATCGTTTCTTTGTGGA 60.244 43.478 0.00 0.00 0.00 4.02
225 230 0.844661 TGCCCCTGTACAAGGTGGAT 60.845 55.000 9.67 0.00 45.78 3.41
344 367 6.710295 CCCCTTTTTAGTTTGGAAGAAATTGG 59.290 38.462 0.00 0.00 0.00 3.16
363 386 6.607004 ATTGGTACTAGTCTTGCTACAAGT 57.393 37.500 0.00 0.00 0.00 3.16
592 649 6.042552 GTGGAGATCCTGAATTCCTAGAATCA 59.957 42.308 2.27 0.00 36.82 2.57
856 914 9.337396 TGAACACCCTGTTTATCATTGTATATC 57.663 33.333 0.00 0.00 41.28 1.63
1357 1415 1.380380 GGGCCCTCCAATCAGGTTG 60.380 63.158 17.04 0.00 39.02 3.77
2182 2240 1.891150 CCAAGCAGTTCAAAGGCAGAT 59.109 47.619 0.00 0.00 0.00 2.90
2193 2251 3.055530 TCAAAGGCAGATCAGTCTCTTCC 60.056 47.826 0.00 0.00 30.42 3.46
2417 2475 3.462483 TCTTTGGTTAACTGACGCTGA 57.538 42.857 5.42 0.00 0.00 4.26
2487 2546 4.084641 TGTTTATGCGCTTGTGAAATTTGC 60.085 37.500 9.73 0.00 0.00 3.68
2488 2547 2.443887 ATGCGCTTGTGAAATTTGCT 57.556 40.000 9.73 0.00 0.00 3.91
2527 2586 9.897744 CTCAAATGCTAATTCTGTTTTAGTGAA 57.102 29.630 0.00 0.00 0.00 3.18
2543 2602 4.708726 AGTGAATTGCAGAACATAAGGC 57.291 40.909 0.00 0.00 0.00 4.35
2677 2824 3.686916 GGACTGTTCCTAGTTTGCTCT 57.313 47.619 0.00 0.00 39.13 4.09
2776 2946 4.004314 TCGTCAGTGTTTTCTTGGTTTCA 58.996 39.130 0.00 0.00 0.00 2.69
2977 3149 2.940410 CAGTTCCTACGAGGAGAGTCTC 59.060 54.545 12.01 12.01 46.73 3.36
3243 3438 2.766263 CTGGTTCAGGTAGCCATACTGA 59.234 50.000 0.00 0.00 37.89 3.41
3244 3439 3.384168 TGGTTCAGGTAGCCATACTGAT 58.616 45.455 0.00 0.00 32.74 2.90
3245 3440 4.552674 TGGTTCAGGTAGCCATACTGATA 58.447 43.478 0.00 0.00 32.74 2.15
3246 3441 4.966168 TGGTTCAGGTAGCCATACTGATAA 59.034 41.667 0.00 0.00 32.74 1.75
3483 3678 9.563748 CCATTGGAGCAATTATCCATTTTTATT 57.436 29.630 11.34 0.00 46.06 1.40
3914 4383 8.534333 TTATGAATTAAGCTATACTCAAGCGG 57.466 34.615 0.00 0.00 44.87 5.52
3994 4463 1.000019 CACCTACTCCCTCCGTCCA 60.000 63.158 0.00 0.00 0.00 4.02
4066 4535 5.948162 AGATGCATCCATTTGAGTAACAAGT 59.052 36.000 23.06 0.00 39.77 3.16
4100 4569 0.911769 TTCGGACGGAGGGAGTACTA 59.088 55.000 0.00 0.00 0.00 1.82
4391 4890 4.518970 TGGTTGTTATCTGTCTTTCTTGGC 59.481 41.667 0.00 0.00 0.00 4.52
4621 5122 0.242017 GCACAAGCAATGGAGTGGTC 59.758 55.000 0.00 0.00 41.58 4.02
4687 5188 1.341679 GGGACAGGGAAAACCCATACC 60.342 57.143 8.05 7.00 41.72 2.73
4822 5323 1.242665 GCTCAGAGGCTTTTGCTGCT 61.243 55.000 0.00 0.00 46.54 4.24
4975 5480 4.451629 TCTTGACCGAGGTTTCATAGAC 57.548 45.455 0.00 0.00 0.00 2.59
5359 5864 0.395173 AAAGCAGGTTCCGTGTTGGT 60.395 50.000 0.00 0.00 39.52 3.67
6230 6735 3.127376 GGTACGTCTCTCTGTCCTCTTTC 59.873 52.174 0.00 0.00 0.00 2.62
6257 6762 1.346395 TGCATCAAGACCACCGTACTT 59.654 47.619 0.00 0.00 0.00 2.24
6258 6763 2.224426 TGCATCAAGACCACCGTACTTT 60.224 45.455 0.00 0.00 0.00 2.66
6259 6764 3.007074 TGCATCAAGACCACCGTACTTTA 59.993 43.478 0.00 0.00 0.00 1.85
6260 6765 4.189231 GCATCAAGACCACCGTACTTTAT 58.811 43.478 0.00 0.00 0.00 1.40
7134 9795 7.682787 AACAGGATACCATCTTTCTCATAGT 57.317 36.000 0.00 0.00 37.17 2.12
7396 10058 2.928801 TTCAGCTGCCTTGTTGTCTA 57.071 45.000 9.47 0.00 0.00 2.59
7454 10116 7.653647 TGTTTTATGTTGTTGGAAGATGGTAC 58.346 34.615 0.00 0.00 0.00 3.34
7664 10326 1.957113 GCCCTGTTTGGATCCTTCTGG 60.957 57.143 14.23 14.74 38.35 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 142 4.023291 GAGGAGAGAGGAGTTTGATGAGT 58.977 47.826 0.00 0.00 0.00 3.41
225 230 3.003173 CGAGGCCCTTCCCAGTGA 61.003 66.667 0.00 0.00 34.51 3.41
420 450 2.285827 TCAACACAAAAGCAAACGGG 57.714 45.000 0.00 0.00 0.00 5.28
592 649 8.910944 CCACTTCATATCCATCTCAAGAAATTT 58.089 33.333 0.00 0.00 0.00 1.82
856 914 6.247903 CAACAACCAGCGTAATATGTTAGTG 58.752 40.000 0.00 0.00 30.48 2.74
1249 1307 7.739825 TCCAAATTCTCTCCTGTATTCATAGG 58.260 38.462 0.00 0.00 34.40 2.57
1262 1320 3.247173 CGCAGTAGCATCCAAATTCTCTC 59.753 47.826 0.00 0.00 42.27 3.20
1357 1415 5.334724 CCTCTTCTCTTTCAACTGATTGTGC 60.335 44.000 0.00 0.00 37.11 4.57
2182 2240 1.076187 TGCTCTCTGGGAAGAGACTGA 59.924 52.381 5.13 0.00 44.67 3.41
2193 2251 2.828520 TCCTGTTAGAAGTGCTCTCTGG 59.171 50.000 0.00 0.00 35.41 3.86
2302 2360 4.260497 CCGTATAAGTCGTTCGACAGATGA 60.260 45.833 23.70 7.40 37.59 2.92
2417 2475 8.517878 CATGACAGAAGTTTCCAGATTAAACAT 58.482 33.333 0.00 0.00 38.92 2.71
2487 2546 5.181748 AGCATTTGAGGAAGTAGCACTAAG 58.818 41.667 0.00 0.00 0.00 2.18
2488 2547 5.165961 AGCATTTGAGGAAGTAGCACTAA 57.834 39.130 0.00 0.00 0.00 2.24
2527 2586 3.960571 AGTGAGCCTTATGTTCTGCAAT 58.039 40.909 0.00 0.00 0.00 3.56
2621 2680 9.363763 CAGAACACAGGCAGACATATATTATAG 57.636 37.037 0.00 0.00 0.00 1.31
2626 2685 5.620738 ACAGAACACAGGCAGACATATAT 57.379 39.130 0.00 0.00 0.00 0.86
2628 2687 3.988976 ACAGAACACAGGCAGACATAT 57.011 42.857 0.00 0.00 0.00 1.78
2677 2824 8.239038 TGTACCAACCATGAAAGAAAAATACA 57.761 30.769 0.00 0.00 0.00 2.29
2718 2865 4.019792 ACAAGGCATGTATTCACACAGA 57.980 40.909 0.00 0.00 41.63 3.41
2776 2946 7.648142 CACACACACTGGTTTTACAATAGAAT 58.352 34.615 0.00 0.00 0.00 2.40
2977 3149 1.875576 GCATCCCTTGATACAGCCTCG 60.876 57.143 0.00 0.00 0.00 4.63
3483 3678 4.889409 GCTACAATCAAATGAATCCCCAGA 59.111 41.667 0.00 0.00 0.00 3.86
3914 4383 3.716872 TCCTGTTAGGATGAGGGGATTTC 59.283 47.826 0.00 0.00 40.06 2.17
3976 4445 0.613853 TTGGACGGAGGGAGTAGGTG 60.614 60.000 0.00 0.00 0.00 4.00
4010 4479 5.824624 ACTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
4046 4515 5.634859 CCAAACTTGTTACTCAAATGGATGC 59.365 40.000 0.00 0.00 36.92 3.91
4100 4569 7.971722 ACAAAGCAAACTAAACGTAACAATCTT 59.028 29.630 0.00 0.00 0.00 2.40
4120 4589 5.985781 TGAATCGAGTCAACTTAACAAAGC 58.014 37.500 14.01 0.00 0.00 3.51
4186 4668 9.981114 AAAAGACAACCAAAAGGATTTAGTATG 57.019 29.630 0.00 0.00 37.28 2.39
4621 5122 2.629617 AGGCCATGGTTCTTGTTTCTTG 59.370 45.455 14.67 0.00 0.00 3.02
4687 5188 4.513198 AACATTTAACATTCCCCACACG 57.487 40.909 0.00 0.00 0.00 4.49
4822 5323 5.076182 TGCAAAACTTCATCAATAGACCCA 58.924 37.500 0.00 0.00 0.00 4.51
4975 5480 2.268298 CGGTAAACCTTCATCTCACCG 58.732 52.381 0.00 0.00 41.12 4.94
6251 6756 9.767684 TCATAGCATGTTTTGAAATAAAGTACG 57.232 29.630 0.35 0.00 0.00 3.67
6259 6764 8.231837 GCATTTGTTCATAGCATGTTTTGAAAT 58.768 29.630 14.99 5.21 30.51 2.17
6260 6765 7.441760 AGCATTTGTTCATAGCATGTTTTGAAA 59.558 29.630 14.99 3.33 30.51 2.69
7134 9795 3.823304 TGCCCATGCGCATGTATTTATAA 59.177 39.130 39.70 18.83 41.78 0.98
7396 10058 4.281182 AGTCTCGAACTAACAACAGGTGAT 59.719 41.667 0.00 0.00 36.07 3.06
7454 10116 8.023128 CAGGTAAGAACATAACTGAAAACATGG 58.977 37.037 0.00 0.00 42.11 3.66
7685 10347 2.107204 CTGGCTTATGCTAACAGGGGAT 59.893 50.000 0.13 0.00 39.59 3.85


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

AutoCloner maintained by Alex Coulton.