Multiple sequence alignment - TraesCS5B01G169600

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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 TraesCS5B01G169600 chr5B 100.000 3771 0 0 1 3771 314275658 314279428 0.000000e+00 6964.0
1 TraesCS5B01G169600 chr5B 92.295 1194 52 19 926 2097 314194069 314192894 0.000000e+00 1659.0
2 TraesCS5B01G169600 chr5B 95.238 756 22 6 2093 2848 314192811 314192070 0.000000e+00 1184.0
3 TraesCS5B01G169600 chr5B 87.629 194 19 2 485 673 528933416 528933223 1.760000e-53 220.0
4 TraesCS5B01G169600 chr5A 94.984 1934 54 24 934 2851 365599413 365601319 0.000000e+00 2994.0
5 TraesCS5B01G169600 chr5A 91.872 1907 106 32 933 2808 365253481 365255369 0.000000e+00 2617.0
6 TraesCS5B01G169600 chr5A 87.129 202 17 3 479 673 648792201 648792002 1.760000e-53 220.0
7 TraesCS5B01G169600 chr5A 98.077 52 0 1 702 752 536799601 536799550 5.190000e-14 89.8
8 TraesCS5B01G169600 chr5A 95.745 47 2 0 814 860 365253176 365253222 4.040000e-10 76.8
9 TraesCS5B01G169600 chr5D 94.093 1947 74 20 933 2848 276924772 276926708 0.000000e+00 2920.0
10 TraesCS5B01G169600 chr5D 92.562 1963 86 25 926 2847 276917417 276919360 0.000000e+00 2761.0
11 TraesCS5B01G169600 chr5D 97.802 182 1 1 760 938 276924566 276924747 1.020000e-80 311.0
12 TraesCS5B01G169600 chr5D 89.683 126 8 4 459 582 550983550 550983672 5.040000e-34 156.0
13 TraesCS5B01G169600 chr5D 100.000 52 0 0 2847 2898 276926733 276926784 3.100000e-16 97.1
14 TraesCS5B01G169600 chr5D 95.745 47 2 0 814 860 276917093 276917139 4.040000e-10 76.8
15 TraesCS5B01G169600 chr4B 97.704 871 13 4 2898 3768 55323140 55324003 0.000000e+00 1491.0
16 TraesCS5B01G169600 chr4B 87.626 396 43 6 1 393 664090589 664090197 4.440000e-124 455.0
17 TraesCS5B01G169600 chr2B 97.600 875 12 2 2897 3771 72979561 72978696 0.000000e+00 1491.0
18 TraesCS5B01G169600 chr2B 84.191 272 26 12 459 719 9011193 9011458 8.090000e-62 248.0
19 TraesCS5B01G169600 chr7A 91.304 874 53 13 2896 3765 728964426 728965280 0.000000e+00 1171.0
20 TraesCS5B01G169600 chr7A 88.990 881 63 13 2896 3768 492419728 492420582 0.000000e+00 1059.0
21 TraesCS5B01G169600 chr7A 87.656 883 58 13 2897 3771 690408848 690408009 0.000000e+00 979.0
22 TraesCS5B01G169600 chr7A 92.857 126 9 0 2896 3021 690408973 690408848 2.310000e-42 183.0
23 TraesCS5B01G169600 chr7A 83.562 146 21 3 1308 1450 158395270 158395415 2.360000e-27 134.0
24 TraesCS5B01G169600 chr7A 94.643 56 1 2 702 755 6871960 6872015 6.710000e-13 86.1
25 TraesCS5B01G169600 chr1B 90.669 493 37 7 1 486 26601578 26601088 0.000000e+00 647.0
26 TraesCS5B01G169600 chr1B 88.940 217 13 5 459 669 26600110 26599899 1.340000e-64 257.0
27 TraesCS5B01G169600 chr1B 83.803 142 11 7 442 582 532148866 532148736 1.420000e-24 124.0
28 TraesCS5B01G169600 chr1B 90.476 63 4 2 702 762 26599729 26599667 8.680000e-12 82.4
29 TraesCS5B01G169600 chr2A 87.097 465 47 9 1 459 550704635 550704178 7.220000e-142 514.0
30 TraesCS5B01G169600 chr2A 98.039 51 0 1 703 752 550703115 550703065 1.870000e-13 87.9
31 TraesCS5B01G169600 chr7B 86.168 441 50 5 54 485 62468105 62468543 2.050000e-127 466.0
32 TraesCS5B01G169600 chr7B 77.369 517 96 19 1309 1816 409712037 409711533 1.710000e-73 287.0
33 TraesCS5B01G169600 chr7B 93.785 177 11 0 2896 3072 60618779 60618955 2.230000e-67 267.0
34 TraesCS5B01G169600 chr7B 80.172 232 42 4 2896 3124 709111174 709111404 1.800000e-38 171.0
35 TraesCS5B01G169600 chr7B 83.562 146 21 2 1308 1450 120586992 120587137 2.360000e-27 134.0
36 TraesCS5B01G169600 chr2D 84.259 432 49 13 22 446 126978812 126978393 1.630000e-108 403.0
37 TraesCS5B01G169600 chr4D 85.326 368 34 4 1 368 43673011 43673358 2.770000e-96 363.0
38 TraesCS5B01G169600 chr4D 96.154 52 1 1 702 752 43674811 43674862 2.410000e-12 84.2
39 TraesCS5B01G169600 chr6D 82.167 443 53 13 54 486 308940897 308941323 1.290000e-94 357.0
40 TraesCS5B01G169600 chr6D 77.215 395 75 14 1310 1698 54238653 54239038 2.280000e-52 217.0
41 TraesCS5B01G169600 chr6D 96.154 52 1 1 702 752 450115904 450115853 2.410000e-12 84.2
42 TraesCS5B01G169600 chr6D 96.970 33 1 0 1786 1818 426336790 426336822 5.260000e-04 56.5
43 TraesCS5B01G169600 chr7D 83.851 322 51 1 2440 2761 400170104 400169784 4.730000e-79 305.0
44 TraesCS5B01G169600 chr7D 77.220 518 95 21 1309 1816 400171046 400170542 7.970000e-72 281.0
45 TraesCS5B01G169600 chr7D 79.528 254 20 17 442 673 629619244 629619001 6.520000e-33 152.0
46 TraesCS5B01G169600 chr7D 83.562 146 21 3 1308 1450 159736611 159736756 2.360000e-27 134.0
47 TraesCS5B01G169600 chr3D 90.576 191 15 3 1 190 72256307 72256119 2.250000e-62 250.0
48 TraesCS5B01G169600 chr3D 96.296 54 0 2 704 755 540128760 540128707 1.870000e-13 87.9
49 TraesCS5B01G169600 chr6A 77.984 377 68 14 1328 1698 61007489 61007122 4.900000e-54 222.0
50 TraesCS5B01G169600 chr1D 78.022 364 63 17 1331 1685 56530509 56530154 2.950000e-51 213.0
51 TraesCS5B01G169600 chr1D 81.855 248 19 15 444 671 329673546 329673787 6.430000e-43 185.0
52 TraesCS5B01G169600 chrUn 77.863 393 46 12 97 488 76828315 76827963 4.940000e-49 206.0
53 TraesCS5B01G169600 chrUn 100.000 111 0 0 3661 3771 479414943 479414833 4.940000e-49 206.0
54 TraesCS5B01G169600 chrUn 83.621 232 23 8 457 673 76827005 76826774 1.780000e-48 204.0
55 TraesCS5B01G169600 chrUn 94.231 52 2 1 702 752 124706512 124706461 1.120000e-10 78.7
56 TraesCS5B01G169600 chr3A 83.582 201 19 7 484 672 84665178 84664980 3.870000e-40 176.0
57 TraesCS5B01G169600 chr6B 82.902 193 25 7 2894 3083 22729513 22729700 2.330000e-37 167.0
58 TraesCS5B01G169600 chr6B 90.756 119 10 1 459 576 76199316 76199198 1.400000e-34 158.0
59 TraesCS5B01G169600 chr6B 98.000 50 0 1 703 751 5321147 5321196 6.710000e-13 86.1
60 TraesCS5B01G169600 chr6B 94.118 51 2 1 3401 3450 172277328 172277278 4.040000e-10 76.8
61 TraesCS5B01G169600 chr3B 79.835 243 23 14 453 671 39593084 39593324 1.810000e-33 154.0
62 TraesCS5B01G169600 chr4A 79.330 179 26 8 62 237 445201060 445200890 8.560000e-22 115.0


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 TraesCS5B01G169600 chr5B 314275658 314279428 3770 False 6964.000000 6964 100.000000 1 3771 1 chr5B.!!$F1 3770
1 TraesCS5B01G169600 chr5B 314192070 314194069 1999 True 1421.500000 1659 93.766500 926 2848 2 chr5B.!!$R2 1922
2 TraesCS5B01G169600 chr5A 365599413 365601319 1906 False 2994.000000 2994 94.984000 934 2851 1 chr5A.!!$F1 1917
3 TraesCS5B01G169600 chr5A 365253176 365255369 2193 False 1346.900000 2617 93.808500 814 2808 2 chr5A.!!$F2 1994
4 TraesCS5B01G169600 chr5D 276917093 276919360 2267 False 1418.900000 2761 94.153500 814 2847 2 chr5D.!!$F2 2033
5 TraesCS5B01G169600 chr5D 276924566 276926784 2218 False 1109.366667 2920 97.298333 760 2898 3 chr5D.!!$F3 2138
6 TraesCS5B01G169600 chr4B 55323140 55324003 863 False 1491.000000 1491 97.704000 2898 3768 1 chr4B.!!$F1 870
7 TraesCS5B01G169600 chr2B 72978696 72979561 865 True 1491.000000 1491 97.600000 2897 3771 1 chr2B.!!$R1 874
8 TraesCS5B01G169600 chr7A 728964426 728965280 854 False 1171.000000 1171 91.304000 2896 3765 1 chr7A.!!$F4 869
9 TraesCS5B01G169600 chr7A 492419728 492420582 854 False 1059.000000 1059 88.990000 2896 3768 1 chr7A.!!$F3 872
10 TraesCS5B01G169600 chr7A 690408009 690408973 964 True 581.000000 979 90.256500 2896 3771 2 chr7A.!!$R1 875
11 TraesCS5B01G169600 chr1B 26599667 26601578 1911 True 328.800000 647 90.028333 1 762 3 chr1B.!!$R2 761
12 TraesCS5B01G169600 chr2A 550703065 550704635 1570 True 300.950000 514 92.568000 1 752 2 chr2A.!!$R1 751
13 TraesCS5B01G169600 chr7B 409711533 409712037 504 True 287.000000 287 77.369000 1309 1816 1 chr7B.!!$R1 507
14 TraesCS5B01G169600 chr4D 43673011 43674862 1851 False 223.600000 363 90.740000 1 752 2 chr4D.!!$F1 751
15 TraesCS5B01G169600 chr7D 400169784 400171046 1262 True 293.000000 305 80.535500 1309 2761 2 chr7D.!!$R2 1452
16 TraesCS5B01G169600 chrUn 76826774 76828315 1541 True 205.000000 206 80.742000 97 673 2 chrUn.!!$R3 576

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
705 2151 2.286365 ATCCAGCCCAAGAACGAAAA 57.714 45.0 0.0 0.0 0.0 2.29 F
1029 2848 0.037975 CCAAAGCTTGCATGTCCACC 60.038 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 3596 0.378962 AGCTGAGCGAGTCGATGTAC 59.621 55.0 18.61 0.00 0.0 2.90 R
2815 4833 0.800683 TCAAGTTCTACCATCGCGCG 60.801 55.0 26.76 26.76 0.0 6.86 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
276 281 6.323739 ACACAATTTACACAGAAGGGTTTCAT 59.676 34.615 0.00 0.00 35.70 2.57
312 317 5.463061 GCACACATTTTACACAGAAATTGCT 59.537 36.000 0.00 0.00 30.66 3.91
314 319 6.696583 CACACATTTTACACAGAAATTGCTCA 59.303 34.615 0.00 0.00 0.00 4.26
354 359 6.560304 AGGACAACCATATGATAGAGGAACAT 59.440 38.462 3.65 0.00 38.94 2.71
705 2151 2.286365 ATCCAGCCCAAGAACGAAAA 57.714 45.000 0.00 0.00 0.00 2.29
706 2152 2.286365 TCCAGCCCAAGAACGAAAAT 57.714 45.000 0.00 0.00 0.00 1.82
710 2276 2.554032 CAGCCCAAGAACGAAAATGACT 59.446 45.455 0.00 0.00 0.00 3.41
755 2321 5.238214 GCTGACTGAAATCTAGCTAAATGGG 59.762 44.000 0.00 0.00 0.00 4.00
756 2322 6.313519 TGACTGAAATCTAGCTAAATGGGT 57.686 37.500 0.00 0.00 0.00 4.51
757 2323 6.349300 TGACTGAAATCTAGCTAAATGGGTC 58.651 40.000 0.00 0.00 0.00 4.46
758 2324 6.156949 TGACTGAAATCTAGCTAAATGGGTCT 59.843 38.462 0.00 0.00 0.00 3.85
807 2373 2.610433 TCAAGCTGCGTCTGTATCTTG 58.390 47.619 0.00 0.00 34.04 3.02
956 2761 6.693545 GCAACTGATCGACCACTATATATAGC 59.306 42.308 18.00 2.97 33.68 2.97
957 2762 7.628580 GCAACTGATCGACCACTATATATAGCA 60.629 40.741 18.00 6.10 33.68 3.49
958 2763 7.939784 ACTGATCGACCACTATATATAGCAA 57.060 36.000 18.00 0.56 33.68 3.91
1029 2848 0.037975 CCAAAGCTTGCATGTCCACC 60.038 55.000 0.00 0.00 0.00 4.61
1050 2869 2.415010 CTGATCGCCGTCCTCTGG 59.585 66.667 0.00 0.00 0.00 3.86
1220 3043 2.190981 CGCCTCCAATGTACGTACTTC 58.809 52.381 25.12 6.49 0.00 3.01
1265 3103 1.512522 CCATGCATGCACGTCGTTG 60.513 57.895 25.37 16.07 0.00 4.10
1291 3129 4.201881 GGGAGTGACCATTAATTTACGTGC 60.202 45.833 0.00 0.00 41.20 5.34
1323 3161 3.559171 GCTTTGATCAGGTGGACCTTGTA 60.559 47.826 0.00 0.00 46.09 2.41
1758 3596 3.834799 GACCGGTACAGGGGCTCG 61.835 72.222 16.82 0.00 35.02 5.03
1860 3748 3.313803 ACACGTTAACACAACATGCATGA 59.686 39.130 32.75 5.74 0.00 3.07
1861 3749 4.023279 ACACGTTAACACAACATGCATGAT 60.023 37.500 32.75 19.24 0.00 2.45
1862 3750 4.321480 CACGTTAACACAACATGCATGATG 59.679 41.667 32.75 30.79 36.73 3.07
1863 3751 3.301379 CGTTAACACAACATGCATGATGC 59.699 43.478 32.75 11.12 45.29 3.91
1866 3754 1.277326 CACAACATGCATGATGCTGC 58.723 50.000 32.75 0.00 45.31 5.25
2814 4832 3.716918 CGTAAACGAAATGTGTGTGTGTG 59.283 43.478 0.00 0.00 43.02 3.82
2815 4833 2.187351 AACGAAATGTGTGTGTGTGC 57.813 45.000 0.00 0.00 0.00 4.57
2816 4834 0.027455 ACGAAATGTGTGTGTGTGCG 59.973 50.000 0.00 0.00 0.00 5.34
2817 4835 1.261510 CGAAATGTGTGTGTGTGCGC 61.262 55.000 0.00 0.00 0.00 6.09
2931 4975 9.127277 ACTATTAAAAGAGCAAACAGGTGTTTA 57.873 29.630 7.75 0.00 45.54 2.01
3504 5697 0.393448 GCCCTCCTCCCGACTAAATC 59.607 60.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 146 8.798402 TCTTAGGAAACTTCTTTGTTGTGAAAA 58.202 29.630 0.00 0.00 43.67 2.29
148 151 7.334844 CCTTCTTAGGAAACTTCTTTGTTGT 57.665 36.000 0.00 0.00 45.05 3.32
230 233 8.864069 TGTGTGTAAGTTTTGTCAATAATTGG 57.136 30.769 0.00 0.00 0.00 3.16
473 1882 9.202273 GTGCTAATTGTGTGGAAAATTTCATTA 57.798 29.630 8.09 1.81 0.00 1.90
477 1886 7.475771 TTGTGCTAATTGTGTGGAAAATTTC 57.524 32.000 0.00 0.00 0.00 2.17
576 1987 7.801104 TGGATGGTGAGTGTGTAAATGTATAT 58.199 34.615 0.00 0.00 0.00 0.86
637 2065 4.212911 TGCACGTGTACGCTTTTATTTTC 58.787 39.130 18.38 0.00 44.43 2.29
705 2151 6.601613 TGACTTTTAGTTTTGTGGTCAGTCAT 59.398 34.615 0.00 0.00 0.00 3.06
706 2152 5.941058 TGACTTTTAGTTTTGTGGTCAGTCA 59.059 36.000 0.00 0.00 0.00 3.41
710 2276 4.947388 AGCTGACTTTTAGTTTTGTGGTCA 59.053 37.500 0.00 0.00 0.00 4.02
755 2321 1.806542 TCCGTACGTAGTGGTCAAGAC 59.193 52.381 15.21 0.00 45.73 3.01
756 2322 2.183478 TCCGTACGTAGTGGTCAAGA 57.817 50.000 15.21 0.00 45.73 3.02
757 2323 2.538333 CGATCCGTACGTAGTGGTCAAG 60.538 54.545 15.21 0.00 45.73 3.02
758 2324 1.398041 CGATCCGTACGTAGTGGTCAA 59.602 52.381 15.21 0.00 45.73 3.18
807 2373 3.368013 CCCTTCCTTTTTAATGTTCGCCC 60.368 47.826 0.00 0.00 0.00 6.13
956 2761 4.447054 GTGCTGAGCTACATACTAGCATTG 59.553 45.833 5.83 0.00 42.32 2.82
957 2762 4.502259 GGTGCTGAGCTACATACTAGCATT 60.502 45.833 5.83 0.00 42.32 3.56
958 2763 3.006323 GGTGCTGAGCTACATACTAGCAT 59.994 47.826 5.83 0.00 42.32 3.79
1029 2848 0.820074 AGAGGACGGCGATCAGGTAG 60.820 60.000 16.62 0.00 0.00 3.18
1220 3043 0.244994 CCAGGACTTGTCGTCTGAGG 59.755 60.000 8.07 0.00 42.44 3.86
1265 3103 4.269363 CGTAAATTAATGGTCACTCCCGTC 59.731 45.833 0.00 0.00 34.77 4.79
1269 3107 4.493545 CGCACGTAAATTAATGGTCACTCC 60.494 45.833 0.00 0.00 0.00 3.85
1274 3112 4.852609 AGACGCACGTAAATTAATGGTC 57.147 40.909 0.00 0.00 0.00 4.02
1275 3113 4.453136 ACAAGACGCACGTAAATTAATGGT 59.547 37.500 0.00 0.00 0.00 3.55
1276 3114 4.965062 ACAAGACGCACGTAAATTAATGG 58.035 39.130 0.00 0.00 0.00 3.16
1277 3115 5.282778 CCAACAAGACGCACGTAAATTAATG 59.717 40.000 0.00 0.00 0.00 1.90
1278 3116 5.387279 CCAACAAGACGCACGTAAATTAAT 58.613 37.500 0.00 0.00 0.00 1.40
1279 3117 4.774586 CCAACAAGACGCACGTAAATTAA 58.225 39.130 0.00 0.00 0.00 1.40
1280 3118 3.364167 GCCAACAAGACGCACGTAAATTA 60.364 43.478 0.00 0.00 0.00 1.40
1281 3119 2.603652 GCCAACAAGACGCACGTAAATT 60.604 45.455 0.00 0.00 0.00 1.82
1285 3123 0.531090 AAGCCAACAAGACGCACGTA 60.531 50.000 0.00 0.00 0.00 3.57
1287 3125 0.929824 CAAAGCCAACAAGACGCACG 60.930 55.000 0.00 0.00 0.00 5.34
1291 3129 2.095567 CCTGATCAAAGCCAACAAGACG 60.096 50.000 0.00 0.00 0.00 4.18
1323 3161 1.452833 GGCGTCGTAGTACCCTCCT 60.453 63.158 0.00 0.00 0.00 3.69
1351 3189 2.044946 GGGCAGGCCGAACTTGAT 60.045 61.111 3.89 0.00 36.85 2.57
1758 3596 0.378962 AGCTGAGCGAGTCGATGTAC 59.621 55.000 18.61 0.00 0.00 2.90
1863 3751 2.358860 ACTCAGCAGCAGCAGCAG 60.359 61.111 12.92 3.97 45.49 4.24
1866 3754 2.776670 TTCCGACTCAGCAGCAGCAG 62.777 60.000 3.17 0.00 45.49 4.24
2814 4832 2.165301 AAGTTCTACCATCGCGCGC 61.165 57.895 27.95 23.91 0.00 6.86
2815 4833 0.800683 TCAAGTTCTACCATCGCGCG 60.801 55.000 26.76 26.76 0.00 6.86
2816 4834 1.060698 GTTCAAGTTCTACCATCGCGC 59.939 52.381 0.00 0.00 0.00 6.86
2817 4835 2.345641 CAGTTCAAGTTCTACCATCGCG 59.654 50.000 0.00 0.00 0.00 5.87
2902 4946 7.390718 ACACCTGTTTGCTCTTTTAATAGTAGG 59.609 37.037 0.00 0.00 0.00 3.18
2931 4975 7.551262 TGTACAGTTTGTTGTGTGACTTTAGAT 59.449 33.333 0.00 0.00 32.56 1.98
3043 5212 8.213679 TGCTAGCCAGAACATTTAATCTAAGAT 58.786 33.333 13.29 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.