Multiple sequence alignment - TraesCS1D01G097900

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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 TraesCS1D01G097900 chr1D 100.000 3092 0 0 1 3092 84729518 84726427 0.000000e+00 5710.0
1 TraesCS1D01G097900 chr1D 93.115 1438 54 25 758 2176 84615792 84614381 0.000000e+00 2065.0
2 TraesCS1D01G097900 chr1D 90.694 1440 84 17 752 2176 84891468 84892872 0.000000e+00 1871.0
3 TraesCS1D01G097900 chr1D 90.213 470 28 7 2628 3092 84614332 84613876 5.710000e-167 597.0
4 TraesCS1D01G097900 chr1D 93.625 251 15 1 2842 3092 84571630 84571381 1.050000e-99 374.0
5 TraesCS1D01G097900 chr1D 81.935 465 46 24 2625 3081 84892918 84893352 2.930000e-95 359.0
6 TraesCS1D01G097900 chr1D 84.706 170 22 3 1930 2095 84573501 84573332 1.910000e-37 167.0
7 TraesCS1D01G097900 chr1D 95.652 46 2 0 2118 2163 84614377 84614332 1.190000e-09 75.0
8 TraesCS1D01G097900 chr1D 82.432 74 3 2 688 751 84615895 84615822 4.310000e-04 56.5
9 TraesCS1D01G097900 chr1D 100.000 30 0 0 722 751 84891421 84891450 4.310000e-04 56.5
10 TraesCS1D01G097900 chr1A 93.828 1604 65 12 1505 3092 78958402 78956817 0.000000e+00 2383.0
11 TraesCS1D01G097900 chr1A 90.797 1456 96 17 752 2176 78551406 78549958 0.000000e+00 1912.0
12 TraesCS1D01G097900 chr1A 92.272 1074 63 14 872 1940 79110396 79111454 0.000000e+00 1506.0
13 TraesCS1D01G097900 chr1A 95.876 679 28 0 1 679 584875407 584876085 0.000000e+00 1099.0
14 TraesCS1D01G097900 chr1A 87.583 604 39 12 2491 3092 78549644 78549075 0.000000e+00 667.0
15 TraesCS1D01G097900 chr1A 84.579 428 50 9 2625 3047 79116592 79117008 7.980000e-111 411.0
16 TraesCS1D01G097900 chr1A 80.077 522 83 15 2581 3092 14162616 14163126 4.870000e-98 368.0
17 TraesCS1D01G097900 chr1A 92.032 251 16 2 2842 3092 78340041 78339795 1.760000e-92 350.0
18 TraesCS1D01G097900 chr1A 91.979 187 7 1 2053 2231 78549838 78549652 3.960000e-64 255.0
19 TraesCS1D01G097900 chr1A 94.915 59 3 0 758 816 79110328 79110386 3.280000e-15 93.5
20 TraesCS1D01G097900 chr1B 92.238 1443 81 8 753 2176 137182446 137181016 0.000000e+00 2015.0
21 TraesCS1D01G097900 chr1B 90.834 1451 88 26 752 2176 137613267 137614698 0.000000e+00 1901.0
22 TraesCS1D01G097900 chr1B 91.132 1387 82 23 793 2163 137450880 137449519 0.000000e+00 1842.0
23 TraesCS1D01G097900 chr1B 89.957 468 36 8 2630 3092 137180913 137180452 7.380000e-166 593.0
24 TraesCS1D01G097900 chr1B 92.073 164 10 1 2842 3005 137162422 137162262 8.630000e-56 228.0
25 TraesCS1D01G097900 chr1B 93.243 148 8 2 2946 3092 137448983 137448837 1.870000e-52 217.0
26 TraesCS1D01G097900 chr1B 86.740 181 18 5 2625 2801 137614775 137614953 2.430000e-46 196.0
27 TraesCS1D01G097900 chr1B 82.941 170 25 3 1930 2095 137172919 137172750 1.920000e-32 150.0
28 TraesCS1D01G097900 chr1B 90.722 97 8 1 2996 3092 137155185 137155090 9.000000e-26 128.0
29 TraesCS1D01G097900 chr1B 93.220 59 4 0 2118 2176 137614671 137614729 1.530000e-13 87.9
30 TraesCS1D01G097900 chr6D 97.206 680 18 1 1 680 464214375 464213697 0.000000e+00 1149.0
31 TraesCS1D01G097900 chr3D 96.793 686 20 2 1 686 214959053 214959736 0.000000e+00 1144.0
32 TraesCS1D01G097900 chr3D 83.936 249 30 6 2239 2486 559226480 559226241 2.400000e-56 230.0
33 TraesCS1D01G097900 chr3D 82.645 242 18 14 2239 2468 8291293 8291522 3.150000e-45 193.0
34 TraesCS1D01G097900 chr3A 96.916 681 20 1 1 681 660861460 660860781 0.000000e+00 1140.0
35 TraesCS1D01G097900 chr7D 96.465 679 23 1 1 679 114467662 114468339 0.000000e+00 1120.0
36 TraesCS1D01G097900 chr7D 95.690 696 27 2 1 696 151540458 151541150 0.000000e+00 1116.0
37 TraesCS1D01G097900 chr7D 82.927 246 23 11 2240 2473 37413372 37413134 1.450000e-48 204.0
38 TraesCS1D01G097900 chr2D 96.029 680 24 3 1 679 70391269 70391946 0.000000e+00 1103.0
39 TraesCS1D01G097900 chr2D 96.024 679 26 1 1 679 161897828 161898505 0.000000e+00 1103.0
40 TraesCS1D01G097900 chr2D 95.876 679 27 1 1 679 101660206 101660883 0.000000e+00 1098.0
41 TraesCS1D01G097900 chr2D 82.138 739 91 23 752 1474 470200269 470200982 2.050000e-166 595.0
42 TraesCS1D01G097900 chr2D 86.400 250 31 3 2239 2488 36426440 36426194 1.410000e-68 270.0
43 TraesCS1D01G097900 chr2D 82.072 251 30 8 2238 2488 648089059 648089294 1.880000e-47 200.0
44 TraesCS1D01G097900 chr2A 83.316 965 113 26 753 1698 611763646 611764581 0.000000e+00 846.0
45 TraesCS1D01G097900 chr2A 82.707 266 26 7 2236 2488 72518575 72518833 5.190000e-53 219.0
46 TraesCS1D01G097900 chrUn 94.845 388 18 2 1601 1987 480029645 480030031 3.410000e-169 604.0
47 TraesCS1D01G097900 chrUn 87.405 262 20 4 2240 2489 369540874 369541134 3.900000e-74 289.0
48 TraesCS1D01G097900 chrUn 87.405 262 20 4 2240 2489 435144129 435144389 3.900000e-74 289.0
49 TraesCS1D01G097900 chrUn 83.071 254 37 6 2236 2486 97140888 97140638 3.100000e-55 226.0
50 TraesCS1D01G097900 chr3B 88.123 261 16 9 2240 2488 779624846 779625103 2.330000e-76 296.0
51 TraesCS1D01G097900 chr3B 91.011 178 15 1 2311 2488 46076954 46077130 3.980000e-59 239.0
52 TraesCS1D01G097900 chr4A 87.405 262 20 4 2240 2489 687514241 687514501 3.900000e-74 289.0
53 TraesCS1D01G097900 chr5D 84.733 262 27 7 2239 2488 498184926 498184666 1.840000e-62 250.0


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 TraesCS1D01G097900 chr1D 84726427 84729518 3091 True 5710.000000 5710 100.000000 1 3092 1 chr1D.!!$R1 3091
1 TraesCS1D01G097900 chr1D 84891421 84893352 1931 False 762.166667 1871 90.876333 722 3081 3 chr1D.!!$F1 2359
2 TraesCS1D01G097900 chr1D 84613876 84615895 2019 True 698.375000 2065 90.353000 688 3092 4 chr1D.!!$R3 2404
3 TraesCS1D01G097900 chr1D 84571381 84573501 2120 True 270.500000 374 89.165500 1930 3092 2 chr1D.!!$R2 1162
4 TraesCS1D01G097900 chr1A 78956817 78958402 1585 True 2383.000000 2383 93.828000 1505 3092 1 chr1A.!!$R2 1587
5 TraesCS1D01G097900 chr1A 584875407 584876085 678 False 1099.000000 1099 95.876000 1 679 1 chr1A.!!$F3 678
6 TraesCS1D01G097900 chr1A 78549075 78551406 2331 True 944.666667 1912 90.119667 752 3092 3 chr1A.!!$R3 2340
7 TraesCS1D01G097900 chr1A 79110328 79111454 1126 False 799.750000 1506 93.593500 758 1940 2 chr1A.!!$F4 1182
8 TraesCS1D01G097900 chr1A 14162616 14163126 510 False 368.000000 368 80.077000 2581 3092 1 chr1A.!!$F1 511
9 TraesCS1D01G097900 chr1B 137180452 137182446 1994 True 1304.000000 2015 91.097500 753 3092 2 chr1B.!!$R4 2339
10 TraesCS1D01G097900 chr1B 137448837 137450880 2043 True 1029.500000 1842 92.187500 793 3092 2 chr1B.!!$R5 2299
11 TraesCS1D01G097900 chr1B 137613267 137614953 1686 False 728.300000 1901 90.264667 752 2801 3 chr1B.!!$F1 2049
12 TraesCS1D01G097900 chr6D 464213697 464214375 678 True 1149.000000 1149 97.206000 1 680 1 chr6D.!!$R1 679
13 TraesCS1D01G097900 chr3D 214959053 214959736 683 False 1144.000000 1144 96.793000 1 686 1 chr3D.!!$F2 685
14 TraesCS1D01G097900 chr3A 660860781 660861460 679 True 1140.000000 1140 96.916000 1 681 1 chr3A.!!$R1 680
15 TraesCS1D01G097900 chr7D 114467662 114468339 677 False 1120.000000 1120 96.465000 1 679 1 chr7D.!!$F1 678
16 TraesCS1D01G097900 chr7D 151540458 151541150 692 False 1116.000000 1116 95.690000 1 696 1 chr7D.!!$F2 695
17 TraesCS1D01G097900 chr2D 70391269 70391946 677 False 1103.000000 1103 96.029000 1 679 1 chr2D.!!$F1 678
18 TraesCS1D01G097900 chr2D 161897828 161898505 677 False 1103.000000 1103 96.024000 1 679 1 chr2D.!!$F3 678
19 TraesCS1D01G097900 chr2D 101660206 101660883 677 False 1098.000000 1098 95.876000 1 679 1 chr2D.!!$F2 678
20 TraesCS1D01G097900 chr2D 470200269 470200982 713 False 595.000000 595 82.138000 752 1474 1 chr2D.!!$F4 722
21 TraesCS1D01G097900 chr2A 611763646 611764581 935 False 846.000000 846 83.316000 753 1698 1 chr2A.!!$F2 945

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
701 706 0.379316 GTTAATTAGTTGCGGCCCCG 59.621 55.0 1.59 1.59 43.09 5.73 F
1815 1938 0.600255 AGCAGCGCGACACTAAGTTT 60.600 50.0 12.10 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1975 0.243907 AGGATCGACACCACGTCTTG 59.756 55.000 12.09 0.0 42.98 3.02 R
2780 4015 6.988580 AGCAATGTCGAAAGATGAAGATATGA 59.011 34.615 0.00 0.0 45.19 2.15 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
515 519 3.191669 CGTGTGGGCGTTATCTATTTCA 58.808 45.455 0.00 0.00 0.00 2.69
616 621 2.755655 CGTGTGGACTGATCCTCTTAGT 59.244 50.000 0.00 0.00 46.43 2.24
624 629 4.357325 ACTGATCCTCTTAGTCACCACAT 58.643 43.478 0.00 0.00 0.00 3.21
682 687 1.659098 GACAGTTATCGGCGTCCAAAG 59.341 52.381 6.85 0.00 0.00 2.77
684 689 2.073816 CAGTTATCGGCGTCCAAAGTT 58.926 47.619 6.85 0.00 0.00 2.66
685 690 3.255725 CAGTTATCGGCGTCCAAAGTTA 58.744 45.455 6.85 0.00 0.00 2.24
687 692 4.331717 CAGTTATCGGCGTCCAAAGTTAAT 59.668 41.667 6.85 0.00 0.00 1.40
688 693 4.939439 AGTTATCGGCGTCCAAAGTTAATT 59.061 37.500 6.85 0.00 0.00 1.40
689 694 6.036300 CAGTTATCGGCGTCCAAAGTTAATTA 59.964 38.462 6.85 0.00 0.00 1.40
691 696 3.929094 TCGGCGTCCAAAGTTAATTAGT 58.071 40.909 6.85 0.00 0.00 2.24
692 697 4.317488 TCGGCGTCCAAAGTTAATTAGTT 58.683 39.130 6.85 0.00 0.00 2.24
694 699 4.163552 GGCGTCCAAAGTTAATTAGTTGC 58.836 43.478 0.00 0.00 0.00 4.17
695 700 3.844099 GCGTCCAAAGTTAATTAGTTGCG 59.156 43.478 0.00 0.00 0.00 4.85
701 706 0.379316 GTTAATTAGTTGCGGCCCCG 59.621 55.000 1.59 1.59 43.09 5.73
784 825 1.808411 ACATGCTTTGTCGGAATCGT 58.192 45.000 0.00 0.00 30.89 3.73
834 879 2.722071 GGAGTCGACTGATTAGCTTCG 58.278 52.381 25.58 0.00 0.00 3.79
836 890 3.003897 GGAGTCGACTGATTAGCTTCGAT 59.996 47.826 25.58 0.00 32.29 3.59
912 1016 2.929531 AGTAGCATAGGCATCGATCG 57.070 50.000 9.36 9.36 44.61 3.69
1708 1831 3.519510 CTCCCCATGGAAAGACTACTTCA 59.480 47.826 15.22 0.00 41.17 3.02
1788 1911 1.128136 CTGCAACAGCTCAAGATCACG 59.872 52.381 0.00 0.00 0.00 4.35
1815 1938 0.600255 AGCAGCGCGACACTAAGTTT 60.600 50.000 12.10 0.00 0.00 2.66
1817 1940 1.419374 CAGCGCGACACTAAGTTTCT 58.581 50.000 12.10 0.00 0.00 2.52
2061 2184 1.066587 GGTGGATCGAGAAGCGGAG 59.933 63.158 0.00 0.00 41.33 4.63
2110 2274 5.701290 AGTTGATACAACAGCTTGTAAGGTC 59.299 40.000 15.29 0.00 44.33 3.85
2254 2506 4.509970 GCGTTGCCAAGGTTTTTAATTTCT 59.490 37.500 0.00 0.00 0.00 2.52
2403 2667 8.984891 TCAAATCAGTTTAAATTTGCATCGAT 57.015 26.923 0.00 0.00 40.85 3.59
2495 2759 3.121496 CGTTGAAATTGTTAAGCGTTGCC 60.121 43.478 0.00 0.00 0.00 4.52
2558 2822 0.593128 GTTGCATTGTGGCGAACTCT 59.407 50.000 0.00 0.00 36.28 3.24
2780 4015 3.315191 GTGACAGTGTAAACAAGGCACAT 59.685 43.478 14.54 0.00 40.10 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.385013 TGTCATCTGCTTACGTGCAT 57.615 45.000 0.00 0.00 42.48 3.96
167 170 1.586422 CAGTTGCCATGTAGCGCTAT 58.414 50.000 21.96 3.06 34.65 2.97
567 572 0.821711 TGGGCAAAACAACTAGCGCT 60.822 50.000 17.26 17.26 40.16 5.92
602 607 3.779444 TGTGGTGACTAAGAGGATCAGT 58.221 45.455 0.00 0.00 37.82 3.41
606 611 5.067936 CGTTCTATGTGGTGACTAAGAGGAT 59.932 44.000 0.00 0.00 0.00 3.24
624 629 2.301870 AGAAATCTGCCCACACGTTCTA 59.698 45.455 0.00 0.00 0.00 2.10
682 687 0.379316 CGGGGCCGCAACTAATTAAC 59.621 55.000 21.08 0.00 0.00 2.01
684 689 1.153127 CCGGGGCCGCAACTAATTA 60.153 57.895 21.08 0.00 38.24 1.40
685 690 2.439519 CCGGGGCCGCAACTAATT 60.440 61.111 21.08 0.00 38.24 1.40
687 692 3.905437 GAACCGGGGCCGCAACTAA 62.905 63.158 21.08 0.00 38.24 2.24
688 693 4.397832 GAACCGGGGCCGCAACTA 62.398 66.667 21.08 0.00 38.24 2.24
714 719 4.914312 TTTCGGTACATACGCTTTTCAG 57.086 40.909 0.00 0.00 0.00 3.02
766 807 4.088648 GTTTACGATTCCGACAAAGCATG 58.911 43.478 0.00 0.00 39.50 4.06
784 825 1.286354 CGAGCCCTTGAACGCGTTTA 61.286 55.000 27.32 20.18 0.00 2.01
834 879 6.783708 ATATAACTACTAGGCAGGCTGATC 57.216 41.667 20.86 9.49 0.00 2.92
836 890 7.893833 TCATTATATAACTACTAGGCAGGCTGA 59.106 37.037 20.86 0.00 0.00 4.26
893 997 1.474478 CCGATCGATGCCTATGCTACT 59.526 52.381 18.66 0.00 38.71 2.57
894 998 1.914634 CCGATCGATGCCTATGCTAC 58.085 55.000 18.66 0.00 38.71 3.58
912 1016 2.970974 GCGTGCTGTTCCTTCTGCC 61.971 63.158 0.00 0.00 0.00 4.85
1284 1404 2.126424 GACTCGTGCCACTCGTCC 60.126 66.667 0.00 0.00 0.00 4.79
1815 1938 0.322187 TCCACGACATCACCTCGAGA 60.322 55.000 15.71 0.00 35.08 4.04
1817 1940 1.880894 GTCCACGACATCACCTCGA 59.119 57.895 0.00 0.00 35.08 4.04
1852 1975 0.243907 AGGATCGACACCACGTCTTG 59.756 55.000 12.09 0.00 42.98 3.02
1961 2084 4.699522 GGTTCTTCCAGCCGGCGT 62.700 66.667 23.20 6.69 35.97 5.68
1988 2111 4.103103 CGTCGTCGAGCAGCTCCA 62.103 66.667 17.16 0.06 39.71 3.86
2061 2184 2.726822 AAACAAGACGGCCGAGGTCC 62.727 60.000 35.90 14.67 34.97 4.46
2110 2274 7.694886 TGATCATAAGTGACTACAAGTCTACG 58.305 38.462 8.42 0.00 45.27 3.51
2254 2506 6.861055 GTGAGCTCCGAAATTATTTTGTTTCA 59.139 34.615 12.15 0.86 34.76 2.69
2462 2726 9.833894 CTTAACAATTTCAACGAAATTTCAGTG 57.166 29.630 17.99 13.86 46.07 3.66
2463 2727 8.539674 GCTTAACAATTTCAACGAAATTTCAGT 58.460 29.630 17.99 13.07 46.07 3.41
2464 2728 7.731302 CGCTTAACAATTTCAACGAAATTTCAG 59.269 33.333 17.99 12.49 46.07 3.02
2469 2733 6.561350 GCAACGCTTAACAATTTCAACGAAAT 60.561 34.615 0.00 0.00 43.07 2.17
2470 2734 5.275974 GCAACGCTTAACAATTTCAACGAAA 60.276 36.000 0.00 0.00 35.94 3.46
2471 2735 4.205385 GCAACGCTTAACAATTTCAACGAA 59.795 37.500 0.00 0.00 0.00 3.85
2472 2736 3.726730 GCAACGCTTAACAATTTCAACGA 59.273 39.130 0.00 0.00 0.00 3.85
2473 2737 3.121496 GGCAACGCTTAACAATTTCAACG 60.121 43.478 0.00 0.00 0.00 4.10
2474 2738 3.799420 TGGCAACGCTTAACAATTTCAAC 59.201 39.130 0.00 0.00 42.51 3.18
2475 2739 4.046938 TGGCAACGCTTAACAATTTCAA 57.953 36.364 0.00 0.00 42.51 2.69
2476 2740 3.717400 TGGCAACGCTTAACAATTTCA 57.283 38.095 0.00 0.00 42.51 2.69
2477 2741 6.529829 TGATAATGGCAACGCTTAACAATTTC 59.470 34.615 0.00 0.00 42.51 2.17
2495 2759 8.223769 GTGTCTTACACTGTCAAGTTGATAATG 58.776 37.037 9.18 9.20 45.27 1.90
2780 4015 6.988580 AGCAATGTCGAAAGATGAAGATATGA 59.011 34.615 0.00 0.00 45.19 2.15


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

AutoCloner maintained by Alex Coulton.