Multiple sequence alignment - TraesCS6D01G308900

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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 TraesCS6D01G308900 chr6D 100.000 3159 0 0 1 3159 419656315 419659473 0.000000e+00 5834
1 TraesCS6D01G308900 chr6D 86.813 1365 115 38 978 2302 419748295 419749634 0.000000e+00 1463
2 TraesCS6D01G308900 chr6D 82.158 1205 156 41 978 2133 419614590 419615784 0.000000e+00 979
3 TraesCS6D01G308900 chr6D 82.616 1116 139 28 974 2066 419447596 419448679 0.000000e+00 935
4 TraesCS6D01G308900 chr6D 84.995 933 107 24 920 1835 419285888 419286804 0.000000e+00 917
5 TraesCS6D01G308900 chr6D 86.441 590 35 20 2584 3159 16717792 16717234 3.490000e-169 604
6 TraesCS6D01G308900 chr6D 91.847 417 22 4 2303 2708 16718212 16717797 3.530000e-159 571
7 TraesCS6D01G308900 chr6D 84.225 355 39 12 1881 2225 419485833 419486180 2.350000e-86 329
8 TraesCS6D01G308900 chr6D 87.245 196 16 3 714 909 419747818 419748004 6.860000e-52 215
9 TraesCS6D01G308900 chr6D 86.286 175 11 6 714 888 419484390 419484551 9.000000e-41 178
10 TraesCS6D01G308900 chr6A 93.338 1546 58 25 788 2304 562869020 562870549 0.000000e+00 2242
11 TraesCS6D01G308900 chr6A 87.657 1353 116 31 979 2302 562920184 562921514 0.000000e+00 1526
12 TraesCS6D01G308900 chr6A 81.434 1395 176 54 978 2304 562813448 562814827 0.000000e+00 1064
13 TraesCS6D01G308900 chr6A 91.761 704 45 8 1 701 146439629 146440322 0.000000e+00 966
14 TraesCS6D01G308900 chr6A 80.102 1367 169 52 974 2301 562762073 562763375 0.000000e+00 922
15 TraesCS6D01G308900 chr6A 86.559 863 82 15 974 1827 562796720 562797557 0.000000e+00 920
16 TraesCS6D01G308900 chr6A 86.111 900 68 21 2301 3159 46071023 46071906 0.000000e+00 917
17 TraesCS6D01G308900 chr6A 83.579 883 110 22 974 1835 562704456 562705324 0.000000e+00 795
18 TraesCS6D01G308900 chr6A 80.220 455 52 21 1880 2304 562797643 562798089 1.100000e-79 307
19 TraesCS6D01G308900 chr6A 85.714 196 15 4 714 909 562919754 562919936 8.940000e-46 195
20 TraesCS6D01G308900 chr6A 85.143 175 13 7 714 888 562796014 562796175 1.950000e-37 167
21 TraesCS6D01G308900 chr6B 90.389 1644 98 24 700 2303 632564983 632566606 0.000000e+00 2106
22 TraesCS6D01G308900 chr6B 87.610 1364 119 29 973 2302 632787101 632788448 0.000000e+00 1537
23 TraesCS6D01G308900 chr6B 83.574 1175 134 36 978 2115 632422196 632423348 0.000000e+00 1046
24 TraesCS6D01G308900 chr6B 83.076 1164 153 32 978 2104 632503469 632504625 0.000000e+00 1018
25 TraesCS6D01G308900 chr6B 81.416 1243 162 42 1094 2301 632304710 632305918 0.000000e+00 952
26 TraesCS6D01G308900 chr6B 84.073 879 110 22 974 1835 632242742 632243607 0.000000e+00 821
27 TraesCS6D01G308900 chr6B 87.056 479 38 5 2305 2761 31279197 31279673 1.300000e-143 520
28 TraesCS6D01G308900 chr6B 87.245 196 12 6 714 909 632786674 632786856 8.880000e-51 211
29 TraesCS6D01G308900 chr6B 86.364 176 10 7 714 888 632421872 632422034 2.500000e-41 180
30 TraesCS6D01G308900 chr5A 90.230 870 58 13 2305 3159 544771848 544772705 0.000000e+00 1110
31 TraesCS6D01G308900 chr5A 92.635 706 39 8 4 706 592400029 592399334 0.000000e+00 1003
32 TraesCS6D01G308900 chr5A 91.773 705 46 9 9 707 611820065 611819367 0.000000e+00 970
33 TraesCS6D01G308900 chr5A 87.348 577 49 13 2305 2867 544794158 544794724 9.550000e-180 640
34 TraesCS6D01G308900 chr2A 89.306 879 58 13 2304 3159 678716655 678715790 0.000000e+00 1070
35 TraesCS6D01G308900 chr2A 86.289 671 51 10 2505 3159 4204146 4203501 0.000000e+00 691
36 TraesCS6D01G308900 chr1D 94.429 700 26 6 1 700 464829775 464830461 0.000000e+00 1064
37 TraesCS6D01G308900 chr1D 88.664 891 50 17 2298 3159 468375453 468376321 0.000000e+00 1038
38 TraesCS6D01G308900 chr1D 88.087 873 52 27 2302 3159 453823861 453824696 0.000000e+00 989
39 TraesCS6D01G308900 chr1D 87.436 589 41 12 2305 2865 83904050 83904633 0.000000e+00 647
40 TraesCS6D01G308900 chr1D 91.387 476 24 7 2316 2781 7581888 7581420 1.240000e-178 636
41 TraesCS6D01G308900 chr2D 93.296 716 38 6 1 710 469245563 469246274 0.000000e+00 1048
42 TraesCS6D01G308900 chr3B 88.915 857 65 7 2305 3159 46302256 46301428 0.000000e+00 1029
43 TraesCS6D01G308900 chr3B 91.105 371 22 8 2793 3159 820944902 820944539 2.830000e-135 492
44 TraesCS6D01G308900 chr5D 88.462 884 46 16 2305 3159 398463969 398463113 0.000000e+00 1016
45 TraesCS6D01G308900 chr5D 88.100 479 32 10 2305 2761 55076334 55075859 2.140000e-151 545
46 TraesCS6D01G308900 chr5D 96.599 294 7 3 2866 3159 440201787 440202077 4.740000e-133 484
47 TraesCS6D01G308900 chr4A 92.867 701 46 4 2 701 530826226 530826923 0.000000e+00 1014
48 TraesCS6D01G308900 chr4A 84.217 868 60 23 2305 3159 729222327 729221524 0.000000e+00 773
49 TraesCS6D01G308900 chr4A 80.615 325 32 13 2580 2893 700994056 700994360 4.100000e-54 222
50 TraesCS6D01G308900 chr7A 92.210 706 42 8 1 702 639278108 639277412 0.000000e+00 987
51 TraesCS6D01G308900 chr7A 91.915 705 44 10 1 700 54941001 54940305 0.000000e+00 974
52 TraesCS6D01G308900 chr7A 90.028 702 49 13 1 700 5758425 5757743 0.000000e+00 889
53 TraesCS6D01G308900 chr7A 94.828 348 15 1 2812 3159 66931304 66930960 9.970000e-150 540
54 TraesCS6D01G308900 chr1B 86.734 897 65 26 2305 3159 621406646 621405762 0.000000e+00 948
55 TraesCS6D01G308900 chr4B 85.953 897 61 25 2305 3159 5246232 5247105 0.000000e+00 898
56 TraesCS6D01G308900 chr3A 84.615 715 64 16 2304 2988 693151074 693150376 0.000000e+00 669
57 TraesCS6D01G308900 chr3D 87.409 548 39 16 2305 2837 5237642 5238174 1.250000e-168 603
58 TraesCS6D01G308900 chr2B 96.166 313 11 1 2847 3159 106634830 106635141 7.820000e-141 510
59 TraesCS6D01G308900 chr4D 91.875 320 20 2 2304 2623 426783325 426783012 2.890000e-120 442
60 TraesCS6D01G308900 chr1A 81.488 578 72 17 2305 2863 3725929 3725368 2.890000e-120 442


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 TraesCS6D01G308900 chr6D 419656315 419659473 3158 False 5834.000000 5834 100.0000 1 3159 1 chr6D.!!$F4 3158
1 TraesCS6D01G308900 chr6D 419614590 419615784 1194 False 979.000000 979 82.1580 978 2133 1 chr6D.!!$F3 1155
2 TraesCS6D01G308900 chr6D 419447596 419448679 1083 False 935.000000 935 82.6160 974 2066 1 chr6D.!!$F2 1092
3 TraesCS6D01G308900 chr6D 419285888 419286804 916 False 917.000000 917 84.9950 920 1835 1 chr6D.!!$F1 915
4 TraesCS6D01G308900 chr6D 419747818 419749634 1816 False 839.000000 1463 87.0290 714 2302 2 chr6D.!!$F6 1588
5 TraesCS6D01G308900 chr6D 16717234 16718212 978 True 587.500000 604 89.1440 2303 3159 2 chr6D.!!$R1 856
6 TraesCS6D01G308900 chr6D 419484390 419486180 1790 False 253.500000 329 85.2555 714 2225 2 chr6D.!!$F5 1511
7 TraesCS6D01G308900 chr6A 562869020 562870549 1529 False 2242.000000 2242 93.3380 788 2304 1 chr6A.!!$F6 1516
8 TraesCS6D01G308900 chr6A 562813448 562814827 1379 False 1064.000000 1064 81.4340 978 2304 1 chr6A.!!$F5 1326
9 TraesCS6D01G308900 chr6A 146439629 146440322 693 False 966.000000 966 91.7610 1 701 1 chr6A.!!$F2 700
10 TraesCS6D01G308900 chr6A 562762073 562763375 1302 False 922.000000 922 80.1020 974 2301 1 chr6A.!!$F4 1327
11 TraesCS6D01G308900 chr6A 46071023 46071906 883 False 917.000000 917 86.1110 2301 3159 1 chr6A.!!$F1 858
12 TraesCS6D01G308900 chr6A 562919754 562921514 1760 False 860.500000 1526 86.6855 714 2302 2 chr6A.!!$F8 1588
13 TraesCS6D01G308900 chr6A 562704456 562705324 868 False 795.000000 795 83.5790 974 1835 1 chr6A.!!$F3 861
14 TraesCS6D01G308900 chr6A 562796014 562798089 2075 False 464.666667 920 83.9740 714 2304 3 chr6A.!!$F7 1590
15 TraesCS6D01G308900 chr6B 632564983 632566606 1623 False 2106.000000 2106 90.3890 700 2303 1 chr6B.!!$F5 1603
16 TraesCS6D01G308900 chr6B 632503469 632504625 1156 False 1018.000000 1018 83.0760 978 2104 1 chr6B.!!$F4 1126
17 TraesCS6D01G308900 chr6B 632304710 632305918 1208 False 952.000000 952 81.4160 1094 2301 1 chr6B.!!$F3 1207
18 TraesCS6D01G308900 chr6B 632786674 632788448 1774 False 874.000000 1537 87.4275 714 2302 2 chr6B.!!$F7 1588
19 TraesCS6D01G308900 chr6B 632242742 632243607 865 False 821.000000 821 84.0730 974 1835 1 chr6B.!!$F2 861
20 TraesCS6D01G308900 chr6B 632421872 632423348 1476 False 613.000000 1046 84.9690 714 2115 2 chr6B.!!$F6 1401
21 TraesCS6D01G308900 chr5A 544771848 544772705 857 False 1110.000000 1110 90.2300 2305 3159 1 chr5A.!!$F1 854
22 TraesCS6D01G308900 chr5A 592399334 592400029 695 True 1003.000000 1003 92.6350 4 706 1 chr5A.!!$R1 702
23 TraesCS6D01G308900 chr5A 611819367 611820065 698 True 970.000000 970 91.7730 9 707 1 chr5A.!!$R2 698
24 TraesCS6D01G308900 chr5A 544794158 544794724 566 False 640.000000 640 87.3480 2305 2867 1 chr5A.!!$F2 562
25 TraesCS6D01G308900 chr2A 678715790 678716655 865 True 1070.000000 1070 89.3060 2304 3159 1 chr2A.!!$R2 855
26 TraesCS6D01G308900 chr2A 4203501 4204146 645 True 691.000000 691 86.2890 2505 3159 1 chr2A.!!$R1 654
27 TraesCS6D01G308900 chr1D 464829775 464830461 686 False 1064.000000 1064 94.4290 1 700 1 chr1D.!!$F3 699
28 TraesCS6D01G308900 chr1D 468375453 468376321 868 False 1038.000000 1038 88.6640 2298 3159 1 chr1D.!!$F4 861
29 TraesCS6D01G308900 chr1D 453823861 453824696 835 False 989.000000 989 88.0870 2302 3159 1 chr1D.!!$F2 857
30 TraesCS6D01G308900 chr1D 83904050 83904633 583 False 647.000000 647 87.4360 2305 2865 1 chr1D.!!$F1 560
31 TraesCS6D01G308900 chr2D 469245563 469246274 711 False 1048.000000 1048 93.2960 1 710 1 chr2D.!!$F1 709
32 TraesCS6D01G308900 chr3B 46301428 46302256 828 True 1029.000000 1029 88.9150 2305 3159 1 chr3B.!!$R1 854
33 TraesCS6D01G308900 chr5D 398463113 398463969 856 True 1016.000000 1016 88.4620 2305 3159 1 chr5D.!!$R2 854
34 TraesCS6D01G308900 chr4A 530826226 530826923 697 False 1014.000000 1014 92.8670 2 701 1 chr4A.!!$F1 699
35 TraesCS6D01G308900 chr4A 729221524 729222327 803 True 773.000000 773 84.2170 2305 3159 1 chr4A.!!$R1 854
36 TraesCS6D01G308900 chr7A 639277412 639278108 696 True 987.000000 987 92.2100 1 702 1 chr7A.!!$R4 701
37 TraesCS6D01G308900 chr7A 54940305 54941001 696 True 974.000000 974 91.9150 1 700 1 chr7A.!!$R2 699
38 TraesCS6D01G308900 chr7A 5757743 5758425 682 True 889.000000 889 90.0280 1 700 1 chr7A.!!$R1 699
39 TraesCS6D01G308900 chr1B 621405762 621406646 884 True 948.000000 948 86.7340 2305 3159 1 chr1B.!!$R1 854
40 TraesCS6D01G308900 chr4B 5246232 5247105 873 False 898.000000 898 85.9530 2305 3159 1 chr4B.!!$F1 854
41 TraesCS6D01G308900 chr3A 693150376 693151074 698 True 669.000000 669 84.6150 2304 2988 1 chr3A.!!$R1 684
42 TraesCS6D01G308900 chr3D 5237642 5238174 532 False 603.000000 603 87.4090 2305 2837 1 chr3D.!!$F1 532
43 TraesCS6D01G308900 chr1A 3725368 3725929 561 True 442.000000 442 81.4880 2305 2863 1 chr1A.!!$R1 558

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
449 460 0.232816 TTCGACGTGCGGTTAAAAGC 59.767 50.000 0.0 0.0 41.33 3.51 F
895 918 1.551430 CATGCATGGAACCCACATGTT 59.449 47.619 19.4 0.0 45.68 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 2114 0.108281 GGTAGCTTCGGAGGGTGTTC 60.108 60.0 1.74 0.0 0.0 3.18 R
2582 3374 0.392706 ATGCCAAGATATGCCGACGA 59.607 50.0 0.00 0.0 0.0 4.20 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
89 90 5.934935 TTACAAGCCAACTAAGCAACTAC 57.065 39.130 0.00 0.00 0.00 2.73
393 404 4.541779 CGGGATCTAGTTTCGAAGATCTG 58.458 47.826 19.29 11.57 44.94 2.90
437 448 2.649331 ACGGATCTGAATTTCGACGT 57.351 45.000 9.00 0.00 0.00 4.34
449 460 0.232816 TTCGACGTGCGGTTAAAAGC 59.767 50.000 0.00 0.00 41.33 3.51
548 559 9.451002 GCTACCTTTCCTTCTAATTATATTCCC 57.549 37.037 0.00 0.00 0.00 3.97
783 797 2.768503 TAACCGGCCTGTACGTGTGC 62.769 60.000 0.00 0.00 0.00 4.57
786 800 4.675029 GGCCTGTACGTGTGCGGT 62.675 66.667 0.00 0.00 43.45 5.68
895 918 1.551430 CATGCATGGAACCCACATGTT 59.449 47.619 19.40 0.00 45.68 2.71
1238 1829 4.096003 AACATCCTCCCGGCCGTG 62.096 66.667 26.12 14.27 0.00 4.94
1309 1900 1.614903 CCTGCATTGTCAAGCCAAGAA 59.385 47.619 0.00 0.00 0.00 2.52
1404 1995 4.290622 CCAAGGGCCAGCACCACT 62.291 66.667 6.18 0.00 0.00 4.00
1511 2114 1.205655 TGCTTCTTCATCCTCCAGTCG 59.794 52.381 0.00 0.00 0.00 4.18
1563 2166 1.079612 CTCACCGTGCTCATCTGCA 60.080 57.895 0.00 0.00 41.05 4.41
1667 2270 2.017559 GCCTCTTCACCGCCGTCTAT 62.018 60.000 0.00 0.00 0.00 1.98
1718 2321 3.127533 GTGCAGGGCATCGTGTCC 61.128 66.667 0.00 0.97 44.07 4.02
1757 2360 2.430367 GTGACGGCCTTCAACCCT 59.570 61.111 14.41 0.00 0.00 4.34
1829 2434 5.848406 GAGATCAATCTCGGAAGGTACATT 58.152 41.667 4.34 0.00 43.29 2.71
2135 2842 0.173935 TACGACCAATGGCCACTACG 59.826 55.000 8.16 12.71 0.00 3.51
2294 3048 3.425659 TCTTGTCAGCTTCTCTCTAGCA 58.574 45.455 0.00 0.00 41.11 3.49
2546 3338 2.186903 CCGTGACCAGCGGCTAAT 59.813 61.111 0.26 0.00 42.82 1.73
2597 3389 1.548973 GCGGTCGTCGGCATATCTTG 61.549 60.000 7.29 0.00 39.26 3.02
2614 3406 1.385756 TTGGCATGCCATGTCATCGG 61.386 55.000 38.78 0.00 45.43 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 3.411446 TGATGTTTAGTTGGCAGGACAG 58.589 45.455 0.00 0.00 0.00 3.51
393 404 2.106683 CATTGGAACCCTCGCGACC 61.107 63.158 3.71 4.99 0.00 4.79
437 448 5.699097 AAAGTCATAAGCTTTTAACCGCA 57.301 34.783 3.20 0.00 32.86 5.69
548 559 1.202348 CGCTCTCACATAGTGGACCAG 60.202 57.143 0.00 0.00 33.87 4.00
630 643 2.125350 CTCCTGGCCACTCGCTTC 60.125 66.667 0.00 0.00 37.74 3.86
652 665 1.094785 ATTTTGATGAACCGAGCGGG 58.905 50.000 14.07 0.00 43.62 6.13
730 743 1.270839 ACATACCTGCCTGTGTGTCAC 60.271 52.381 0.00 0.00 35.99 3.67
783 797 1.994779 GTAAACACACATACCGGACCG 59.005 52.381 9.46 6.99 0.00 4.79
784 798 1.994779 CGTAAACACACATACCGGACC 59.005 52.381 9.46 0.00 0.00 4.46
785 799 2.676076 ACGTAAACACACATACCGGAC 58.324 47.619 9.46 0.00 0.00 4.79
786 800 3.669290 CGTACGTAAACACACATACCGGA 60.669 47.826 9.46 0.00 0.00 5.14
860 874 1.694169 CATGGTAGGCCCTCCACCT 60.694 63.158 17.19 1.87 41.57 4.00
953 1438 4.529377 AGTTGGAGCATGAACCATGATTTT 59.471 37.500 10.77 0.00 40.71 1.82
1211 1802 1.596934 GAGGATGTTGACGAGGGCA 59.403 57.895 0.00 0.00 0.00 5.36
1238 1829 3.959991 GAGGGCCAGCACGAAGGTC 62.960 68.421 6.18 0.00 0.00 3.85
1296 1887 2.250939 CGGCGTTCTTGGCTTGACA 61.251 57.895 0.00 0.00 0.00 3.58
1511 2114 0.108281 GGTAGCTTCGGAGGGTGTTC 60.108 60.000 1.74 0.00 0.00 3.18
1563 2166 1.065647 CTCATGAGGGATCCCATGCT 58.934 55.000 32.69 12.24 39.82 3.79
1612 2215 3.357079 CCCACGCCTGAGTGTTGC 61.357 66.667 0.48 0.00 40.33 4.17
1757 2360 2.548707 GGCGGTTATGATCATGCAGAGA 60.549 50.000 18.72 0.00 0.00 3.10
1829 2434 3.429492 TCCATCTTGGCAGCACAAATTA 58.571 40.909 0.00 0.00 37.47 1.40
1900 2571 2.362077 ACCAATCACACTGAAAGCAACC 59.638 45.455 0.00 0.00 37.60 3.77
2135 2842 0.879400 TCGCTACTCCGGTCGATCTC 60.879 60.000 0.00 0.00 0.00 2.75
2294 3048 2.425143 TCCGGTAGTGTAGGATCGTT 57.575 50.000 0.00 0.00 0.00 3.85
2369 3123 1.796190 TAGGCTGTCGGCATAGCTCG 61.796 60.000 5.89 0.00 44.01 5.03
2455 3210 1.078497 TAGGTCGACGGCCGTTCTA 60.078 57.895 34.65 25.43 39.75 2.10
2491 3248 2.897350 GGTATGCCGACAGCTGCC 60.897 66.667 15.27 0.16 44.23 4.85
2546 3338 1.743623 CGGCATAGGTTTGACGGCA 60.744 57.895 0.00 0.00 44.46 5.69
2582 3374 0.392706 ATGCCAAGATATGCCGACGA 59.607 50.000 0.00 0.00 0.00 4.20
2597 3389 1.789078 GACCGATGACATGGCATGCC 61.789 60.000 30.54 30.54 0.00 4.40
2614 3406 2.087009 GCATATCTACGCCGCGGAC 61.087 63.158 33.48 19.66 0.00 4.79
2637 3439 2.978452 GATGTCGTGGCGCCTATGCT 62.978 60.000 29.70 7.90 34.43 3.79
2652 3464 3.838271 AGTGCCGCGGATCGATGT 61.838 61.111 33.48 1.43 41.67 3.06


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

AutoCloner maintained by Alex Coulton.