Multiple sequence alignment - TraesCS6A01G301200

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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 TraesCS6A01G301200 chr6A 100.000 6227 0 0 1 6227 534781295 534787521 0.000000e+00 11500.0
1 TraesCS6A01G301200 chr6A 98.116 743 13 1 1 742 534774467 534775209 0.000000e+00 1293.0
2 TraesCS6A01G301200 chr6A 92.557 309 23 0 5002 5310 2346119 2345811 1.590000e-120 444.0
3 TraesCS6A01G301200 chr3D 96.388 4125 73 17 2136 6227 144285990 144290071 0.000000e+00 6722.0
4 TraesCS6A01G301200 chr3D 96.614 2156 43 12 1298 3447 144283854 144285985 0.000000e+00 3550.0
5 TraesCS6A01G301200 chr3D 96.240 1250 23 2 5002 6227 438458755 438457506 0.000000e+00 2026.0
6 TraesCS6A01G301200 chr3D 92.356 798 50 9 1 791 562451125 562451918 0.000000e+00 1125.0
7 TraesCS6A01G301200 chr3D 95.914 514 21 0 792 1305 144281388 144281901 0.000000e+00 833.0
8 TraesCS6A01G301200 chr3D 88.060 67 7 1 2460 2525 144285097 144285163 1.860000e-10 78.7
9 TraesCS6A01G301200 chr3A 97.912 2778 33 10 798 3572 572463377 572460622 0.000000e+00 4785.0
10 TraesCS6A01G301200 chr3A 97.052 1289 20 6 4076 5350 572460491 572459207 0.000000e+00 2154.0
11 TraesCS6A01G301200 chr3A 98.164 926 16 1 5303 6227 572459211 572458286 0.000000e+00 1615.0
12 TraesCS6A01G301200 chr3A 98.250 743 10 3 1 742 693309759 693309019 0.000000e+00 1297.0
13 TraesCS6A01G301200 chr3A 100.000 137 0 0 3648 3784 572460624 572460488 2.880000e-63 254.0
14 TraesCS6A01G301200 chr7B 92.260 2442 112 27 1265 3661 347314408 347311999 0.000000e+00 3391.0
15 TraesCS6A01G301200 chr7B 92.430 1321 80 13 3686 5002 347311803 347310499 0.000000e+00 1868.0
16 TraesCS6A01G301200 chr7B 90.300 1402 80 14 2326 3690 347308968 347307586 0.000000e+00 1784.0
17 TraesCS6A01G301200 chr7B 89.888 1345 102 17 3686 5002 347307430 347306092 0.000000e+00 1700.0
18 TraesCS6A01G301200 chr7B 91.935 248 19 1 856 1103 347314960 347314714 4.620000e-91 346.0
19 TraesCS6A01G301200 chr7B 95.122 41 2 0 3650 3690 347311999 347311959 1.450000e-06 65.8
20 TraesCS6A01G301200 chr5D 96.000 1250 25 2 5002 6227 447256214 447257462 0.000000e+00 2008.0
21 TraesCS6A01G301200 chr5D 95.377 1233 32 2 5002 6210 175959597 175960828 0.000000e+00 1938.0
22 TraesCS6A01G301200 chr5D 90.717 1228 82 13 3785 5002 101227509 101226304 0.000000e+00 1607.0
23 TraesCS6A01G301200 chr5D 90.709 1227 83 15 3785 5002 101196252 101195048 0.000000e+00 1605.0
24 TraesCS6A01G301200 chr5D 93.325 794 47 6 1 791 227295831 227296621 0.000000e+00 1168.0
25 TraesCS6A01G301200 chr5D 94.681 470 23 2 2909 3378 101198263 101197796 0.000000e+00 728.0
26 TraesCS6A01G301200 chr5D 94.268 471 24 3 2909 3378 101229509 101229041 0.000000e+00 717.0
27 TraesCS6A01G301200 chr5D 91.610 441 32 4 2061 2498 100944185 100944623 6.900000e-169 604.0
28 TraesCS6A01G301200 chr5D 89.562 297 27 3 856 1150 100943599 100943893 2.120000e-99 374.0
29 TraesCS6A01G301200 chr5D 87.576 330 23 5 2546 2875 100944635 100944946 3.550000e-97 366.0
30 TraesCS6A01G301200 chr7D 95.760 1250 29 1 5002 6227 38022018 38023267 0.000000e+00 1993.0
31 TraesCS6A01G301200 chr7D 94.387 962 20 2 5290 6227 426550126 426549175 0.000000e+00 1447.0
32 TraesCS6A01G301200 chr7D 92.588 796 48 8 3 790 57916311 57917103 0.000000e+00 1133.0
33 TraesCS6A01G301200 chr7D 87.838 444 41 7 3381 3815 571296366 571295927 5.570000e-140 508.0
34 TraesCS6A01G301200 chr6D 96.041 1086 18 3 5167 6227 19896577 19897662 0.000000e+00 1744.0
35 TraesCS6A01G301200 chr6D 88.653 802 73 17 1 791 241371348 241370554 0.000000e+00 961.0
36 TraesCS6A01G301200 chr6D 85.963 805 94 16 1 792 338423598 338424396 0.000000e+00 843.0
37 TraesCS6A01G301200 chr2D 95.385 1040 24 1 5212 6227 643061263 643060224 0.000000e+00 1633.0
38 TraesCS6A01G301200 chr2D 87.563 1190 77 20 3818 4989 564929875 564931011 0.000000e+00 1312.0
39 TraesCS6A01G301200 chr2D 87.958 191 23 0 857 1047 222196923 222196733 6.280000e-55 226.0
40 TraesCS6A01G301200 chr1B 87.594 1201 91 21 3818 5002 159157987 159159145 0.000000e+00 1339.0
41 TraesCS6A01G301200 chr1B 90.068 443 37 6 2060 2497 28256642 28257082 9.060000e-158 568.0
42 TraesCS6A01G301200 chr1B 85.271 129 13 4 3658 3786 651885888 651885766 1.820000e-25 128.0
43 TraesCS6A01G301200 chr4D 87.861 1178 83 23 3818 4975 81365978 81367115 0.000000e+00 1328.0
44 TraesCS6A01G301200 chr4D 85.143 175 21 4 856 1030 220907667 220907498 2.310000e-39 174.0
45 TraesCS6A01G301200 chr4D 80.829 193 33 3 4482 4670 278291628 278291436 1.400000e-31 148.0
46 TraesCS6A01G301200 chr2A 98.250 743 12 1 1 742 8425142 8425884 0.000000e+00 1299.0
47 TraesCS6A01G301200 chr2A 97.981 743 14 1 1 742 8445811 8446553 0.000000e+00 1288.0
48 TraesCS6A01G301200 chr2A 86.420 162 16 5 871 1030 762334875 762335032 8.300000e-39 172.0
49 TraesCS6A01G301200 chr5A 97.981 743 14 1 1 742 605136381 605137123 0.000000e+00 1288.0
50 TraesCS6A01G301200 chr5A 80.769 104 16 4 2173 2275 458222762 458222662 1.860000e-10 78.7
51 TraesCS6A01G301200 chr4A 97.847 743 15 1 1 742 12649038 12649780 0.000000e+00 1282.0
52 TraesCS6A01G301200 chr4A 87.765 801 78 16 1 789 496076768 496077560 0.000000e+00 918.0
53 TraesCS6A01G301200 chr4A 88.136 295 32 3 857 1150 504861275 504861567 1.280000e-91 348.0
54 TraesCS6A01G301200 chr4A 79.389 131 22 5 2149 2278 75435794 75435668 3.090000e-13 87.9
55 TraesCS6A01G301200 chr1A 95.000 800 30 5 1 791 543745174 543745972 0.000000e+00 1247.0
56 TraesCS6A01G301200 chr1A 92.880 309 22 0 5002 5310 544726397 544726705 3.420000e-122 449.0
57 TraesCS6A01G301200 chr1A 84.536 97 9 5 742 837 240813083 240813174 2.390000e-14 91.6
58 TraesCS6A01G301200 chr1D 87.824 1002 71 17 3818 4811 60144837 60145795 0.000000e+00 1127.0
59 TraesCS6A01G301200 chr5B 96.880 641 18 1 5589 6227 689113737 689114377 0.000000e+00 1072.0
60 TraesCS6A01G301200 chr5B 92.557 309 23 0 5002 5310 412708918 412708610 1.590000e-120 444.0
61 TraesCS6A01G301200 chr7A 85.910 802 95 17 1 791 122811910 122811116 0.000000e+00 839.0
62 TraesCS6A01G301200 chr3B 84.375 288 31 9 3503 3785 42027017 42027295 2.860000e-68 270.0
63 TraesCS6A01G301200 chr3B 83.391 289 30 9 3503 3786 42042905 42043180 1.040000e-62 252.0
64 TraesCS6A01G301200 chrUn 80.176 227 36 7 874 1092 2686445 2686220 1.800000e-35 161.0


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 TraesCS6A01G301200 chr6A 534781295 534787521 6226 False 11500.000 11500 100.000000 1 6227 1 chr6A.!!$F2 6226
1 TraesCS6A01G301200 chr6A 534774467 534775209 742 False 1293.000 1293 98.116000 1 742 1 chr6A.!!$F1 741
2 TraesCS6A01G301200 chr3D 144281388 144290071 8683 False 2795.925 6722 94.244000 792 6227 4 chr3D.!!$F2 5435
3 TraesCS6A01G301200 chr3D 438457506 438458755 1249 True 2026.000 2026 96.240000 5002 6227 1 chr3D.!!$R1 1225
4 TraesCS6A01G301200 chr3D 562451125 562451918 793 False 1125.000 1125 92.356000 1 791 1 chr3D.!!$F1 790
5 TraesCS6A01G301200 chr3A 572458286 572463377 5091 True 2202.000 4785 98.282000 798 6227 4 chr3A.!!$R2 5429
6 TraesCS6A01G301200 chr3A 693309019 693309759 740 True 1297.000 1297 98.250000 1 742 1 chr3A.!!$R1 741
7 TraesCS6A01G301200 chr7B 347306092 347314960 8868 True 1525.800 3391 91.989167 856 5002 6 chr7B.!!$R1 4146
8 TraesCS6A01G301200 chr5D 447256214 447257462 1248 False 2008.000 2008 96.000000 5002 6227 1 chr5D.!!$F3 1225
9 TraesCS6A01G301200 chr5D 175959597 175960828 1231 False 1938.000 1938 95.377000 5002 6210 1 chr5D.!!$F1 1208
10 TraesCS6A01G301200 chr5D 227295831 227296621 790 False 1168.000 1168 93.325000 1 791 1 chr5D.!!$F2 790
11 TraesCS6A01G301200 chr5D 101195048 101198263 3215 True 1166.500 1605 92.695000 2909 5002 2 chr5D.!!$R1 2093
12 TraesCS6A01G301200 chr5D 101226304 101229509 3205 True 1162.000 1607 92.492500 2909 5002 2 chr5D.!!$R2 2093
13 TraesCS6A01G301200 chr5D 100943599 100944946 1347 False 448.000 604 89.582667 856 2875 3 chr5D.!!$F4 2019
14 TraesCS6A01G301200 chr7D 38022018 38023267 1249 False 1993.000 1993 95.760000 5002 6227 1 chr7D.!!$F1 1225
15 TraesCS6A01G301200 chr7D 426549175 426550126 951 True 1447.000 1447 94.387000 5290 6227 1 chr7D.!!$R1 937
16 TraesCS6A01G301200 chr7D 57916311 57917103 792 False 1133.000 1133 92.588000 3 790 1 chr7D.!!$F2 787
17 TraesCS6A01G301200 chr6D 19896577 19897662 1085 False 1744.000 1744 96.041000 5167 6227 1 chr6D.!!$F1 1060
18 TraesCS6A01G301200 chr6D 241370554 241371348 794 True 961.000 961 88.653000 1 791 1 chr6D.!!$R1 790
19 TraesCS6A01G301200 chr6D 338423598 338424396 798 False 843.000 843 85.963000 1 792 1 chr6D.!!$F2 791
20 TraesCS6A01G301200 chr2D 643060224 643061263 1039 True 1633.000 1633 95.385000 5212 6227 1 chr2D.!!$R2 1015
21 TraesCS6A01G301200 chr2D 564929875 564931011 1136 False 1312.000 1312 87.563000 3818 4989 1 chr2D.!!$F1 1171
22 TraesCS6A01G301200 chr1B 159157987 159159145 1158 False 1339.000 1339 87.594000 3818 5002 1 chr1B.!!$F2 1184
23 TraesCS6A01G301200 chr4D 81365978 81367115 1137 False 1328.000 1328 87.861000 3818 4975 1 chr4D.!!$F1 1157
24 TraesCS6A01G301200 chr2A 8425142 8425884 742 False 1299.000 1299 98.250000 1 742 1 chr2A.!!$F1 741
25 TraesCS6A01G301200 chr2A 8445811 8446553 742 False 1288.000 1288 97.981000 1 742 1 chr2A.!!$F2 741
26 TraesCS6A01G301200 chr5A 605136381 605137123 742 False 1288.000 1288 97.981000 1 742 1 chr5A.!!$F1 741
27 TraesCS6A01G301200 chr4A 12649038 12649780 742 False 1282.000 1282 97.847000 1 742 1 chr4A.!!$F1 741
28 TraesCS6A01G301200 chr4A 496076768 496077560 792 False 918.000 918 87.765000 1 789 1 chr4A.!!$F2 788
29 TraesCS6A01G301200 chr1A 543745174 543745972 798 False 1247.000 1247 95.000000 1 791 1 chr1A.!!$F2 790
30 TraesCS6A01G301200 chr1D 60144837 60145795 958 False 1127.000 1127 87.824000 3818 4811 1 chr1D.!!$F1 993
31 TraesCS6A01G301200 chr5B 689113737 689114377 640 False 1072.000 1072 96.880000 5589 6227 1 chr5B.!!$F1 638
32 TraesCS6A01G301200 chr7A 122811116 122811910 794 True 839.000 839 85.910000 1 791 1 chr7A.!!$R1 790

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
928 957 1.001517 TCTCTCCTCTGAGCTGCGT 60.002 57.895 0.0 0.0 38.58 5.24 F
1459 3592 2.222796 CGTGTCGTTCGTCGGTATAAGA 60.223 50.000 0.0 0.0 40.32 2.10 F
2221 4363 0.773644 ATGGAGGTGAAGCAAGTGGT 59.226 50.000 0.0 0.0 0.00 4.16 F
2241 4383 1.623311 TCAAGTCAGGGAAATGCTCGA 59.377 47.619 0.0 0.0 0.00 4.04 F
3608 7090 1.502163 GCGCTGACTCATGTATGGGC 61.502 60.000 0.0 0.0 33.34 5.36 F
3945 8948 1.768275 TCTCAAGTGTGGGAGCTGAAA 59.232 47.619 0.0 0.0 28.16 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 4363 1.623311 TCGAGCATTTCCCTGACTTGA 59.377 47.619 0.0 0.0 0.00 3.02 R
2972 6448 0.815734 TACTCGGCTCTTGGTGCTAC 59.184 55.000 0.0 0.0 0.00 3.58 R
3553 7035 2.229792 TGGCACTTGAAAGACATGGTC 58.770 47.619 0.0 0.0 0.00 4.02 R
4001 9004 2.821969 GGTGATGTGTCTCCAAAGCAAT 59.178 45.455 0.0 0.0 37.82 3.56 R
4736 14188 2.698274 TGCTACGCTTGAGATATTCCCA 59.302 45.455 0.0 0.0 0.00 4.37 R
6048 15628 4.161377 AGCCTGCAAAACAAGAGGTAAAAA 59.839 37.500 0.0 0.0 0.00 1.94 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
793 822 7.962995 CCTCTAGGGCATATATCTTTCACTA 57.037 40.000 0.00 0.00 0.00 2.74
893 922 1.219824 TCCGTCTCCCCCTACTCCTT 61.220 60.000 0.00 0.00 0.00 3.36
928 957 1.001517 TCTCTCCTCTGAGCTGCGT 60.002 57.895 0.00 0.00 38.58 5.24
1178 1208 4.410400 GCCCCCTCCAGGAACACG 62.410 72.222 0.00 0.00 38.24 4.49
1459 3592 2.222796 CGTGTCGTTCGTCGGTATAAGA 60.223 50.000 0.00 0.00 40.32 2.10
2221 4363 0.773644 ATGGAGGTGAAGCAAGTGGT 59.226 50.000 0.00 0.00 0.00 4.16
2241 4383 1.623311 TCAAGTCAGGGAAATGCTCGA 59.377 47.619 0.00 0.00 0.00 4.04
2826 4986 6.348950 CGTTTGGACACAACCATATGTACAAT 60.349 38.462 0.00 0.00 46.47 2.71
2851 5011 5.076182 TGAAGCCTTCATTTGGTATTGACA 58.924 37.500 2.24 0.00 34.08 3.58
2949 6425 5.309638 TCGTGTGGGAAAAATACATGAAGA 58.690 37.500 0.00 0.00 37.40 2.87
3608 7090 1.502163 GCGCTGACTCATGTATGGGC 61.502 60.000 0.00 0.00 33.34 5.36
3797 8796 4.770010 TCAACTAAGGGGGCACTTTAATTG 59.230 41.667 6.49 6.49 32.02 2.32
3850 8849 8.246180 TCTTCAATCTTTTAGGATTCATGCAAC 58.754 33.333 0.00 0.00 34.15 4.17
3890 8889 3.445096 GCATGCTATTTTGGGTTCTCAGT 59.555 43.478 11.37 0.00 0.00 3.41
3945 8948 1.768275 TCTCAAGTGTGGGAGCTGAAA 59.232 47.619 0.00 0.00 28.16 2.69
3946 8949 2.373169 TCTCAAGTGTGGGAGCTGAAAT 59.627 45.455 0.00 0.00 28.16 2.17
5210 14684 1.141254 TGTTTTCTCACCACCGGCTAA 59.859 47.619 0.00 0.00 0.00 3.09
6201 15781 0.786435 AATGTCTTGGGGCTCCCTTT 59.214 50.000 0.00 0.00 45.70 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 191 4.765273 ACATATGTTGTATGCGGTCTGAA 58.235 39.130 1.41 0.00 36.57 3.02
783 812 1.076332 GTTGGCGCGTAGTGAAAGAT 58.924 50.000 8.43 0.00 43.07 2.40
786 815 1.300003 TCGTTGGCGCGTAGTGAAA 60.300 52.632 8.43 0.00 43.07 2.69
867 896 4.554036 GGGGAGACGGAGGCATGC 62.554 72.222 9.90 9.90 0.00 4.06
893 922 4.341520 GGAGAGAGATAGGTAGCGGAAAAA 59.658 45.833 0.00 0.00 0.00 1.94
928 957 0.827925 ACCTGCAGAGAGGAACGACA 60.828 55.000 17.39 0.00 36.51 4.35
985 1014 4.776322 CATCGGAGGGGCACGCAA 62.776 66.667 0.00 0.00 46.88 4.85
1195 1225 1.531578 GGAGAAGCAAAACAGGACGAC 59.468 52.381 0.00 0.00 0.00 4.34
1459 3592 1.813753 CATCGACCGTCCGGCAATT 60.814 57.895 5.47 0.00 39.32 2.32
2221 4363 1.623311 TCGAGCATTTCCCTGACTTGA 59.377 47.619 0.00 0.00 0.00 3.02
2241 4383 4.098044 TCGTTGATCTTCTCGATAGCCTTT 59.902 41.667 0.00 0.00 30.84 3.11
2826 4986 6.041409 TGTCAATACCAAATGAAGGCTTCAAA 59.959 34.615 31.57 11.84 43.95 2.69
2972 6448 0.815734 TACTCGGCTCTTGGTGCTAC 59.184 55.000 0.00 0.00 0.00 3.58
3553 7035 2.229792 TGGCACTTGAAAGACATGGTC 58.770 47.619 0.00 0.00 0.00 4.02
3850 8849 2.896243 GCAGATGCAGACACTCAAAG 57.104 50.000 0.00 0.00 41.59 2.77
4001 9004 2.821969 GGTGATGTGTCTCCAAAGCAAT 59.178 45.455 0.00 0.00 37.82 3.56
4157 9178 9.589111 CCTCTAGAAGTTTTCAGTTATTACTCC 57.411 37.037 0.00 0.00 30.26 3.85
4569 13998 5.270853 GTGCAACAAAGAATACTCAACGTT 58.729 37.500 0.00 0.00 36.32 3.99
4736 14188 2.698274 TGCTACGCTTGAGATATTCCCA 59.302 45.455 0.00 0.00 0.00 4.37
6048 15628 4.161377 AGCCTGCAAAACAAGAGGTAAAAA 59.839 37.500 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.