Multiple sequence alignment - TraesCS6A01G175400

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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 TraesCS6A01G175400 chr6A 100.000 5588 0 0 1 5588 190691502 190685915 0.000000e+00 10283.0
1 TraesCS6A01G175400 chr6A 99.446 2886 14 2 2704 5588 190661533 190658649 0.000000e+00 5240.0
2 TraesCS6A01G175400 chr6A 98.814 2698 23 5 1 2693 190742603 190739910 0.000000e+00 4796.0
3 TraesCS6A01G175400 chr6A 99.098 2551 20 3 2704 5253 190739456 190736908 0.000000e+00 4580.0
4 TraesCS6A01G175400 chr6A 98.660 2314 21 3 104 2412 190664161 190661853 0.000000e+00 4093.0
5 TraesCS6A01G175400 chr6A 92.308 130 6 3 1317 1446 130415770 130415895 1.240000e-41 182.0
6 TraesCS6A01G175400 chr6A 87.356 87 7 1 3847 3933 62810626 62810544 4.610000e-16 97.1
7 TraesCS6A01G175400 chr6A 92.982 57 4 0 434 490 94353133 94353189 3.590000e-12 84.2
8 TraesCS6A01G175400 chr6A 97.917 48 1 0 3893 3940 190660390 190660343 3.590000e-12 84.2
9 TraesCS6A01G175400 chr6A 97.917 48 1 0 3893 3940 190738313 190738266 3.590000e-12 84.2
10 TraesCS6A01G175400 chr6B 97.064 1090 28 2 1430 2519 276732222 276733307 0.000000e+00 1832.0
11 TraesCS6A01G175400 chr6B 95.887 924 10 4 2898 3804 276734766 276735678 0.000000e+00 1471.0
12 TraesCS6A01G175400 chr6B 88.388 1042 66 18 4394 5399 532140266 532139244 0.000000e+00 1203.0
13 TraesCS6A01G175400 chr6B 95.447 593 17 3 741 1326 276731634 276732223 0.000000e+00 937.0
14 TraesCS6A01G175400 chr6B 98.721 469 3 1 3930 4395 276735678 276736146 0.000000e+00 830.0
15 TraesCS6A01G175400 chr6B 97.633 169 4 0 2525 2693 276733600 276733768 1.970000e-74 291.0
16 TraesCS6A01G175400 chr6B 96.512 86 2 1 5395 5480 276736143 276736227 2.100000e-29 141.0
17 TraesCS6A01G175400 chr6B 79.137 139 22 6 526 659 54900194 54900330 7.710000e-14 89.8
18 TraesCS6A01G175400 chr6D 96.574 1080 20 7 1440 2519 152256280 152257342 0.000000e+00 1773.0
19 TraesCS6A01G175400 chr6D 95.540 1121 23 5 2704 3807 152258001 152259111 0.000000e+00 1768.0
20 TraesCS6A01G175400 chr6D 96.939 588 15 2 741 1326 152255641 152256227 0.000000e+00 983.0
21 TraesCS6A01G175400 chr6D 98.498 466 7 0 3930 4395 152259104 152259569 0.000000e+00 822.0
22 TraesCS6A01G175400 chr6D 96.392 194 7 0 5395 5588 152259566 152259759 2.510000e-83 320.0
23 TraesCS6A01G175400 chr6D 97.753 178 4 0 2516 2693 152257373 152257550 1.960000e-79 307.0
24 TraesCS6A01G175400 chr6D 84.831 178 26 1 5225 5401 93881270 93881093 1.600000e-40 178.0
25 TraesCS6A01G175400 chr6D 85.106 94 8 4 571 659 418629722 418629814 2.140000e-14 91.6
26 TraesCS6A01G175400 chr3A 91.715 1038 40 8 4394 5395 251369407 251368380 0.000000e+00 1399.0
27 TraesCS6A01G175400 chr3A 88.068 176 19 2 1430 1604 9129664 9129490 2.040000e-49 207.0
28 TraesCS6A01G175400 chr3A 82.569 218 27 10 20 229 679704889 679704675 1.240000e-41 182.0
29 TraesCS6A01G175400 chr3A 92.453 53 4 0 434 486 747931819 747931767 6.000000e-10 76.8
30 TraesCS6A01G175400 chr7A 91.040 1038 46 18 4395 5395 534408804 534407777 0.000000e+00 1358.0
31 TraesCS6A01G175400 chr7A 92.248 129 8 1 1194 1320 671938885 671938757 1.240000e-41 182.0
32 TraesCS6A01G175400 chr7A 89.313 131 12 1 3803 3933 7041022 7041150 4.480000e-36 163.0
33 TraesCS6A01G175400 chr7A 78.519 270 40 14 6 265 195481790 195481529 1.610000e-35 161.0
34 TraesCS6A01G175400 chr7A 94.444 54 0 3 3888 3940 42986167 42986116 4.640000e-11 80.5
35 TraesCS6A01G175400 chr1A 91.080 1009 71 10 4393 5400 231644203 231643213 0.000000e+00 1347.0
36 TraesCS6A01G175400 chr1A 94.545 55 3 0 434 488 573443614 573443560 9.970000e-13 86.1
37 TraesCS6A01G175400 chr7B 90.388 1030 58 17 4389 5398 509508330 509509338 0.000000e+00 1315.0
38 TraesCS6A01G175400 chr7B 83.691 233 28 9 16 243 64065353 64065126 1.580000e-50 211.0
39 TraesCS6A01G175400 chr7B 92.366 131 8 1 1192 1320 678657221 678657091 9.560000e-43 185.0
40 TraesCS6A01G175400 chr7B 81.333 150 20 6 526 669 120371942 120372089 1.270000e-21 115.0
41 TraesCS6A01G175400 chrUn 100.000 557 0 0 2704 3260 451646435 451645879 0.000000e+00 1029.0
42 TraesCS6A01G175400 chrUn 100.000 397 0 0 4820 5216 479104263 479104659 0.000000e+00 734.0
43 TraesCS6A01G175400 chrUn 79.920 249 38 10 4 249 308002699 308002938 7.440000e-39 172.0
44 TraesCS6A01G175400 chrUn 84.146 164 21 3 491 653 210625836 210625995 2.700000e-33 154.0
45 TraesCS6A01G175400 chr4B 90.859 722 47 7 4690 5395 340551380 340550662 0.000000e+00 950.0
46 TraesCS6A01G175400 chr4B 82.759 174 24 4 491 659 604620589 604620761 3.490000e-32 150.0
47 TraesCS6A01G175400 chr4B 97.959 49 1 0 3893 3941 474386378 474386330 9.970000e-13 86.1
48 TraesCS6A01G175400 chr1D 78.835 1082 138 48 4393 5394 186715317 186716387 0.000000e+00 645.0
49 TraesCS6A01G175400 chr1D 80.000 245 36 11 16 249 244622357 244622115 9.630000e-38 169.0
50 TraesCS6A01G175400 chr4D 80.593 809 95 32 4400 5172 495110694 495109912 8.120000e-158 568.0
51 TraesCS6A01G175400 chr4D 80.501 359 33 21 1 326 379232473 379232827 2.010000e-59 241.0
52 TraesCS6A01G175400 chr2B 91.503 153 10 3 1443 1593 236703604 236703453 2.040000e-49 207.0
53 TraesCS6A01G175400 chr2B 87.791 172 17 3 1436 1606 636136726 636136894 1.230000e-46 198.0
54 TraesCS6A01G175400 chr2B 93.600 125 6 1 1192 1314 164025001 164025125 9.560000e-43 185.0
55 TraesCS6A01G175400 chr2B 83.051 177 22 5 491 660 11039068 11039243 2.700000e-33 154.0
56 TraesCS6A01G175400 chr2B 91.667 60 4 1 434 492 545348916 545348975 1.290000e-11 82.4
57 TraesCS6A01G175400 chr5A 88.372 172 16 4 1435 1605 328688804 328688636 2.640000e-48 204.0
58 TraesCS6A01G175400 chr5A 91.111 135 9 3 1325 1456 6567664 6567798 4.450000e-41 180.0
59 TraesCS6A01G175400 chr5A 91.837 98 8 0 3798 3895 649435088 649434991 2.720000e-28 137.0
60 TraesCS6A01G175400 chr5A 82.609 138 18 4 526 658 19674084 19674220 3.540000e-22 117.0
61 TraesCS6A01G175400 chr5B 97.436 117 3 0 1315 1431 278886870 278886986 3.410000e-47 200.0
62 TraesCS6A01G175400 chr5B 87.356 174 20 2 1431 1603 28234959 28234787 1.230000e-46 198.0
63 TraesCS6A01G175400 chr5B 92.727 55 4 0 434 488 418683989 418684043 4.640000e-11 80.5
64 TraesCS6A01G175400 chr4A 97.368 114 3 0 1318 1431 381221440 381221327 1.590000e-45 195.0
65 TraesCS6A01G175400 chr4A 92.366 131 8 1 1192 1320 166836881 166836751 9.560000e-43 185.0
66 TraesCS6A01G175400 chr4A 79.920 249 38 10 4 249 729058737 729058498 7.440000e-39 172.0
67 TraesCS6A01G175400 chr4A 79.377 257 24 17 16 249 56511749 56511999 2.700000e-33 154.0
68 TraesCS6A01G175400 chr4A 81.622 185 23 10 114 292 615191522 615191701 5.840000e-30 143.0
69 TraesCS6A01G175400 chr4A 88.288 111 11 2 3779 3889 542275954 542276062 1.260000e-26 132.0
70 TraesCS6A01G175400 chr4A 91.379 58 5 0 433 490 503637025 503636968 4.640000e-11 80.5
71 TraesCS6A01G175400 chr2A 86.932 176 19 3 1436 1609 350530302 350530475 1.590000e-45 195.0
72 TraesCS6A01G175400 chr2A 85.246 122 17 1 5225 5345 88723324 88723203 2.110000e-24 124.0
73 TraesCS6A01G175400 chr2A 84.416 77 7 5 3893 3965 607600077 607600002 2.790000e-08 71.3
74 TraesCS6A01G175400 chr7D 96.522 115 4 0 1318 1432 248393399 248393513 2.050000e-44 191.0
75 TraesCS6A01G175400 chr7D 92.727 55 4 0 434 488 296512561 296512615 4.640000e-11 80.5
76 TraesCS6A01G175400 chr7D 92.727 55 4 0 434 488 614406280 614406226 4.640000e-11 80.5
77 TraesCS6A01G175400 chr7D 100.000 29 0 0 739 767 593026826 593026854 3.000000e-03 54.7
78 TraesCS6A01G175400 chr1B 95.082 122 5 1 1315 1436 687253933 687254053 2.050000e-44 191.0
79 TraesCS6A01G175400 chr1B 77.744 328 55 14 1 322 636561800 636562115 9.560000e-43 185.0
80 TraesCS6A01G175400 chr1B 94.262 122 6 1 1315 1436 651523707 651523587 9.560000e-43 185.0
81 TraesCS6A01G175400 chr5D 94.309 123 5 2 1312 1432 134808259 134808381 2.660000e-43 187.0
82 TraesCS6A01G175400 chr5D 92.800 125 7 1 1192 1314 13239763 13239887 4.450000e-41 180.0
83 TraesCS6A01G175400 chr5D 91.603 131 9 1 1192 1320 461454289 461454159 4.450000e-41 180.0
84 TraesCS6A01G175400 chr5D 96.591 88 3 0 3800 3887 446918258 446918171 4.510000e-31 147.0
85 TraesCS6A01G175400 chr2D 83.815 173 22 5 491 660 417546672 417546503 5.790000e-35 159.0
86 TraesCS6A01G175400 chr2D 94.681 94 4 1 3794 3887 150380745 150380653 1.620000e-30 145.0
87 TraesCS6A01G175400 chr2D 90.566 106 8 2 3798 3902 100900316 100900212 7.550000e-29 139.0
88 TraesCS6A01G175400 chr2D 83.893 149 19 5 518 662 568780641 568780494 2.720000e-28 137.0
89 TraesCS6A01G175400 chr3B 93.617 94 6 0 3796 3889 200860774 200860681 2.100000e-29 141.0


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 TraesCS6A01G175400 chr6A 190685915 190691502 5587 True 10283.000000 10283 100.000000 1 5588 1 chr6A.!!$R2 5587
1 TraesCS6A01G175400 chr6A 190736908 190742603 5695 True 3153.400000 4796 98.609667 1 5253 3 chr6A.!!$R4 5252
2 TraesCS6A01G175400 chr6A 190658649 190664161 5512 True 3139.066667 5240 98.674333 104 5588 3 chr6A.!!$R3 5484
3 TraesCS6A01G175400 chr6B 532139244 532140266 1022 True 1203.000000 1203 88.388000 4394 5399 1 chr6B.!!$R1 1005
4 TraesCS6A01G175400 chr6B 276731634 276736227 4593 False 917.000000 1832 96.877333 741 5480 6 chr6B.!!$F2 4739
5 TraesCS6A01G175400 chr6D 152255641 152259759 4118 False 995.500000 1773 96.949333 741 5588 6 chr6D.!!$F2 4847
6 TraesCS6A01G175400 chr3A 251368380 251369407 1027 True 1399.000000 1399 91.715000 4394 5395 1 chr3A.!!$R2 1001
7 TraesCS6A01G175400 chr7A 534407777 534408804 1027 True 1358.000000 1358 91.040000 4395 5395 1 chr7A.!!$R3 1000
8 TraesCS6A01G175400 chr1A 231643213 231644203 990 True 1347.000000 1347 91.080000 4393 5400 1 chr1A.!!$R1 1007
9 TraesCS6A01G175400 chr7B 509508330 509509338 1008 False 1315.000000 1315 90.388000 4389 5398 1 chr7B.!!$F2 1009
10 TraesCS6A01G175400 chrUn 451645879 451646435 556 True 1029.000000 1029 100.000000 2704 3260 1 chrUn.!!$R1 556
11 TraesCS6A01G175400 chr4B 340550662 340551380 718 True 950.000000 950 90.859000 4690 5395 1 chr4B.!!$R1 705
12 TraesCS6A01G175400 chr1D 186715317 186716387 1070 False 645.000000 645 78.835000 4393 5394 1 chr1D.!!$F1 1001
13 TraesCS6A01G175400 chr4D 495109912 495110694 782 True 568.000000 568 80.593000 4400 5172 1 chr4D.!!$R1 772

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
523 528 0.248539 GACGATGAGGTGACTACGGC 60.249 60.000 0.0 0.0 44.43 5.68 F
524 529 0.963856 ACGATGAGGTGACTACGGCA 60.964 55.000 0.0 0.0 44.43 5.69 F
530 535 1.000506 GAGGTGACTACGGCAACTTCA 59.999 52.381 0.0 0.0 44.43 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3838 5233 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.0 37.82 1.82 R
3881 5276 6.411492 GCGTTTAGATCACTAAGAGTTACTCG 59.589 42.308 6.73 0.0 39.36 4.18 R
4653 6058 1.079405 GTGGGGATCGAGCGTTTGA 60.079 57.895 0.00 0.0 0.00 2.69 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
128 129 9.434420 TGAACAAGTTTTTGAGAAATGTTGAAT 57.566 25.926 0.00 0.00 37.73 2.57
516 521 0.955905 TCACGTTGACGATGAGGTGA 59.044 50.000 10.87 0.00 43.02 4.02
523 528 0.248539 GACGATGAGGTGACTACGGC 60.249 60.000 0.00 0.00 44.43 5.68
524 529 0.963856 ACGATGAGGTGACTACGGCA 60.964 55.000 0.00 0.00 44.43 5.69
530 535 1.000506 GAGGTGACTACGGCAACTTCA 59.999 52.381 0.00 0.00 44.43 3.02
644 650 2.225068 ATAAGCGCTTGCGTCTGTAT 57.775 45.000 32.23 12.36 45.69 2.29
827 833 4.996434 GCCCTCGCACAGCACTGT 62.996 66.667 0.00 0.00 46.17 3.55
3649 5029 2.680339 GGTGTTTCCATAGAGCTTCAGC 59.320 50.000 0.00 0.00 37.47 4.26
3881 5276 7.190920 ACGCTCTTATATTTGTTTATGGAGC 57.809 36.000 0.00 0.00 36.51 4.70
4548 5947 6.725364 ACATAGATTTTCACAGAATCCCAGT 58.275 36.000 0.00 0.00 34.74 4.00
4653 6058 2.047274 CACGACTGAACGGCCCAT 60.047 61.111 0.00 0.00 37.61 4.00
4740 6167 4.394712 GCAGCCCAGCCTACACGT 62.395 66.667 0.00 0.00 0.00 4.49
4818 6245 2.426023 GGAACACCGACAGCACCT 59.574 61.111 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
516 521 6.811253 TGAAATTTATGAAGTTGCCGTAGT 57.189 33.333 0.00 0.00 0.00 2.73
552 557 4.002316 GAGCATCTTCAAAAGACTGAGCT 58.998 43.478 0.00 0.00 41.01 4.09
556 561 7.606858 TTCTATGAGCATCTTCAAAAGACTG 57.393 36.000 0.00 0.00 41.01 3.51
827 833 4.758251 CGATGTCGGGCAGTGGCA 62.758 66.667 19.48 0.00 43.71 4.92
1079 1093 4.662961 TGTGGTGACTGAGCGGCG 62.663 66.667 0.51 0.51 0.00 6.46
3838 5233 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
3881 5276 6.411492 GCGTTTAGATCACTAAGAGTTACTCG 59.589 42.308 6.73 0.00 39.36 4.18
4653 6058 1.079405 GTGGGGATCGAGCGTTTGA 60.079 57.895 0.00 0.00 0.00 2.69
4740 6167 3.702048 CCCCAAGGCGAGAACCGA 61.702 66.667 0.00 0.00 41.76 4.69


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

AutoCloner maintained by Alex Coulton.