Multiple sequence alignment - TraesCS1B01G112900

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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 TraesCS1B01G112900 chr1B 100.000 9343 0 0 1 9343 131455949 131465291 0.000000e+00 17254.0
1 TraesCS1B01G112900 chr1B 92.583 1200 58 8 7196 8367 131783732 131784928 0.000000e+00 1694.0
2 TraesCS1B01G112900 chr1B 91.962 1157 51 19 6060 7191 131782540 131783679 0.000000e+00 1583.0
3 TraesCS1B01G112900 chr1B 84.385 1505 126 50 2412 3870 131777007 131778448 0.000000e+00 1376.0
4 TraesCS1B01G112900 chr1B 95.115 737 13 10 917 1637 131775539 131776268 0.000000e+00 1140.0
5 TraesCS1B01G112900 chr1B 88.382 921 86 10 4668 5573 131781298 131782212 0.000000e+00 1088.0
6 TraesCS1B01G112900 chr1B 93.054 763 12 6 1 724 131774787 131775547 0.000000e+00 1077.0
7 TraesCS1B01G112900 chr1B 85.154 714 63 22 1638 2327 131776304 131776998 0.000000e+00 691.0
8 TraesCS1B01G112900 chr1B 84.538 498 41 12 4056 4536 131778438 131778916 2.380000e-125 460.0
9 TraesCS1B01G112900 chr1B 97.073 205 6 0 717 921 588495267 588495063 6.940000e-91 346.0
10 TraesCS1B01G112900 chr1B 96.618 207 6 1 720 926 562160291 562160086 8.980000e-90 342.0
11 TraesCS1B01G112900 chr1B 96.237 186 7 0 1 186 130666079 130666264 1.180000e-78 305.0
12 TraesCS1B01G112900 chr1B 88.350 206 23 1 4461 4665 131778954 131779159 7.250000e-61 246.0
13 TraesCS1B01G112900 chr1B 92.727 110 7 1 5942 6051 131782198 131782306 3.490000e-34 158.0
14 TraesCS1B01G112900 chr1D 91.414 1910 110 22 6045 7928 79812549 79814430 0.000000e+00 2569.0
15 TraesCS1B01G112900 chr1D 87.695 1991 191 22 4092 6035 79810369 79812352 0.000000e+00 2270.0
16 TraesCS1B01G112900 chr1D 84.998 2173 188 60 1733 3870 79938258 79940327 0.000000e+00 2080.0
17 TraesCS1B01G112900 chr1D 86.131 1990 203 28 4092 6035 79940366 79942328 0.000000e+00 2078.0
18 TraesCS1B01G112900 chr1D 87.971 1222 79 30 7193 8362 79943667 79944872 0.000000e+00 1380.0
19 TraesCS1B01G112900 chr1D 86.469 1212 97 37 1638 2816 79803091 79804268 0.000000e+00 1267.0
20 TraesCS1B01G112900 chr1D 93.581 592 21 11 1063 1638 79937568 79938158 0.000000e+00 867.0
21 TraesCS1B01G112900 chr1D 89.339 666 43 12 6526 7170 79942938 79943596 0.000000e+00 811.0
22 TraesCS1B01G112900 chr1D 92.203 513 21 12 1 507 79757558 79758057 0.000000e+00 708.0
23 TraesCS1B01G112900 chr1D 94.794 461 11 9 46 496 79936376 79936833 0.000000e+00 706.0
24 TraesCS1B01G112900 chr1D 94.889 450 19 4 1156 1602 79802150 79802598 0.000000e+00 701.0
25 TraesCS1B01G112900 chr1D 93.636 440 21 3 7929 8362 79814554 79814992 0.000000e+00 651.0
26 TraesCS1B01G112900 chr1D 92.237 438 18 6 6045 6480 79942517 79942940 2.890000e-169 606.0
27 TraesCS1B01G112900 chr1D 83.961 611 63 20 3278 3870 79809737 79810330 3.810000e-153 553.0
28 TraesCS1B01G112900 chr1D 91.667 348 25 2 2899 3245 79804294 79804638 6.560000e-131 479.0
29 TraesCS1B01G112900 chr1D 91.787 207 15 2 3860 4065 308699073 308698868 4.270000e-73 287.0
30 TraesCS1B01G112900 chr1D 79.384 422 53 24 1849 2252 328821807 328822212 5.560000e-67 267.0
31 TraesCS1B01G112900 chr1D 94.048 168 9 1 937 1103 79799004 79799171 4.330000e-63 254.0
32 TraesCS1B01G112900 chr1D 94.118 153 5 3 488 636 79936902 79937054 7.300000e-56 230.0
33 TraesCS1B01G112900 chr1D 91.667 132 3 1 601 724 79798850 79798981 9.640000e-40 176.0
34 TraesCS1B01G112900 chr1D 100.000 46 0 0 1593 1638 79803011 79803056 1.670000e-12 86.1
35 TraesCS1B01G112900 chr1A 88.955 2010 169 26 4508 6480 98587608 98589601 0.000000e+00 2433.0
36 TraesCS1B01G112900 chr1A 90.980 1419 101 12 6526 7928 98589599 98591006 0.000000e+00 1886.0
37 TraesCS1B01G112900 chr1A 84.457 1023 99 26 2879 3870 98586194 98587187 0.000000e+00 953.0
38 TraesCS1B01G112900 chr1A 88.273 776 26 15 1 724 98583967 98584729 0.000000e+00 869.0
39 TraesCS1B01G112900 chr1A 91.266 561 19 8 7782 8312 98515364 98515924 0.000000e+00 737.0
40 TraesCS1B01G112900 chr1A 95.943 419 8 3 1229 1638 98585017 98585435 0.000000e+00 671.0
41 TraesCS1B01G112900 chr1A 93.151 438 21 2 7930 8367 98591040 98591468 1.320000e-177 634.0
42 TraesCS1B01G112900 chr1A 95.213 188 9 0 3869 4056 420523364 420523551 1.970000e-76 298.0
43 TraesCS1B01G112900 chr1A 87.550 249 18 11 917 1152 98584721 98584969 9.240000e-70 276.0
44 TraesCS1B01G112900 chr1A 82.927 164 26 2 2082 2243 62255679 62255516 7.560000e-31 147.0
45 TraesCS1B01G112900 chrUn 96.047 936 36 1 8400 9334 31729999 31730934 0.000000e+00 1522.0
46 TraesCS1B01G112900 chrUn 96.047 936 36 1 8400 9334 278206986 278207921 0.000000e+00 1522.0
47 TraesCS1B01G112900 chrUn 90.861 941 81 4 8403 9342 240818656 240819592 0.000000e+00 1256.0
48 TraesCS1B01G112900 chrUn 98.980 196 2 0 721 916 76852845 76853040 1.490000e-92 351.0
49 TraesCS1B01G112900 chrUn 80.153 393 52 12 1849 2221 33664369 33663983 4.300000e-68 270.0
50 TraesCS1B01G112900 chrUn 79.898 393 53 12 1849 2221 33372488 33372102 2.000000e-66 265.0
51 TraesCS1B01G112900 chr5B 91.459 925 77 2 8419 9342 227948460 227949383 0.000000e+00 1269.0
52 TraesCS1B01G112900 chr5B 78.274 336 42 15 1921 2240 94051055 94051375 4.450000e-43 187.0
53 TraesCS1B01G112900 chr2B 90.899 923 83 1 8420 9342 669200536 669201457 0.000000e+00 1238.0
54 TraesCS1B01G112900 chr2B 90.889 922 82 2 8422 9342 140159192 140160112 0.000000e+00 1236.0
55 TraesCS1B01G112900 chr2B 99.485 194 1 0 723 916 38432289 38432096 4.150000e-93 353.0
56 TraesCS1B01G112900 chr5A 89.577 921 92 2 8415 9335 538772090 538771174 0.000000e+00 1166.0
57 TraesCS1B01G112900 chr5A 95.238 189 9 0 3868 4056 358173074 358172886 5.480000e-77 300.0
58 TraesCS1B01G112900 chr5A 92.195 205 13 3 3863 4065 600091113 600090910 4.270000e-73 287.0
59 TraesCS1B01G112900 chr3A 87.354 941 119 0 8403 9343 108951137 108950197 0.000000e+00 1079.0
60 TraesCS1B01G112900 chr3A 79.592 392 55 11 1849 2221 747882792 747882407 3.350000e-64 257.0
61 TraesCS1B01G112900 chr2A 87.261 942 118 2 8403 9343 686036205 686037145 0.000000e+00 1074.0
62 TraesCS1B01G112900 chr2A 93.069 202 12 2 3861 4061 673952733 673952533 2.550000e-75 294.0
63 TraesCS1B01G112900 chr2A 73.003 626 120 38 4092 4678 202345367 202344752 3.470000e-39 174.0
64 TraesCS1B01G112900 chr7B 99.487 195 1 0 722 916 10919925 10920119 1.150000e-93 355.0
65 TraesCS1B01G112900 chr7B 96.667 210 5 2 712 920 691275956 691275748 1.930000e-91 348.0
66 TraesCS1B01G112900 chr7B 96.635 208 5 2 717 923 744140281 744140487 2.500000e-90 344.0
67 TraesCS1B01G112900 chr7B 94.792 192 10 0 3868 4059 496407367 496407558 5.480000e-77 300.0
68 TraesCS1B01G112900 chr7B 79.947 379 51 19 1848 2214 395259927 395260292 1.200000e-63 255.0
69 TraesCS1B01G112900 chr6B 98.974 195 2 0 722 916 30629797 30629603 5.370000e-92 350.0
70 TraesCS1B01G112900 chr4A 97.073 205 6 0 717 921 731617248 731617044 6.940000e-91 346.0
71 TraesCS1B01G112900 chr3B 94.792 192 10 0 3868 4059 697349342 697349151 5.480000e-77 300.0
72 TraesCS1B01G112900 chr3B 78.697 399 58 11 1841 2218 545059981 545060373 3.370000e-59 241.0
73 TraesCS1B01G112900 chr3B 80.808 297 55 2 4483 4778 625319300 625319595 2.030000e-56 231.0
74 TraesCS1B01G112900 chr3B 75.298 336 58 8 1905 2221 704258733 704258404 4.550000e-28 137.0
75 TraesCS1B01G112900 chr4B 95.213 188 9 0 3869 4056 582621177 582621364 1.970000e-76 298.0
76 TraesCS1B01G112900 chr7A 91.038 212 15 4 3855 4063 576494574 576494784 5.520000e-72 283.0
77 TraesCS1B01G112900 chr6A 79.277 415 64 8 1848 2240 617185634 617186048 4.300000e-68 270.0


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 TraesCS1B01G112900 chr1B 131455949 131465291 9342 False 17254.000000 17254 100.000000 1 9343 1 chr1B.!!$F2 9342
1 TraesCS1B01G112900 chr1B 131774787 131784928 10141 False 951.300000 1694 89.625000 1 8367 10 chr1B.!!$F3 8366
2 TraesCS1B01G112900 chr1D 79809737 79814992 5255 False 1510.750000 2569 89.176500 3278 8362 4 chr1D.!!$F4 5084
3 TraesCS1B01G112900 chr1D 79936376 79944872 8496 False 1094.750000 2080 90.396125 46 8362 8 chr1D.!!$F5 8316
4 TraesCS1B01G112900 chr1D 79798850 79804638 5788 False 493.850000 1267 93.123333 601 3245 6 chr1D.!!$F3 2644
5 TraesCS1B01G112900 chr1A 98583967 98591468 7501 False 1103.142857 2433 89.901286 1 8367 7 chr1A.!!$F3 8366
6 TraesCS1B01G112900 chr1A 98515364 98515924 560 False 737.000000 737 91.266000 7782 8312 1 chr1A.!!$F1 530
7 TraesCS1B01G112900 chrUn 31729999 31730934 935 False 1522.000000 1522 96.047000 8400 9334 1 chrUn.!!$F1 934
8 TraesCS1B01G112900 chrUn 278206986 278207921 935 False 1522.000000 1522 96.047000 8400 9334 1 chrUn.!!$F4 934
9 TraesCS1B01G112900 chrUn 240818656 240819592 936 False 1256.000000 1256 90.861000 8403 9342 1 chrUn.!!$F3 939
10 TraesCS1B01G112900 chr5B 227948460 227949383 923 False 1269.000000 1269 91.459000 8419 9342 1 chr5B.!!$F2 923
11 TraesCS1B01G112900 chr2B 669200536 669201457 921 False 1238.000000 1238 90.899000 8420 9342 1 chr2B.!!$F2 922
12 TraesCS1B01G112900 chr2B 140159192 140160112 920 False 1236.000000 1236 90.889000 8422 9342 1 chr2B.!!$F1 920
13 TraesCS1B01G112900 chr5A 538771174 538772090 916 True 1166.000000 1166 89.577000 8415 9335 1 chr5A.!!$R2 920
14 TraesCS1B01G112900 chr3A 108950197 108951137 940 True 1079.000000 1079 87.354000 8403 9343 1 chr3A.!!$R1 940
15 TraesCS1B01G112900 chr2A 686036205 686037145 940 False 1074.000000 1074 87.261000 8403 9343 1 chr2A.!!$F1 940


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
761 882 0.032130 CTAAGCATCTTAGCGCCGGA 59.968 55.0 5.05 0.00 40.15 5.14 F
775 896 0.171231 GCCGGACCTCTTTCAAATGC 59.829 55.0 5.05 0.00 0.00 3.56 F
796 917 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.0 22.98 22.98 45.83 4.70 F
861 982 0.324943 TCTCTTAGCGCAAGGCCTTT 59.675 50.0 17.61 3.50 45.17 3.11 F
2826 6536 0.107703 CCGGCAAAGCATGGAGTCTA 60.108 55.0 0.00 0.00 0.00 2.59 F
2849 6559 0.036765 ATGCGAGCAAACGGTCCTAA 60.037 50.0 0.57 0.00 0.00 2.69 F
3919 7687 0.032515 TCGGAGCTCCAATGGTAGGA 60.033 55.0 31.67 15.40 35.14 2.94 F
4923 10978 0.107017 CCGCCATGATGTTTCCTCCT 60.107 55.0 0.00 0.00 0.00 3.69 F
5901 11975 0.040351 TGACCTCCTCCTCCTCTGTG 59.960 60.0 0.00 0.00 0.00 3.66 F
5902 11976 0.333312 GACCTCCTCCTCCTCTGTGA 59.667 60.0 0.00 0.00 0.00 3.58 F
7512 14139 0.403271 AGCTGCAGGTGAGAACCAAT 59.597 50.0 19.45 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 5348 0.036306 ACACCTTTCACGATGGGGAC 59.964 55.000 0.00 0.00 30.59 4.46 R
2707 6392 0.469144 GGCCCCACAGTTCTTTTGGA 60.469 55.000 0.00 0.00 31.39 3.53 R
2708 6393 0.758685 TGGCCCCACAGTTCTTTTGG 60.759 55.000 0.00 0.00 0.00 3.28 R
2830 6540 0.036765 TTAGGACCGTTTGCTCGCAT 60.037 50.000 0.00 0.00 0.00 4.73 R
3900 7668 0.032515 TCCTACCATTGGAGCTCCGA 60.033 55.000 25.33 25.33 39.43 4.55 R
4037 7805 0.179215 GCAAGGTTGTCAGAATCGCG 60.179 55.000 0.00 0.00 0.00 5.87 R
5689 11760 0.029035 AGTATCATCGACACGACCGC 59.971 55.000 0.00 0.00 39.18 5.68 R
6777 13328 0.179084 ATTTCCATGACGCCGTCGAT 60.179 50.000 13.18 4.65 39.41 3.59 R
7548 14175 0.673333 TTGCGATGCAGGATCAACGT 60.673 50.000 2.47 0.00 40.61 3.99 R
7640 14267 2.944075 GATGCCAGCATCCCATCTC 58.056 57.895 19.71 0.00 45.06 2.75 R
8377 15160 0.317160 CAAGTCCCGTCACTACTGCA 59.683 55.000 0.00 0.00 0.00 4.41 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)



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AutoCloner maintained by Alex Coulton.