Multiple sequence alignment - TraesCS1B01G112900
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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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 primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.