Multiple sequence alignment - TraesCS7B01G028900

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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 TraesCS7B01G028900 chr7B 100.000 2321 0 0 1 2321 27389933 27392253 0.000000e+00 4287.0
1 TraesCS7B01G028900 chr7B 95.177 1721 66 5 1 1717 27350180 27351887 0.000000e+00 2702.0
2 TraesCS7B01G028900 chr7B 91.899 1432 105 9 897 2320 654097009 654098437 0.000000e+00 1991.0
3 TraesCS7B01G028900 chr7B 93.155 1344 83 7 985 2321 654081685 654083026 0.000000e+00 1964.0
4 TraesCS7B01G028900 chr6B 90.288 1668 130 16 682 2321 575831765 575833428 0.000000e+00 2154.0
5 TraesCS7B01G028900 chrUn 92.878 1348 87 7 983 2321 55591867 55590520 0.000000e+00 1949.0
6 TraesCS7B01G028900 chrUn 91.982 1347 100 6 983 2321 55581164 55579818 0.000000e+00 1882.0
7 TraesCS7B01G028900 chr5B 92.719 1346 88 8 983 2321 600573707 600575049 0.000000e+00 1934.0
8 TraesCS7B01G028900 chr5B 90.291 1442 107 12 910 2321 600592267 600593705 0.000000e+00 1857.0
9 TraesCS7B01G028900 chr5B 93.697 1174 66 3 332 1504 295628462 295627296 0.000000e+00 1751.0
10 TraesCS7B01G028900 chr1B 90.865 1445 89 17 906 2321 173329990 173331420 0.000000e+00 1897.0
11 TraesCS7B01G028900 chr1B 90.895 1329 116 4 983 2307 514436616 514437943 0.000000e+00 1779.0
12 TraesCS7B01G028900 chr1B 86.567 67 7 2 293 358 392065526 392065591 3.200000e-09 73.1
13 TraesCS7B01G028900 chr1B 97.297 37 1 0 294 330 514377724 514377760 1.930000e-06 63.9
14 TraesCS7B01G028900 chr3B 94.143 1161 65 3 350 1508 341402378 341401219 0.000000e+00 1764.0
15 TraesCS7B01G028900 chr3B 93.454 1161 72 4 350 1508 341417379 341416221 0.000000e+00 1720.0
16 TraesCS7B01G028900 chr3B 96.264 803 28 2 350 1151 148684109 148683308 0.000000e+00 1315.0
17 TraesCS7B01G028900 chr3B 95.890 803 31 2 350 1151 148668686 148667885 0.000000e+00 1299.0
18 TraesCS7B01G028900 chr3B 84.752 564 46 14 293 830 390922332 390921783 1.580000e-146 529.0
19 TraesCS7B01G028900 chr2A 92.790 1165 81 3 346 1508 401688248 401689411 0.000000e+00 1683.0
20 TraesCS7B01G028900 chr2A 92.704 1165 80 5 346 1508 401715455 401716616 0.000000e+00 1676.0
21 TraesCS7B01G028900 chr2A 92.446 1165 83 5 346 1508 403700448 403701609 0.000000e+00 1659.0
22 TraesCS7B01G028900 chr2D 81.510 768 65 42 291 999 429336004 429335255 5.600000e-156 560.0
23 TraesCS7B01G028900 chr2D 94.366 284 14 2 3 284 335705834 335706117 3.540000e-118 435.0
24 TraesCS7B01G028900 chr4A 92.010 388 30 1 443 830 658828204 658828590 5.640000e-151 544.0
25 TraesCS7B01G028900 chr4A 90.979 388 34 1 443 830 248942701 248942315 2.640000e-144 521.0
26 TraesCS7B01G028900 chr3D 94.406 286 14 2 1 284 249669082 249668797 2.740000e-119 438.0
27 TraesCS7B01G028900 chr3D 93.031 287 17 3 1 284 249653726 249653440 1.280000e-112 416.0
28 TraesCS7B01G028900 chr3D 92.226 283 20 2 4 284 249281406 249281124 1.290000e-107 399.0


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 TraesCS7B01G028900 chr7B 27389933 27392253 2320 False 4287 4287 100.000 1 2321 1 chr7B.!!$F2 2320
1 TraesCS7B01G028900 chr7B 27350180 27351887 1707 False 2702 2702 95.177 1 1717 1 chr7B.!!$F1 1716
2 TraesCS7B01G028900 chr7B 654097009 654098437 1428 False 1991 1991 91.899 897 2320 1 chr7B.!!$F4 1423
3 TraesCS7B01G028900 chr7B 654081685 654083026 1341 False 1964 1964 93.155 985 2321 1 chr7B.!!$F3 1336
4 TraesCS7B01G028900 chr6B 575831765 575833428 1663 False 2154 2154 90.288 682 2321 1 chr6B.!!$F1 1639
5 TraesCS7B01G028900 chrUn 55590520 55591867 1347 True 1949 1949 92.878 983 2321 1 chrUn.!!$R2 1338
6 TraesCS7B01G028900 chrUn 55579818 55581164 1346 True 1882 1882 91.982 983 2321 1 chrUn.!!$R1 1338
7 TraesCS7B01G028900 chr5B 600573707 600575049 1342 False 1934 1934 92.719 983 2321 1 chr5B.!!$F1 1338
8 TraesCS7B01G028900 chr5B 600592267 600593705 1438 False 1857 1857 90.291 910 2321 1 chr5B.!!$F2 1411
9 TraesCS7B01G028900 chr5B 295627296 295628462 1166 True 1751 1751 93.697 332 1504 1 chr5B.!!$R1 1172
10 TraesCS7B01G028900 chr1B 173329990 173331420 1430 False 1897 1897 90.865 906 2321 1 chr1B.!!$F1 1415
11 TraesCS7B01G028900 chr1B 514436616 514437943 1327 False 1779 1779 90.895 983 2307 1 chr1B.!!$F4 1324
12 TraesCS7B01G028900 chr3B 341401219 341402378 1159 True 1764 1764 94.143 350 1508 1 chr3B.!!$R3 1158
13 TraesCS7B01G028900 chr3B 341416221 341417379 1158 True 1720 1720 93.454 350 1508 1 chr3B.!!$R4 1158
14 TraesCS7B01G028900 chr3B 148683308 148684109 801 True 1315 1315 96.264 350 1151 1 chr3B.!!$R2 801
15 TraesCS7B01G028900 chr3B 148667885 148668686 801 True 1299 1299 95.890 350 1151 1 chr3B.!!$R1 801
16 TraesCS7B01G028900 chr3B 390921783 390922332 549 True 529 529 84.752 293 830 1 chr3B.!!$R5 537
17 TraesCS7B01G028900 chr2A 401688248 401689411 1163 False 1683 1683 92.790 346 1508 1 chr2A.!!$F1 1162
18 TraesCS7B01G028900 chr2A 401715455 401716616 1161 False 1676 1676 92.704 346 1508 1 chr2A.!!$F2 1162
19 TraesCS7B01G028900 chr2A 403700448 403701609 1161 False 1659 1659 92.446 346 1508 1 chr2A.!!$F3 1162
20 TraesCS7B01G028900 chr2D 429335255 429336004 749 True 560 560 81.510 291 999 1 chr2D.!!$R1 708

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
402 406 1.078214 ACATCCAGCCACCACGATG 60.078 57.895 0.0 0.0 38.44 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1507 1.005037 AGCTTCACGCCGTGATTCA 60.005 52.632 21.92 5.27 42.4 2.57 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
200 203 3.973973 AGGATGATCGGGTGATTTCCTTA 59.026 43.478 5.40 0.00 41.29 2.69
286 289 2.711009 AGACAATCAGAACAACCCAGGA 59.289 45.455 0.00 0.00 0.00 3.86
287 290 3.138283 AGACAATCAGAACAACCCAGGAA 59.862 43.478 0.00 0.00 0.00 3.36
402 406 1.078214 ACATCCAGCCACCACGATG 60.078 57.895 0.00 0.00 38.44 3.84
470 500 1.335964 CGGCGATCATCCGTACAAGAT 60.336 52.381 0.00 0.00 41.85 2.40
625 655 1.196808 CAGCACTTCGTTGGCGTTATT 59.803 47.619 0.00 0.00 39.49 1.40
1085 1165 1.956477 GTCAACAGCATCAACCTGGTT 59.044 47.619 6.18 6.18 34.65 3.67
1153 1233 1.550524 ACTTCGTCATGCTGGAGCTAA 59.449 47.619 0.00 0.00 42.66 3.09
1315 1395 1.709147 CTTCTTCATCAAGCCGGCGG 61.709 60.000 24.35 24.35 0.00 6.13
1319 1400 0.753867 TTCATCAAGCCGGCGGTATA 59.246 50.000 28.82 11.30 0.00 1.47
1334 1415 2.543238 CGGTATAGAGGACAAAGGCGTC 60.543 54.545 0.00 0.00 35.03 5.19
1421 1502 2.062177 AGCGCCAATACCGGGTACT 61.062 57.895 9.50 0.00 0.00 2.73
1440 1521 2.431771 CGGTGAATCACGGCGTGA 60.432 61.111 40.35 40.35 46.90 4.35
1446 1527 1.005037 AATCACGGCGTGAAGCTCA 60.005 52.632 41.49 21.95 45.96 4.26
1696 1798 2.360801 GCTTTGCCAACACTAACTTCCA 59.639 45.455 0.00 0.00 0.00 3.53
1745 1848 1.739196 GAGGACCGCCGTAAACACC 60.739 63.158 0.00 0.00 39.96 4.16
1841 1944 3.895656 CGGTCTCCATAAGAATACTCCCA 59.104 47.826 0.00 0.00 35.21 4.37
1852 1955 0.981183 ATACTCCCACAAGGCGAACA 59.019 50.000 0.00 0.00 34.51 3.18
1898 2002 3.798202 ACATCATAAAGAAGTCCGAGCC 58.202 45.455 0.00 0.00 0.00 4.70
1925 2029 1.680735 GACCCATGCAACTTCAACACA 59.319 47.619 0.00 0.00 0.00 3.72
2006 2112 1.216178 GCCATGTTTTGAGCGGCAT 59.784 52.632 1.45 0.00 42.50 4.40
2314 2423 6.905736 TGAAATACTTGCTTCCCATACCATA 58.094 36.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
286 289 0.555769 TGGCTGGGTGTCTCCTTTTT 59.444 50.000 0.00 0.00 36.25 1.94
287 290 0.178990 GTGGCTGGGTGTCTCCTTTT 60.179 55.000 0.00 0.00 36.25 2.27
330 333 0.038343 GTTGTACGTGGGTTCGGCTA 60.038 55.000 0.00 0.00 34.94 3.93
402 406 2.180131 CTTGCTGCGTGAGTTCTGGC 62.180 60.000 0.00 0.00 0.00 4.85
625 655 7.712639 GTCTTGGTTAGCTTGATGAAGATGATA 59.287 37.037 0.00 0.00 0.00 2.15
1085 1165 2.264480 CACCACGATCCTTGCGGA 59.736 61.111 0.00 0.00 45.16 5.54
1315 1395 2.357009 TCGACGCCTTTGTCCTCTATAC 59.643 50.000 0.00 0.00 35.40 1.47
1319 1400 1.587054 CTCGACGCCTTTGTCCTCT 59.413 57.895 0.00 0.00 35.40 3.69
1334 1415 2.456119 GGCATCGTTGTGAGCCTCG 61.456 63.158 0.00 0.00 43.70 4.63
1421 1502 4.673298 ACGCCGTGATTCACCGCA 62.673 61.111 23.51 0.00 38.20 5.69
1426 1507 1.005037 AGCTTCACGCCGTGATTCA 60.005 52.632 21.92 5.27 42.40 2.57
1440 1521 2.551270 TGGTATCCTCCTTGTGAGCTT 58.449 47.619 0.00 0.00 39.98 3.74
1446 1527 2.838202 ACGTTGATGGTATCCTCCTTGT 59.162 45.455 0.00 0.00 0.00 3.16
1670 1771 1.837538 TAGTGTTGGCAAAGCGACGC 61.838 55.000 13.03 13.03 0.00 5.19
1818 1921 4.150359 GGGAGTATTCTTATGGAGACCGA 58.850 47.826 0.00 0.00 33.02 4.69
1852 1955 1.747206 GCTTCATCGGGTATGCAAGGT 60.747 52.381 0.00 0.00 35.38 3.50
1898 2002 2.046023 TTGCATGGGTCCTGCTCG 60.046 61.111 4.85 0.00 40.34 5.03
1925 2029 3.562505 GTCGACAACGTTGATGTAGTCT 58.437 45.455 33.66 9.45 40.69 3.24
1977 2083 3.055530 TCAAAACATGGCTTTGTGTTGGT 60.056 39.130 17.98 2.28 42.59 3.67
2006 2112 1.844771 CGTGTCCTCGTCGGTACACA 61.845 60.000 18.81 5.29 40.66 3.72


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

AutoCloner maintained by Alex Coulton.