Multiple sequence alignment - TraesCS7A01G289600

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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 TraesCS7A01G289600 chr7A 100.000 2216 0 0 1 2216 352181992 352184207 0.000000e+00 4093.0
1 TraesCS7A01G289600 chrUn 95.011 2245 81 8 2 2216 93409792 93412035 0.000000e+00 3496.0
2 TraesCS7A01G289600 chrUn 94.335 1518 61 5 2 1494 216518763 216520280 0.000000e+00 2303.0
3 TraesCS7A01G289600 chrUn 94.792 960 30 3 1277 2216 453004432 453003473 0.000000e+00 1478.0
4 TraesCS7A01G289600 chrUn 95.093 428 21 0 1789 2216 403667276 403667703 0.000000e+00 675.0
5 TraesCS7A01G289600 chrUn 96.620 355 9 1 1720 2071 23290057 23290411 8.820000e-164 586.0
6 TraesCS7A01G289600 chrUn 94.828 58 3 0 1721 1778 60723217 60723160 8.430000e-15 91.6
7 TraesCS7A01G289600 chr5D 94.784 2243 89 6 2 2216 503218057 503215815 0.000000e+00 3469.0
8 TraesCS7A01G289600 chr5D 94.869 1832 85 7 393 2216 329120677 329122507 0.000000e+00 2854.0
9 TraesCS7A01G289600 chr5D 93.784 1287 57 4 2 1265 503278387 503279673 0.000000e+00 1912.0
10 TraesCS7A01G289600 chr5D 93.711 1288 57 6 2 1265 6188779 6187492 0.000000e+00 1908.0
11 TraesCS7A01G289600 chr2D 94.742 2244 89 8 2 2216 272794054 272796297 0.000000e+00 3463.0
12 TraesCS7A01G289600 chr6D 94.561 2243 91 9 2 2215 168251377 168249137 0.000000e+00 3437.0
13 TraesCS7A01G289600 chr6D 94.056 1329 54 6 2 1305 168251925 168253253 0.000000e+00 1993.0
14 TraesCS7A01G289600 chr3A 93.987 2245 104 11 2 2216 672910168 672912411 0.000000e+00 3369.0
15 TraesCS7A01G289600 chr3B 93.891 2259 93 10 2 2216 201526863 201524606 0.000000e+00 3365.0
16 TraesCS7A01G289600 chr6A 93.856 2246 107 10 2 2216 260116441 260118686 0.000000e+00 3354.0
17 TraesCS7A01G289600 chr5A 93.353 1715 87 5 2 1690 619266210 619264497 0.000000e+00 2510.0
18 TraesCS7A01G289600 chr3D 93.866 1288 54 5 2 1265 589279703 589280989 0.000000e+00 1917.0
19 TraesCS7A01G289600 chr3D 93.436 1173 52 6 2 1150 571592161 571593332 0.000000e+00 1716.0
20 TraesCS7A01G289600 chr4D 93.029 1291 62 7 2 1264 19928414 19927124 0.000000e+00 1860.0
21 TraesCS7A01G289600 chr2B 94.027 519 26 2 1702 2216 696668925 696669442 0.000000e+00 782.0


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 TraesCS7A01G289600 chr7A 352181992 352184207 2215 False 4093 4093 100.000 1 2216 1 chr7A.!!$F1 2215
1 TraesCS7A01G289600 chrUn 93409792 93412035 2243 False 3496 3496 95.011 2 2216 1 chrUn.!!$F2 2214
2 TraesCS7A01G289600 chrUn 216518763 216520280 1517 False 2303 2303 94.335 2 1494 1 chrUn.!!$F3 1492
3 TraesCS7A01G289600 chrUn 453003473 453004432 959 True 1478 1478 94.792 1277 2216 1 chrUn.!!$R2 939
4 TraesCS7A01G289600 chr5D 503215815 503218057 2242 True 3469 3469 94.784 2 2216 1 chr5D.!!$R2 2214
5 TraesCS7A01G289600 chr5D 329120677 329122507 1830 False 2854 2854 94.869 393 2216 1 chr5D.!!$F1 1823
6 TraesCS7A01G289600 chr5D 503278387 503279673 1286 False 1912 1912 93.784 2 1265 1 chr5D.!!$F2 1263
7 TraesCS7A01G289600 chr5D 6187492 6188779 1287 True 1908 1908 93.711 2 1265 1 chr5D.!!$R1 1263
8 TraesCS7A01G289600 chr2D 272794054 272796297 2243 False 3463 3463 94.742 2 2216 1 chr2D.!!$F1 2214
9 TraesCS7A01G289600 chr6D 168249137 168251377 2240 True 3437 3437 94.561 2 2215 1 chr6D.!!$R1 2213
10 TraesCS7A01G289600 chr6D 168251925 168253253 1328 False 1993 1993 94.056 2 1305 1 chr6D.!!$F1 1303
11 TraesCS7A01G289600 chr3A 672910168 672912411 2243 False 3369 3369 93.987 2 2216 1 chr3A.!!$F1 2214
12 TraesCS7A01G289600 chr3B 201524606 201526863 2257 True 3365 3365 93.891 2 2216 1 chr3B.!!$R1 2214
13 TraesCS7A01G289600 chr6A 260116441 260118686 2245 False 3354 3354 93.856 2 2216 1 chr6A.!!$F1 2214
14 TraesCS7A01G289600 chr5A 619264497 619266210 1713 True 2510 2510 93.353 2 1690 1 chr5A.!!$R1 1688
15 TraesCS7A01G289600 chr3D 589279703 589280989 1286 False 1917 1917 93.866 2 1265 1 chr3D.!!$F2 1263
16 TraesCS7A01G289600 chr3D 571592161 571593332 1171 False 1716 1716 93.436 2 1150 1 chr3D.!!$F1 1148
17 TraesCS7A01G289600 chr4D 19927124 19928414 1290 True 1860 1860 93.029 2 1264 1 chr4D.!!$R1 1262
18 TraesCS7A01G289600 chr2B 696668925 696669442 517 False 782 782 94.027 1702 2216 1 chr2B.!!$F1 514

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
819 846 0.769873 ATCTGCCCCTTATCCAGCTG 59.23 55.0 6.78 6.78 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1901 5.376756 TGGGTTGTACCAAGTCTAAAACT 57.623 39.13 0.0 0.0 41.02 2.66 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
166 186 7.768582 CCATCTGTCTAGAGATCGTCATATACT 59.231 40.741 0.00 0.00 36.14 2.12
177 197 8.630054 AGATCGTCATATACTTCTAGAAAGCT 57.370 34.615 6.63 0.00 0.00 3.74
250 270 9.267084 GAGAAAAGAAGAATCTACTTCAACTGT 57.733 33.333 0.00 0.00 45.83 3.55
366 386 1.749063 CAAAAGAGGGTAAATCGGCCC 59.251 52.381 0.00 0.00 45.16 5.80
527 547 7.014038 CACGTAGTAAGAGGGGTAGTTATGAAT 59.986 40.741 0.00 0.00 41.61 2.57
669 696 4.085210 CGATAGTTTTATTCTTCGTCGCCC 60.085 45.833 0.00 0.00 0.00 6.13
760 787 2.631580 GGGAATTGAACCCGCGCAA 61.632 57.895 8.75 0.00 37.85 4.85
819 846 0.769873 ATCTGCCCCTTATCCAGCTG 59.230 55.000 6.78 6.78 0.00 4.24
878 906 9.729281 TTCTATTTATTCCAACCTTCGTACTTT 57.271 29.630 0.00 0.00 0.00 2.66
898 926 9.862371 GTACTTTGATCGAGATATTGGACATAT 57.138 33.333 3.20 0.00 0.00 1.78
909 937 7.341805 AGATATTGGACATATAATGCCACTCC 58.658 38.462 0.00 0.00 36.60 3.85
916 944 7.502226 TGGACATATAATGCCACTCCTTAAAAG 59.498 37.037 0.00 0.00 33.56 2.27
1012 1051 5.379706 AAAGGTCAATATGAAGGAGGAGG 57.620 43.478 0.00 0.00 0.00 4.30
1035 1074 5.930569 GGAAGAAACAATAGTAACGTGGTCT 59.069 40.000 0.00 0.00 0.00 3.85
1038 1077 4.771590 AACAATAGTAACGTGGTCTCGA 57.228 40.909 0.00 0.00 34.70 4.04
1039 1078 4.771590 ACAATAGTAACGTGGTCTCGAA 57.228 40.909 0.00 0.00 34.70 3.71
1061 1100 4.770795 ACATCTAGCATTCTACCCACAAC 58.229 43.478 0.00 0.00 0.00 3.32
1063 1102 2.829720 TCTAGCATTCTACCCACAACGT 59.170 45.455 0.00 0.00 0.00 3.99
1145 1184 5.376625 TCCTATGGTAGATCACAAATTGGC 58.623 41.667 0.00 0.00 0.00 4.52
1186 1225 7.151308 TCGGCATTTCACAAGTTATGAAAATT 58.849 30.769 13.00 0.00 46.26 1.82
1275 1316 9.807921 AAGATTCAAAATGAAGTAAAGGTAGGA 57.192 29.630 0.00 0.00 40.05 2.94
1346 1387 7.339482 TCCCTAGGATAAAGAAGAAGAAAAGC 58.661 38.462 11.48 0.00 0.00 3.51
1416 1457 5.059833 AGTTCGAGAGAGTTTTCAAAGCAT 58.940 37.500 0.00 0.00 43.69 3.79
1422 1463 8.567948 TCGAGAGAGTTTTCAAAGCATAAAAAT 58.432 29.630 0.00 0.00 34.84 1.82
1458 1499 7.027161 GTCTGTTTTCAAAGCACAAAGAGTTA 58.973 34.615 0.00 0.00 0.00 2.24
1463 1504 9.034544 GTTTTCAAAGCACAAAGAGTTATTGAT 57.965 29.630 0.00 0.00 0.00 2.57
1470 1511 8.345724 AGCACAAAGAGTTATTGATGAGATTT 57.654 30.769 0.00 0.00 0.00 2.17
1865 1947 2.661718 ACACCATTCCTTTTGGTTCGT 58.338 42.857 0.00 0.00 45.19 3.85
1866 1948 2.360801 ACACCATTCCTTTTGGTTCGTG 59.639 45.455 0.00 0.00 45.19 4.35
1963 2047 4.884164 AGAATAGGAAAAAGGGCTCGAATG 59.116 41.667 0.00 0.00 0.00 2.67
1965 2049 0.817654 GGAAAAAGGGCTCGAATGGG 59.182 55.000 0.00 0.00 0.00 4.00
2083 2167 7.555914 TCCAAAAAGAAATCGATATGATCCACA 59.444 33.333 0.00 0.00 35.84 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.261826 GGCTTATGTTCTTCATGTAGCATTCT 59.738 38.462 13.97 0.00 42.20 2.40
281 301 1.165270 CCCTTCCACGTGTGATTTCC 58.835 55.000 15.65 0.00 0.00 3.13
386 406 3.104519 TGGGATACTAAACGGACCTCA 57.895 47.619 0.00 0.00 0.00 3.86
502 522 6.006275 TCATAACTACCCCTCTTACTACGT 57.994 41.667 0.00 0.00 0.00 3.57
527 547 4.194497 TGGGGGTGGTCCACAGGA 62.194 66.667 23.48 1.39 45.78 3.86
864 892 4.482386 TCTCGATCAAAGTACGAAGGTTG 58.518 43.478 0.00 0.00 35.70 3.77
865 893 4.778534 TCTCGATCAAAGTACGAAGGTT 57.221 40.909 0.00 0.00 35.70 3.50
870 898 6.038936 TGTCCAATATCTCGATCAAAGTACGA 59.961 38.462 0.00 0.00 34.90 3.43
878 906 7.928167 GGCATTATATGTCCAATATCTCGATCA 59.072 37.037 0.00 0.00 0.00 2.92
909 937 7.606839 AGTCGATTACTCCTTTTCCCTTTTAAG 59.393 37.037 0.00 0.00 30.33 1.85
954 993 7.631377 GCCAATAAATGATGAGCTACAAAAGGT 60.631 37.037 0.00 0.00 39.11 3.50
1012 1051 6.183359 CGAGACCACGTTACTATTGTTTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
1035 1074 3.958147 TGGGTAGAATGCTAGATGTTCGA 59.042 43.478 0.00 0.00 0.00 3.71
1038 1077 5.186198 GTTGTGGGTAGAATGCTAGATGTT 58.814 41.667 0.00 0.00 0.00 2.71
1039 1078 4.680708 CGTTGTGGGTAGAATGCTAGATGT 60.681 45.833 0.00 0.00 0.00 3.06
1061 1100 0.588730 CGCGATTGTATGGCCAAACG 60.589 55.000 10.96 4.74 41.68 3.60
1063 1102 1.674359 ATCGCGATTGTATGGCCAAA 58.326 45.000 17.62 0.00 0.00 3.28
1133 1172 2.491693 ACGAATTCCGCCAATTTGTGAT 59.508 40.909 9.17 0.00 44.49 3.06
1136 1175 1.668628 GCACGAATTCCGCCAATTTGT 60.669 47.619 0.00 5.51 46.36 2.83
1145 1184 0.870307 CCGAGTAGGCACGAATTCCG 60.870 60.000 0.00 0.00 45.44 4.30
1186 1225 8.311836 ACAACGAGATTTAGTATCCTTTCTTGA 58.688 33.333 0.00 0.00 0.00 3.02
1261 1302 6.409005 GGTTATTCCCCTCCTACCTTTACTTC 60.409 46.154 0.00 0.00 0.00 3.01
1275 1316 8.566109 ACTTGTCATAAATAAGGTTATTCCCCT 58.434 33.333 0.00 0.00 36.75 4.79
1346 1387 0.672401 TTGCGAGTTTCCTTAGCCCG 60.672 55.000 0.00 0.00 0.00 6.13
1380 1421 8.113173 ACTCTCTCGAACTTAAGTAGACAATT 57.887 34.615 8.92 0.00 0.00 2.32
1383 1424 7.507733 AAACTCTCTCGAACTTAAGTAGACA 57.492 36.000 8.92 0.00 0.00 3.41
1422 1463 6.374333 GCTTTGAAAACAGACATAGGGATACA 59.626 38.462 0.00 0.00 39.74 2.29
1458 1499 2.372264 ACGCCAGCAAATCTCATCAAT 58.628 42.857 0.00 0.00 0.00 2.57
1463 1504 2.472695 AGTAACGCCAGCAAATCTCA 57.527 45.000 0.00 0.00 0.00 3.27
1494 1535 5.311649 AGGGCATGAGGTTCAGTATCATAAT 59.688 40.000 0.00 0.00 32.51 1.28
1819 1901 5.376756 TGGGTTGTACCAAGTCTAAAACT 57.623 39.130 0.00 0.00 41.02 2.66
1963 2047 7.066404 GGAACTTGAGTCTGATTCTATTTTCCC 59.934 40.741 1.79 0.00 0.00 3.97
1965 2049 7.545965 TCGGAACTTGAGTCTGATTCTATTTTC 59.454 37.037 1.79 1.22 0.00 2.29
2075 2159 7.931046 TCCAATATGGATTATGATGTGGATCA 58.069 34.615 0.00 0.00 42.67 2.92


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

AutoCloner maintained by Alex Coulton.