Multiple sequence alignment - TraesCS5B01G247200

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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 TraesCS5B01G247200 chr5B 100.000 2192 0 0 1 2192 429065479 429063288 0.000000e+00 4012
1 TraesCS5B01G247200 chr5A 97.691 1732 28 8 357 2083 482022166 482023890 0.000000e+00 2966
2 TraesCS5B01G247200 chr5A 98.006 351 2 1 1 346 482022133 482022483 2.410000e-169 604
3 TraesCS5B01G247200 chr3D 96.888 1735 39 9 357 2083 589250062 589248335 0.000000e+00 2891
4 TraesCS5B01G247200 chr3D 95.935 1550 46 11 543 2083 158932532 158930991 0.000000e+00 2497
5 TraesCS5B01G247200 chr3D 95.690 1508 44 11 588 2083 158938604 158937106 0.000000e+00 2405
6 TraesCS5B01G247200 chr3D 99.145 468 4 0 357 824 158939082 158938615 0.000000e+00 843
7 TraesCS5B01G247200 chr3D 98.844 346 4 0 1 346 158939110 158938765 3.090000e-173 617
8 TraesCS5B01G247200 chr3D 98.555 346 5 0 1 346 589250090 589249745 1.440000e-171 612
9 TraesCS5B01G247200 chr3B 97.356 1475 27 7 615 2083 201553833 201555301 0.000000e+00 2497
10 TraesCS5B01G247200 chr4A 94.805 1617 52 16 474 2083 219302935 219304526 0.000000e+00 2492
11 TraesCS5B01G247200 chr4A 94.161 137 4 4 2056 2192 414602608 414602740 2.850000e-49 206
12 TraesCS5B01G247200 chr7B 94.893 1586 66 13 504 2083 105212551 105210975 0.000000e+00 2466
13 TraesCS5B01G247200 chrUn 95.837 1273 34 11 822 2083 371791801 371790537 0.000000e+00 2039
14 TraesCS5B01G247200 chrUn 99.143 467 4 0 358 824 355920579 355921045 0.000000e+00 841
15 TraesCS5B01G247200 chrUn 98.844 346 4 0 1 346 341019341 341019686 3.090000e-173 617
16 TraesCS5B01G247200 chrUn 97.110 346 4 1 1 346 362350991 362351330 1.460000e-161 579
17 TraesCS5B01G247200 chrUn 97.110 346 3 1 1 346 355920557 355920895 5.250000e-161 577
18 TraesCS5B01G247200 chr1D 95.940 1207 38 8 357 1559 200552758 200551559 0.000000e+00 1947
19 TraesCS5B01G247200 chr1D 98.834 343 3 1 1 343 200552786 200552445 5.170000e-171 610
20 TraesCS5B01G247200 chr5D 95.104 1062 38 9 1030 2083 432405876 432406931 0.000000e+00 1661
21 TraesCS5B01G247200 chr5D 95.214 982 33 8 619 1591 523037748 523036772 0.000000e+00 1541
22 TraesCS5B01G247200 chr5D 91.483 681 39 7 360 1040 424172462 424171801 0.000000e+00 918
23 TraesCS5B01G247200 chr5D 98.844 346 4 0 1 346 503254650 503254305 3.090000e-173 617
24 TraesCS5B01G247200 chr6D 95.137 946 34 10 357 1299 431006021 431005085 0.000000e+00 1482
25 TraesCS5B01G247200 chr6D 97.101 345 9 1 1 345 431006049 431005706 4.060000e-162 580
26 TraesCS5B01G247200 chr2D 97.110 346 4 1 1 346 591995782 591996121 1.460000e-161 579
27 TraesCS5B01G247200 chr2D 94.286 140 3 5 2058 2192 645338921 645338782 2.210000e-50 209
28 TraesCS5B01G247200 chr6B 93.103 145 6 4 2052 2192 477159804 477159660 2.210000e-50 209
29 TraesCS5B01G247200 chr3A 95.489 133 3 3 2061 2192 481631447 481631317 2.210000e-50 209
30 TraesCS5B01G247200 chr3A 94.815 135 3 3 2059 2192 481432933 481433064 7.930000e-50 207
31 TraesCS5B01G247200 chr2B 93.103 145 4 5 2052 2192 590039465 590039323 7.930000e-50 207
32 TraesCS5B01G247200 chr4B 93.571 140 5 4 2053 2192 602791997 602791862 2.850000e-49 206
33 TraesCS5B01G247200 chr7A 100.000 110 0 0 2083 2192 484450324 484450215 1.030000e-48 204
34 TraesCS5B01G247200 chr6A 91.156 147 11 2 2048 2192 47610467 47610613 4.770000e-47 198


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 TraesCS5B01G247200 chr5B 429063288 429065479 2191 True 4012.000000 4012 100.0000 1 2192 1 chr5B.!!$R1 2191
1 TraesCS5B01G247200 chr5A 482022133 482023890 1757 False 1785.000000 2966 97.8485 1 2083 2 chr5A.!!$F1 2082
2 TraesCS5B01G247200 chr3D 158930991 158932532 1541 True 2497.000000 2497 95.9350 543 2083 1 chr3D.!!$R1 1540
3 TraesCS5B01G247200 chr3D 589248335 589250090 1755 True 1751.500000 2891 97.7215 1 2083 2 chr3D.!!$R3 2082
4 TraesCS5B01G247200 chr3D 158937106 158939110 2004 True 1288.333333 2405 97.8930 1 2083 3 chr3D.!!$R2 2082
5 TraesCS5B01G247200 chr3B 201553833 201555301 1468 False 2497.000000 2497 97.3560 615 2083 1 chr3B.!!$F1 1468
6 TraesCS5B01G247200 chr4A 219302935 219304526 1591 False 2492.000000 2492 94.8050 474 2083 1 chr4A.!!$F1 1609
7 TraesCS5B01G247200 chr7B 105210975 105212551 1576 True 2466.000000 2466 94.8930 504 2083 1 chr7B.!!$R1 1579
8 TraesCS5B01G247200 chrUn 371790537 371791801 1264 True 2039.000000 2039 95.8370 822 2083 1 chrUn.!!$R1 1261
9 TraesCS5B01G247200 chr1D 200551559 200552786 1227 True 1278.500000 1947 97.3870 1 1559 2 chr1D.!!$R1 1558
10 TraesCS5B01G247200 chr5D 432405876 432406931 1055 False 1661.000000 1661 95.1040 1030 2083 1 chr5D.!!$F1 1053
11 TraesCS5B01G247200 chr5D 523036772 523037748 976 True 1541.000000 1541 95.2140 619 1591 1 chr5D.!!$R3 972
12 TraesCS5B01G247200 chr5D 424171801 424172462 661 True 918.000000 918 91.4830 360 1040 1 chr5D.!!$R1 680
13 TraesCS5B01G247200 chr6D 431005085 431006049 964 True 1031.000000 1482 96.1190 1 1299 2 chr6D.!!$R1 1298

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
342 348 5.72437 TCATTTTCCCTTCTTTTTATCCCCC 59.276 40.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2243 0.953471 CGCCACTCGGATTCAAACCA 60.953 55.0 0.0 0.0 33.78 3.67 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
121 127 8.635765 AACAGCTCTCTTGTTCCATAATTAAA 57.364 30.769 0.00 0.00 0.00 1.52
340 346 9.739276 ATTTTCATTTTCCCTTCTTTTTATCCC 57.261 29.630 0.00 0.00 0.00 3.85
341 347 6.867519 TCATTTTCCCTTCTTTTTATCCCC 57.132 37.500 0.00 0.00 0.00 4.81
342 348 5.724370 TCATTTTCCCTTCTTTTTATCCCCC 59.276 40.000 0.00 0.00 0.00 5.40
448 454 8.635765 AAACAGCTCTCTTGTTCCATAATTAA 57.364 30.769 0.00 0.00 0.00 1.40
449 455 8.635765 AACAGCTCTCTTGTTCCATAATTAAA 57.364 30.769 0.00 0.00 0.00 1.52
962 1220 6.097839 AGGATTGATTTGCAGCAATAGATGTT 59.902 34.615 9.12 0.00 35.05 2.71
1171 1433 2.935849 GGTTTTTCTGGGCAACAAACAG 59.064 45.455 0.00 0.00 39.74 3.16
1475 1748 9.181061 GACTTACAACTTCTACCTATCTTCTCT 57.819 37.037 0.00 0.00 0.00 3.10
1720 2002 6.456795 AAAGAAGTTCCAACTCTTTCAAGG 57.543 37.500 0.00 0.00 38.57 3.61
1761 2043 4.830046 TGGGCAAAGCAAGAGTTTATTGTA 59.170 37.500 0.00 0.00 0.00 2.41
2087 2370 8.492673 TGCAACTTTAGAACATATACTGAAGG 57.507 34.615 0.00 0.00 35.18 3.46
2088 2371 8.318412 TGCAACTTTAGAACATATACTGAAGGA 58.682 33.333 0.00 0.00 35.18 3.36
2089 2372 9.162764 GCAACTTTAGAACATATACTGAAGGAA 57.837 33.333 0.00 0.00 35.18 3.36
2096 2379 8.854614 AGAACATATACTGAAGGAAATATGCC 57.145 34.615 0.00 0.00 36.29 4.40
2097 2380 7.885399 AGAACATATACTGAAGGAAATATGCCC 59.115 37.037 0.00 0.00 36.29 5.36
2098 2381 7.335127 ACATATACTGAAGGAAATATGCCCT 57.665 36.000 0.00 0.00 36.29 5.19
2099 2382 8.449423 ACATATACTGAAGGAAATATGCCCTA 57.551 34.615 0.00 0.00 36.29 3.53
2100 2383 8.543774 ACATATACTGAAGGAAATATGCCCTAG 58.456 37.037 0.00 0.00 36.29 3.02
2101 2384 8.762645 CATATACTGAAGGAAATATGCCCTAGA 58.237 37.037 0.00 0.00 31.36 2.43
2102 2385 5.559148 ACTGAAGGAAATATGCCCTAGAG 57.441 43.478 0.00 0.46 31.36 2.43
2103 2386 4.349342 ACTGAAGGAAATATGCCCTAGAGG 59.651 45.833 0.00 0.00 39.47 3.69
2178 2461 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
2179 2462 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
2180 2463 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
2181 2464 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
2182 2465 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
2183 2466 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
2184 2467 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
2185 2468 9.048446 GCTAGAATTGTATTAACCGGAAACATA 57.952 33.333 9.46 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 127 7.820872 GGTTTTCATTGGAATTCACTCAATCAT 59.179 33.333 7.93 0.0 31.93 2.45
448 454 9.211485 GTTTTCATTGGAATTCACTCAATCATT 57.789 29.630 7.93 0.0 31.93 2.57
449 455 7.820872 GGTTTTCATTGGAATTCACTCAATCAT 59.179 33.333 7.93 0.0 31.93 2.45
934 1192 3.598019 TTGCTGCAAATCAATCCTTCC 57.402 42.857 13.51 0.0 0.00 3.46
1720 2002 4.037446 TGCCCAATAGAAACACAAACACTC 59.963 41.667 0.00 0.0 0.00 3.51
1826 2109 5.405571 CGTCGATATTGGGAAAGTCCATAAG 59.594 44.000 0.00 0.0 38.64 1.73
1960 2243 0.953471 CGCCACTCGGATTCAAACCA 60.953 55.000 0.00 0.0 33.78 3.67
2094 2377 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.6 44.71 5.19
2152 2435 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.0 35.82 1.75
2153 2436 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.0 38.19 2.57
2154 2437 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.0 0.00 2.57
2155 2438 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.0 0.00 3.07
2156 2439 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.0 0.00 4.06
2157 2440 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.0 0.00 3.79
2158 2441 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.0 0.00 3.49
2159 2442 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.0 0.00 3.42


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

AutoCloner maintained by Alex Coulton.