Multiple sequence alignment - TraesCS5A01G245500

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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 TraesCS5A01G245500 chr5A 100.000 2697 0 0 1 2697 458924640 458921944 0.000000e+00 4981.0
1 TraesCS5A01G245500 chr5A 98.981 687 5 2 1 687 174600910 174601594 0.000000e+00 1229.0
2 TraesCS5A01G245500 chr5A 99.563 229 1 0 2469 2697 458914851 458914623 4.150000e-113 418.0
3 TraesCS5A01G245500 chr2B 97.243 1052 29 0 686 1737 667279651 667280702 0.000000e+00 1783.0
4 TraesCS5A01G245500 chr2B 98.696 690 7 2 1 690 465129105 465129792 0.000000e+00 1223.0
5 TraesCS5A01G245500 chr2B 95.687 626 20 5 1906 2524 667280696 667281321 0.000000e+00 1000.0
6 TraesCS5A01G245500 chr2B 88.947 190 7 1 2522 2697 667281424 667281613 3.490000e-54 222.0
7 TraesCS5A01G245500 chr3D 92.034 1067 79 5 686 1752 49439056 49440116 0.000000e+00 1495.0
8 TraesCS5A01G245500 chr3D 81.915 376 27 20 2337 2688 603452216 603451858 2.040000e-71 279.0
9 TraesCS5A01G245500 chr7D 90.317 1074 99 4 686 1758 503074597 503073528 0.000000e+00 1402.0
10 TraesCS5A01G245500 chr7D 86.498 711 66 15 2012 2697 58190339 58189634 0.000000e+00 754.0
11 TraesCS5A01G245500 chr7D 76.939 490 72 27 2138 2610 178951341 178950876 9.650000e-60 241.0
12 TraesCS5A01G245500 chr6B 98.981 687 5 2 1 687 606302580 606303264 0.000000e+00 1229.0
13 TraesCS5A01G245500 chr2A 98.981 687 5 2 1 687 518943531 518944215 0.000000e+00 1229.0
14 TraesCS5A01G245500 chr5B 98.980 686 5 2 1 686 48315595 48316278 0.000000e+00 1227.0
15 TraesCS5A01G245500 chr3B 98.980 686 5 2 1 686 389958275 389957592 0.000000e+00 1227.0
16 TraesCS5A01G245500 chr3B 98.417 695 8 3 1 694 476291550 476292242 0.000000e+00 1219.0
17 TraesCS5A01G245500 chr3A 98.696 690 7 2 1 690 586878437 586877750 0.000000e+00 1223.0
18 TraesCS5A01G245500 chr3A 81.322 696 58 36 2051 2688 638009863 638010544 1.440000e-137 499.0
19 TraesCS5A01G245500 chr6A 98.555 692 8 2 1 692 75295938 75295249 0.000000e+00 1221.0
20 TraesCS5A01G245500 chr7B 94.207 794 27 10 1923 2697 570910276 570911069 0.000000e+00 1194.0
21 TraesCS5A01G245500 chr7B 84.972 1078 136 16 686 1748 123775547 123776613 0.000000e+00 1070.0
22 TraesCS5A01G245500 chr7B 84.137 1078 145 16 686 1748 716356793 716357859 0.000000e+00 1020.0
23 TraesCS5A01G245500 chr4B 84.112 1070 147 17 686 1748 63685366 63686419 0.000000e+00 1013.0
24 TraesCS5A01G245500 chr4B 84.310 1007 140 14 686 1688 63652348 63653340 0.000000e+00 968.0
25 TraesCS5A01G245500 chr7A 83.946 1034 143 15 686 1705 309668997 309667973 0.000000e+00 968.0
26 TraesCS5A01G245500 chrUn 82.746 1078 161 16 686 1751 357104390 357103326 0.000000e+00 937.0
27 TraesCS5A01G245500 chrUn 95.431 569 24 1 1692 2260 308001954 308002520 0.000000e+00 905.0
28 TraesCS5A01G245500 chr4A 95.431 569 24 1 1692 2260 729059482 729058916 0.000000e+00 905.0
29 TraesCS5A01G245500 chr4A 85.437 412 32 19 2296 2688 646291918 646291516 1.160000e-108 403.0
30 TraesCS5A01G245500 chr1D 78.818 203 26 10 2410 2610 3417477 3417664 1.310000e-23 121.0
31 TraesCS5A01G245500 chr2D 96.970 33 0 1 2210 2242 448154882 448154913 1.000000e-03 54.7


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 TraesCS5A01G245500 chr5A 458921944 458924640 2696 True 4981.000000 4981 100.000 1 2697 1 chr5A.!!$R2 2696
1 TraesCS5A01G245500 chr5A 174600910 174601594 684 False 1229.000000 1229 98.981 1 687 1 chr5A.!!$F1 686
2 TraesCS5A01G245500 chr2B 465129105 465129792 687 False 1223.000000 1223 98.696 1 690 1 chr2B.!!$F1 689
3 TraesCS5A01G245500 chr2B 667279651 667281613 1962 False 1001.666667 1783 93.959 686 2697 3 chr2B.!!$F2 2011
4 TraesCS5A01G245500 chr3D 49439056 49440116 1060 False 1495.000000 1495 92.034 686 1752 1 chr3D.!!$F1 1066
5 TraesCS5A01G245500 chr7D 503073528 503074597 1069 True 1402.000000 1402 90.317 686 1758 1 chr7D.!!$R3 1072
6 TraesCS5A01G245500 chr7D 58189634 58190339 705 True 754.000000 754 86.498 2012 2697 1 chr7D.!!$R1 685
7 TraesCS5A01G245500 chr6B 606302580 606303264 684 False 1229.000000 1229 98.981 1 687 1 chr6B.!!$F1 686
8 TraesCS5A01G245500 chr2A 518943531 518944215 684 False 1229.000000 1229 98.981 1 687 1 chr2A.!!$F1 686
9 TraesCS5A01G245500 chr5B 48315595 48316278 683 False 1227.000000 1227 98.980 1 686 1 chr5B.!!$F1 685
10 TraesCS5A01G245500 chr3B 389957592 389958275 683 True 1227.000000 1227 98.980 1 686 1 chr3B.!!$R1 685
11 TraesCS5A01G245500 chr3B 476291550 476292242 692 False 1219.000000 1219 98.417 1 694 1 chr3B.!!$F1 693
12 TraesCS5A01G245500 chr3A 586877750 586878437 687 True 1223.000000 1223 98.696 1 690 1 chr3A.!!$R1 689
13 TraesCS5A01G245500 chr3A 638009863 638010544 681 False 499.000000 499 81.322 2051 2688 1 chr3A.!!$F1 637
14 TraesCS5A01G245500 chr6A 75295249 75295938 689 True 1221.000000 1221 98.555 1 692 1 chr6A.!!$R1 691
15 TraesCS5A01G245500 chr7B 570910276 570911069 793 False 1194.000000 1194 94.207 1923 2697 1 chr7B.!!$F2 774
16 TraesCS5A01G245500 chr7B 123775547 123776613 1066 False 1070.000000 1070 84.972 686 1748 1 chr7B.!!$F1 1062
17 TraesCS5A01G245500 chr7B 716356793 716357859 1066 False 1020.000000 1020 84.137 686 1748 1 chr7B.!!$F3 1062
18 TraesCS5A01G245500 chr4B 63685366 63686419 1053 False 1013.000000 1013 84.112 686 1748 1 chr4B.!!$F2 1062
19 TraesCS5A01G245500 chr4B 63652348 63653340 992 False 968.000000 968 84.310 686 1688 1 chr4B.!!$F1 1002
20 TraesCS5A01G245500 chr7A 309667973 309668997 1024 True 968.000000 968 83.946 686 1705 1 chr7A.!!$R1 1019
21 TraesCS5A01G245500 chrUn 357103326 357104390 1064 True 937.000000 937 82.746 686 1751 1 chrUn.!!$R1 1065
22 TraesCS5A01G245500 chrUn 308001954 308002520 566 False 905.000000 905 95.431 1692 2260 1 chrUn.!!$F1 568
23 TraesCS5A01G245500 chr4A 729058916 729059482 566 True 905.000000 905 95.431 1692 2260 1 chr4A.!!$R2 568

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
486 487 0.036671 GGGGTCGACCGATTTTGACT 60.037 55.0 27.68 0.0 41.6 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1854 0.240145 AGACGATCGCTTGAACACGA 59.76 50.0 16.6 0.0 43.33 4.35 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
49 50 2.823154 CGGTATTTGGGGTCAATGTTGT 59.177 45.455 0.00 0.00 32.28 3.32
187 188 0.320160 GTTCTACAGGACGGCGGTTT 60.320 55.000 13.24 0.00 0.00 3.27
210 211 1.136356 CGCAATGTTGTATGGCGCA 59.864 52.632 10.83 0.00 41.27 6.09
486 487 0.036671 GGGGTCGACCGATTTTGACT 60.037 55.000 27.68 0.00 41.60 3.41
641 642 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
674 675 4.384940 AGGCTTTGTTGTTGTTGTTGTTT 58.615 34.783 0.00 0.00 0.00 2.83
708 709 2.080286 TCTGTCGCAAGCTTACCTTC 57.920 50.000 0.00 0.00 37.18 3.46
919 921 2.900716 TTGTGATGTTCAGGACACGA 57.099 45.000 0.00 0.00 42.04 4.35
932 934 4.002982 CAGGACACGAAAAATCATGAGGA 58.997 43.478 0.09 0.00 0.00 3.71
1508 1518 1.270625 ACGTTACCATCCACACACCTG 60.271 52.381 0.00 0.00 0.00 4.00
1585 1595 0.966920 GGAGTGGGTCGAGTGAGAAA 59.033 55.000 0.00 0.00 0.00 2.52
1706 1716 8.458573 AATGACACAACAATAGAGGTTTGTAA 57.541 30.769 0.00 0.00 36.32 2.41
1755 1767 9.595357 GTTCTTTTTGTCTTGCTATTACTACAC 57.405 33.333 0.00 0.00 0.00 2.90
1822 1834 0.036388 ACCGATGTTGAAGTGCCGAT 60.036 50.000 0.00 0.00 0.00 4.18
1843 1855 4.560136 TGTCGCAACATCTATCTCTCTC 57.440 45.455 0.00 0.00 0.00 3.20
1859 1871 0.240145 TCTCGTGTTCAAGCGATCGT 59.760 50.000 17.81 0.26 36.50 3.73
1867 1879 3.190744 TGTTCAAGCGATCGTCTAGAAGT 59.809 43.478 17.81 0.00 0.00 3.01
1878 1890 2.820787 CGTCTAGAAGTCAGGGACAAGT 59.179 50.000 0.00 0.00 34.60 3.16
1886 1898 0.843309 TCAGGGACAAGTGGCTCAAA 59.157 50.000 0.00 0.00 0.00 2.69
2163 2182 6.900568 TTTAGGTTGTGTTTTGCAATGAAG 57.099 33.333 0.00 0.00 0.00 3.02
2283 2305 3.728845 AGTAGAAACGCATGACACTTGT 58.271 40.909 0.00 0.00 0.00 3.16
2294 2316 4.622933 GCATGACACTTGTATGGACCTGTA 60.623 45.833 0.00 0.00 0.00 2.74
2567 2731 6.653740 TGTCGTCTCTATTCTGTTCTGTTCTA 59.346 38.462 0.00 0.00 0.00 2.10
2692 2873 5.072055 TGGAGTTCTTGCATGATTCTGAAA 58.928 37.500 2.75 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.145861 TCATCAATACCCCCATCCTCCTA 59.854 47.826 0.00 0.00 0.00 2.94
187 188 1.458398 CCATACAACATTGCGGGTCA 58.542 50.000 0.00 0.00 0.00 4.02
210 211 2.550208 CCTTTTAGTCGGCCAACACTCT 60.550 50.000 2.24 0.00 0.00 3.24
486 487 2.176889 CTCTTAACGGACTCCTCCCAA 58.823 52.381 0.00 0.00 31.93 4.12
641 642 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
674 675 3.486708 GCGACAGATGAACAACAACAACA 60.487 43.478 0.00 0.00 0.00 3.33
708 709 3.982576 AACCTTAGCCAAAACTCAACG 57.017 42.857 0.00 0.00 0.00 4.10
994 996 7.412853 CAAGAACATTTAGCAGTCATGGATAC 58.587 38.462 0.00 0.00 0.00 2.24
1508 1518 1.271656 GCCCCTTGCATTGATATCAGC 59.728 52.381 5.39 7.70 40.77 4.26
1585 1595 1.203125 TGGATTCCGGGCCTTCTTTTT 60.203 47.619 0.84 0.00 0.00 1.94
1597 1607 2.161410 TGCGACTTTTTGATGGATTCCG 59.839 45.455 0.00 0.00 0.00 4.30
1706 1716 7.992754 ACAGATAGTCTTCAAAAGCAAGAAT 57.007 32.000 0.00 0.00 31.60 2.40
1726 1738 8.677148 AGTAATAGCAAGACAAAAAGAACAGA 57.323 30.769 0.00 0.00 0.00 3.41
1822 1834 3.002759 CGAGAGAGATAGATGTTGCGACA 59.997 47.826 9.77 9.77 40.71 4.35
1835 1847 1.813178 TCGCTTGAACACGAGAGAGAT 59.187 47.619 0.00 0.00 33.69 2.75
1837 1849 2.181205 GATCGCTTGAACACGAGAGAG 58.819 52.381 0.00 0.00 42.31 3.20
1841 1853 0.635731 GACGATCGCTTGAACACGAG 59.364 55.000 16.60 0.00 42.31 4.18
1842 1854 0.240145 AGACGATCGCTTGAACACGA 59.760 50.000 16.60 0.00 43.33 4.35
1843 1855 1.840741 CTAGACGATCGCTTGAACACG 59.159 52.381 16.60 0.00 0.00 4.49
1859 1871 3.165875 CCACTTGTCCCTGACTTCTAGA 58.834 50.000 0.00 0.00 33.15 2.43
1867 1879 0.843309 TTTGAGCCACTTGTCCCTGA 59.157 50.000 0.00 0.00 0.00 3.86
2163 2182 7.308435 CACATGGAAGGAAAATTAGAGACAAC 58.692 38.462 0.00 0.00 0.00 3.32
2207 2226 9.701098 ATGAATATGCATCAACAATACCATTTC 57.299 29.630 0.19 0.00 0.00 2.17
2266 2287 3.435327 TCCATACAAGTGTCATGCGTTTC 59.565 43.478 0.00 0.00 0.00 2.78
2267 2288 3.188460 GTCCATACAAGTGTCATGCGTTT 59.812 43.478 0.00 0.00 0.00 3.60
2283 2305 6.262496 CGAGATTCAGTTAGTACAGGTCCATA 59.738 42.308 0.00 0.00 0.00 2.74
2294 2316 5.047235 ACCTAGCAAACGAGATTCAGTTAGT 60.047 40.000 0.00 0.00 0.00 2.24
2539 2703 5.009710 ACAGAACAGAATAGAGACGACACAA 59.990 40.000 0.00 0.00 0.00 3.33
2567 2731 5.913137 TTTTAAATTGCACGATCCCAGAT 57.087 34.783 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.