Multiple sequence alignment - TraesCS5D01G527400

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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 TraesCS5D01G527400 chr5D 100.000 2627 0 0 1 2627 544628047 544630673 0.000000e+00 4852.0
1 TraesCS5D01G527400 chr5D 87.351 1842 174 31 2 1795 544620371 544622201 0.000000e+00 2056.0
2 TraesCS5D01G527400 chr5D 75.243 1648 307 68 5 1596 544457641 544459243 0.000000e+00 689.0
3 TraesCS5D01G527400 chr5D 80.740 784 124 18 920 1694 544772524 544773289 1.050000e-163 586.0
4 TraesCS5D01G527400 chr5D 94.706 170 5 1 1886 2051 544666937 544667106 7.210000e-66 261.0
5 TraesCS5D01G527400 chr5D 77.632 456 44 28 2205 2627 403146412 403145982 9.460000e-55 224.0
6 TraesCS5D01G527400 chr4A 95.670 970 30 4 1 959 624619723 624620691 0.000000e+00 1548.0
7 TraesCS5D01G527400 chr4A 94.415 931 45 5 956 1883 624620991 624621917 0.000000e+00 1424.0
8 TraesCS5D01G527400 chr4A 79.365 819 159 10 5 818 624228154 624228967 3.790000e-158 568.0
9 TraesCS5D01G527400 chr4A 78.902 820 162 11 13 827 625200984 625201797 1.780000e-151 545.0
10 TraesCS5D01G527400 chr4A 79.044 816 153 17 12 818 624343005 624343811 6.390000e-151 544.0
11 TraesCS5D01G527400 chr4A 79.545 308 45 9 898 1202 624664021 624664313 1.230000e-48 204.0
12 TraesCS5D01G527400 chr4A 74.468 470 70 31 2103 2534 690137196 690136739 9.730000e-35 158.0
13 TraesCS5D01G527400 chr1A 95.567 970 31 4 1 959 569464135 569463167 0.000000e+00 1543.0
14 TraesCS5D01G527400 chr1A 94.307 931 46 5 956 1883 569462867 569461941 0.000000e+00 1419.0
15 TraesCS5D01G527400 chr1A 80.064 311 44 9 901 1208 569419721 569419426 5.690000e-52 215.0
16 TraesCS5D01G527400 chr1A 84.507 71 7 3 2007 2075 49112270 49112202 1.690000e-07 67.6
17 TraesCS5D01G527400 chr5B 96.016 728 26 3 1901 2627 687028222 687028947 0.000000e+00 1181.0
18 TraesCS5D01G527400 chr5B 90.059 845 72 8 879 1715 687026058 687026898 0.000000e+00 1085.0
19 TraesCS5D01G527400 chr5B 81.137 827 127 19 879 1694 687112892 687112084 1.030000e-178 636.0
20 TraesCS5D01G527400 chr5B 78.954 822 158 15 5 818 686541994 686542808 1.780000e-151 545.0
21 TraesCS5D01G527400 chr5B 75.849 530 74 39 2096 2586 337980551 337980037 1.220000e-53 220.0
22 TraesCS5D01G527400 chr5B 96.850 127 3 1 1776 1902 687026905 687027030 7.370000e-51 211.0
23 TraesCS5D01G527400 chr3D 93.739 559 28 4 2071 2627 611592864 611593417 0.000000e+00 832.0
24 TraesCS5D01G527400 chr3D 82.444 843 139 8 34 870 581536653 581537492 0.000000e+00 728.0
25 TraesCS5D01G527400 chr3D 95.288 191 4 2 1886 2073 611596280 611596468 5.500000e-77 298.0
26 TraesCS5D01G527400 chr7D 93.705 556 29 3 2074 2627 514100426 514099875 0.000000e+00 828.0
27 TraesCS5D01G527400 chr7D 91.250 560 26 7 2074 2627 597544527 597543985 0.000000e+00 741.0
28 TraesCS5D01G527400 chr7D 95.337 193 7 2 1886 2077 514097119 514096928 3.280000e-79 305.0
29 TraesCS5D01G527400 chr6B 91.547 556 27 6 2074 2627 184033672 184033135 0.000000e+00 749.0
30 TraesCS5D01G527400 chr6B 93.506 154 4 1 1920 2073 184030841 184030694 9.460000e-55 224.0
31 TraesCS5D01G527400 chrUn 79.975 814 160 3 12 824 48437712 48438523 4.840000e-167 597.0
32 TraesCS5D01G527400 chr7A 92.670 382 24 3 2249 2627 690567752 690567372 4.940000e-152 547.0
33 TraesCS5D01G527400 chr7A 88.372 172 12 3 1904 2075 690564897 690564734 1.590000e-47 200.0
34 TraesCS5D01G527400 chr2D 94.737 190 8 1 1886 2075 592378164 592377977 7.110000e-76 294.0
35 TraesCS5D01G527400 chr3B 76.862 376 50 11 2127 2470 308425427 308425057 7.470000e-41 178.0
36 TraesCS5D01G527400 chr3A 77.850 307 51 14 2267 2569 749608681 749608974 9.660000e-40 174.0
37 TraesCS5D01G527400 chr6D 92.727 110 6 2 2074 2181 469582874 469582765 9.730000e-35 158.0
38 TraesCS5D01G527400 chr2A 84.722 72 7 3 2007 2076 383877589 383877520 4.690000e-08 69.4


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 TraesCS5D01G527400 chr5D 544628047 544630673 2626 False 4852.000000 4852 100.000000 1 2627 1 chr5D.!!$F3 2626
1 TraesCS5D01G527400 chr5D 544620371 544622201 1830 False 2056.000000 2056 87.351000 2 1795 1 chr5D.!!$F2 1793
2 TraesCS5D01G527400 chr5D 544457641 544459243 1602 False 689.000000 689 75.243000 5 1596 1 chr5D.!!$F1 1591
3 TraesCS5D01G527400 chr5D 544772524 544773289 765 False 586.000000 586 80.740000 920 1694 1 chr5D.!!$F5 774
4 TraesCS5D01G527400 chr4A 624619723 624621917 2194 False 1486.000000 1548 95.042500 1 1883 2 chr4A.!!$F5 1882
5 TraesCS5D01G527400 chr4A 624228154 624228967 813 False 568.000000 568 79.365000 5 818 1 chr4A.!!$F1 813
6 TraesCS5D01G527400 chr4A 625200984 625201797 813 False 545.000000 545 78.902000 13 827 1 chr4A.!!$F4 814
7 TraesCS5D01G527400 chr4A 624343005 624343811 806 False 544.000000 544 79.044000 12 818 1 chr4A.!!$F2 806
8 TraesCS5D01G527400 chr1A 569461941 569464135 2194 True 1481.000000 1543 94.937000 1 1883 2 chr1A.!!$R3 1882
9 TraesCS5D01G527400 chr5B 687026058 687028947 2889 False 825.666667 1181 94.308333 879 2627 3 chr5B.!!$F2 1748
10 TraesCS5D01G527400 chr5B 687112084 687112892 808 True 636.000000 636 81.137000 879 1694 1 chr5B.!!$R2 815
11 TraesCS5D01G527400 chr5B 686541994 686542808 814 False 545.000000 545 78.954000 5 818 1 chr5B.!!$F1 813
12 TraesCS5D01G527400 chr5B 337980037 337980551 514 True 220.000000 220 75.849000 2096 2586 1 chr5B.!!$R1 490
13 TraesCS5D01G527400 chr3D 581536653 581537492 839 False 728.000000 728 82.444000 34 870 1 chr3D.!!$F1 836
14 TraesCS5D01G527400 chr3D 611592864 611596468 3604 False 565.000000 832 94.513500 1886 2627 2 chr3D.!!$F2 741
15 TraesCS5D01G527400 chr7D 597543985 597544527 542 True 741.000000 741 91.250000 2074 2627 1 chr7D.!!$R1 553
16 TraesCS5D01G527400 chr7D 514096928 514100426 3498 True 566.500000 828 94.521000 1886 2627 2 chr7D.!!$R2 741
17 TraesCS5D01G527400 chr6B 184030694 184033672 2978 True 486.500000 749 92.526500 1920 2627 2 chr6B.!!$R1 707
18 TraesCS5D01G527400 chrUn 48437712 48438523 811 False 597.000000 597 79.975000 12 824 1 chrUn.!!$F1 812
19 TraesCS5D01G527400 chr7A 690564734 690567752 3018 True 373.500000 547 90.521000 1904 2627 2 chr7A.!!$R1 723

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
269 281 1.032114 GTTGGCCCACTCATAGGTGC 61.032 60.0 0.0 0.0 36.03 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 3487 1.12478 GCCTCTTAACCTCTCCTCCC 58.875 60.0 0.0 0.0 0.0 4.3 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
162 169 1.464997 GCCTCTCTAACCAAAGCAACG 59.535 52.381 0.00 0.00 0.00 4.10
269 281 1.032114 GTTGGCCCACTCATAGGTGC 61.032 60.000 0.00 0.00 36.03 5.01
462 481 6.094742 ATGTACGCATTGACAAATTGGATACA 59.905 34.615 0.00 0.00 36.97 2.29
718 737 4.081642 CGTCTCTTGGGGAACTAGAATTCA 60.082 45.833 8.44 0.00 0.00 2.57
1069 1433 4.341806 TGTGTGGCATCTTTGTTGAATTCT 59.658 37.500 7.05 0.00 0.00 2.40
1124 1488 5.163663 CGGCACCATGTATTGAAATGTTACT 60.164 40.000 0.00 0.00 0.00 2.24
1214 1585 9.915629 ACATTTAGAGCTTACTATAGATTTCCG 57.084 33.333 6.78 0.00 0.00 4.30
1415 1804 6.920569 ATTTATTGGCTTTAGGTCACTACG 57.079 37.500 0.00 0.00 0.00 3.51
1462 1851 3.432051 CTAGAGCGAGCCCCCAACG 62.432 68.421 0.00 0.00 0.00 4.10
1706 2097 7.624360 TTTAGGCTGTAATAAACTCCATGTG 57.376 36.000 0.00 0.00 0.00 3.21
1913 3498 0.568697 GGGGATTAGGGAGGAGAGGT 59.431 60.000 0.00 0.00 0.00 3.85
1992 3577 4.372656 ACATACGAGGCAGAATCTTAAGC 58.627 43.478 0.00 0.00 0.00 3.09
2066 3651 6.431543 TCTTTCCAGACTATAGATAGGAAGCG 59.568 42.308 6.78 10.36 36.59 4.68
2241 3841 6.704310 AGAAGCATCCTTTTATGTTGCAATT 58.296 32.000 0.59 0.00 35.79 2.32
2260 3873 7.318893 TGCAATTGGAACATATTTTTCGATCA 58.681 30.769 7.72 0.00 39.30 2.92
2599 4240 1.757118 TGCCTAGTACTGCATCTCACC 59.243 52.381 5.39 0.00 31.31 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.672356 GCGCCTCCACTGTGTTGAT 60.672 57.895 7.08 0.00 0.00 2.57
99 106 2.103153 CCTCTATAGGGTTGAGGCCA 57.897 55.000 5.01 0.00 41.76 5.36
162 169 1.025113 GGTTACCCAAGAAGCTCCGC 61.025 60.000 0.00 0.00 0.00 5.54
168 175 2.702592 TATGCCGGTTACCCAAGAAG 57.297 50.000 1.90 0.00 0.00 2.85
269 281 1.745087 ACAAACCACTGTCAGTTGCAG 59.255 47.619 1.67 0.00 39.67 4.41
718 737 3.133691 GACCACACATCGCATCACATAT 58.866 45.455 0.00 0.00 0.00 1.78
924 973 7.352079 TCTCAAGCACAGTGATGAGATTATA 57.648 36.000 24.81 11.00 42.36 0.98
1069 1433 7.175104 AGAAAAGCTATTGTCCATTCAAGGTA 58.825 34.615 0.00 0.00 0.00 3.08
1124 1488 4.943705 GTGCCAAAGAGATCACCTCAATAA 59.056 41.667 0.00 0.00 44.40 1.40
1462 1851 4.081420 TCCTTTCAGAACTATCCTCTGCAC 60.081 45.833 0.00 0.00 40.18 4.57
1706 2097 7.549147 TTCACTACCATATAATACCACCCTC 57.451 40.000 0.00 0.00 0.00 4.30
1895 2287 2.498473 AACCTCTCCTCCCTAATCCC 57.502 55.000 0.00 0.00 0.00 3.85
1902 3487 1.124780 GCCTCTTAACCTCTCCTCCC 58.875 60.000 0.00 0.00 0.00 4.30
1913 3498 1.153249 CGCAATCCCCGCCTCTTAA 60.153 57.895 0.00 0.00 0.00 1.85
1975 3560 1.855360 GACGCTTAAGATTCTGCCTCG 59.145 52.381 6.67 0.00 0.00 4.63
1992 3577 5.023920 CGTTGATTCAATTGAGATTGGACG 58.976 41.667 8.41 11.31 42.36 4.79
2061 3646 5.709966 ACAAAAGATATTGGGAAACGCTTC 58.290 37.500 0.00 0.00 34.56 3.86


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

AutoCloner maintained by Alex Coulton.