Multiple sequence alignment - TraesCS5B01G421000

Loading Multiple Alignment...

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 TraesCS5B01G421000 chr5B 100.000 2678 0 0 1 2678 596826635 596823958 0.000000e+00 4946.0
1 TraesCS5B01G421000 chr5B 98.362 1282 20 1 1398 2678 596223409 596224690 0.000000e+00 2250.0
2 TraesCS5B01G421000 chr5B 96.914 875 25 2 552 1426 596210870 596211742 0.000000e+00 1465.0
3 TraesCS5B01G421000 chr5B 94.374 711 37 3 1969 2678 596393689 596394397 0.000000e+00 1088.0
4 TraesCS5B01G421000 chr5B 94.640 541 20 2 29 561 596205212 596205751 0.000000e+00 830.0
5 TraesCS5B01G421000 chr5B 94.694 245 11 2 1736 1980 596388706 596388948 1.950000e-101 379.0
6 TraesCS5B01G421000 chr5B 76.950 577 119 12 2107 2676 280650159 280649590 1.550000e-82 316.0
7 TraesCS5B01G421000 chr5B 74.936 786 115 51 345 1104 596349466 596350195 4.360000e-73 285.0
8 TraesCS5B01G421000 chr5B 76.103 544 117 13 1121 1656 280651107 280650569 3.400000e-69 272.0
9 TraesCS5B01G421000 chr5B 90.306 196 19 0 1255 1450 596832144 596831949 9.510000e-65 257.0
10 TraesCS5B01G421000 chr5B 74.919 618 109 32 141 740 596833337 596832748 9.580000e-60 241.0
11 TraesCS5B01G421000 chr5B 89.655 174 18 0 1277 1450 596199404 596199577 3.470000e-54 222.0
12 TraesCS5B01G421000 chr5B 87.179 156 20 0 1295 1450 596204059 596204214 7.620000e-41 178.0
13 TraesCS5B01G421000 chr5B 79.147 211 40 4 1707 1915 280650559 280650351 2.780000e-30 143.0
14 TraesCS5B01G421000 chr5B 90.278 72 7 0 1033 1104 596723391 596723320 7.890000e-16 95.3
15 TraesCS5B01G421000 chr5B 96.000 50 2 0 100 149 596205234 596205283 6.140000e-12 82.4
16 TraesCS5B01G421000 chr5B 96.000 50 2 0 51 100 596826536 596826487 6.140000e-12 82.4
17 TraesCS5B01G421000 chr5B 96.000 50 2 0 100 149 596826585 596826536 6.140000e-12 82.4
18 TraesCS5B01G421000 chr5D 95.577 2600 87 10 100 2678 485062107 485059515 0.000000e+00 4139.0
19 TraesCS5B01G421000 chr5D 79.339 968 139 32 538 1450 485092586 485091625 8.140000e-175 623.0
20 TraesCS5B01G421000 chr5D 76.481 540 111 11 2143 2676 246012369 246011840 2.030000e-71 279.0
21 TraesCS5B01G421000 chr5D 93.056 72 5 0 29 100 485062129 485062058 3.650000e-19 106.0
22 TraesCS5B01G421000 chr5D 81.148 122 23 0 1829 1950 501365809 501365688 6.100000e-17 99.0
23 TraesCS5B01G421000 chr5A 96.642 1995 52 6 685 2678 606354318 606352338 0.000000e+00 3299.0
24 TraesCS5B01G421000 chr5A 92.841 447 23 3 100 541 606354980 606354538 8.080000e-180 640.0
25 TraesCS5B01G421000 chr5A 76.083 577 123 13 2107 2676 329994849 329994281 1.210000e-73 287.0
26 TraesCS5B01G421000 chr5A 95.614 114 4 1 538 651 606354425 606354313 5.890000e-42 182.0
27 TraesCS5B01G421000 chr5A 94.444 72 4 0 29 100 606355002 606354931 7.840000e-21 111.0
28 TraesCS5B01G421000 chr5A 94.340 53 3 0 48 100 606362698 606362646 6.140000e-12 82.4
29 TraesCS5B01G421000 chr5A 90.909 55 5 0 100 154 606362695 606362641 1.030000e-09 75.0
30 TraesCS5B01G421000 chr4A 75.000 228 55 2 1831 2057 740603553 740603327 1.310000e-18 104.0


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 TraesCS5B01G421000 chr5B 596823958 596826635 2677 True 1703.600000 4946 97.333333 1 2678 3 chr5B.!!$R3 2677
1 TraesCS5B01G421000 chr5B 596223409 596224690 1281 False 2250.000000 2250 98.362000 1398 2678 1 chr5B.!!$F3 1280
2 TraesCS5B01G421000 chr5B 596210870 596211742 872 False 1465.000000 1465 96.914000 552 1426 1 chr5B.!!$F2 874
3 TraesCS5B01G421000 chr5B 596393689 596394397 708 False 1088.000000 1088 94.374000 1969 2678 1 chr5B.!!$F6 709
4 TraesCS5B01G421000 chr5B 596204059 596205751 1692 False 363.466667 830 92.606333 29 1450 3 chr5B.!!$F7 1421
5 TraesCS5B01G421000 chr5B 596349466 596350195 729 False 285.000000 285 74.936000 345 1104 1 chr5B.!!$F4 759
6 TraesCS5B01G421000 chr5B 596831949 596833337 1388 True 249.000000 257 82.612500 141 1450 2 chr5B.!!$R4 1309
7 TraesCS5B01G421000 chr5B 280649590 280651107 1517 True 243.666667 316 77.400000 1121 2676 3 chr5B.!!$R2 1555
8 TraesCS5B01G421000 chr5D 485059515 485062129 2614 True 2122.500000 4139 94.316500 29 2678 2 chr5D.!!$R4 2649
9 TraesCS5B01G421000 chr5D 485091625 485092586 961 True 623.000000 623 79.339000 538 1450 1 chr5D.!!$R2 912
10 TraesCS5B01G421000 chr5D 246011840 246012369 529 True 279.000000 279 76.481000 2143 2676 1 chr5D.!!$R1 533
11 TraesCS5B01G421000 chr5A 606352338 606355002 2664 True 1058.000000 3299 94.885250 29 2678 4 chr5A.!!$R2 2649
12 TraesCS5B01G421000 chr5A 329994281 329994849 568 True 287.000000 287 76.083000 2107 2676 1 chr5A.!!$R1 569

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
446 1591 0.318699 CTTCGCCACTGTCAAGACGA 60.319 55.0 0.0 0.0 0.0 4.20 F
865 2478 1.551452 AAGGAACGAGAGGGACAGAG 58.449 55.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 2928 1.534235 AAGTGTCCCTCTCAGCCGT 60.534 57.895 0.0 0.0 0.0 5.68 R
1958 3774 4.039488 ACGGAACCAGATAGTGTGTTGTTA 59.961 41.667 0.0 0.0 0.0 2.41 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
163 1289 1.271840 TTAATGGCCTCCACCGCTCT 61.272 55.000 3.32 0.0 35.80 4.09
216 1342 4.090930 CACAAAATGCAACATAAGCTGAGC 59.909 41.667 0.00 0.0 0.00 4.26
335 1466 3.181491 GGTGTTAACAGCTCAAAACTGCA 60.181 43.478 26.48 0.0 40.88 4.41
446 1591 0.318699 CTTCGCCACTGTCAAGACGA 60.319 55.000 0.00 0.0 0.00 4.20
476 1626 4.600111 AGTGGACATAAGGAAAGTACCCAA 59.400 41.667 0.00 0.0 0.00 4.12
638 1914 1.902508 CTTTGCACCAGGTCCTCTAGA 59.097 52.381 0.00 0.0 0.00 2.43
753 2030 6.538945 ACATGTTTGGGTTCTGTAACTTTT 57.461 33.333 0.00 0.0 35.81 2.27
865 2478 1.551452 AAGGAACGAGAGGGACAGAG 58.449 55.000 0.00 0.0 0.00 3.35
1214 2874 2.359850 GCAAGGCATCCGGTGTGA 60.360 61.111 12.69 0.0 0.00 3.58
1580 3251 5.285401 TGGTCCTATCCCTTGTGAAATAGA 58.715 41.667 0.00 0.0 0.00 1.98
1785 3457 7.559897 GTCCCATTCCCAAAGATATAGTGAAAA 59.440 37.037 0.00 0.0 0.00 2.29
1866 3538 6.911308 AGCAATATAGGTAACCTGACCAAAT 58.089 36.000 0.00 0.0 42.47 2.32
1958 3774 5.505181 TTTTAGAGGACTTGAGGCTCAAT 57.495 39.130 28.67 18.7 35.59 2.57
2051 3867 3.207778 CCGTAACCAACTTTCTGGACAA 58.792 45.455 0.00 0.0 38.96 3.18
2453 4269 1.275573 GGAGGCCGACTACAGTTTCTT 59.724 52.381 0.00 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.394767 TGCTTCTAAATTATGACATGCTTCTAA 57.605 29.630 0.00 0.00 0.00 2.10
10 11 8.962884 TGCTTCTAAATTATGACATGCTTCTA 57.037 30.769 0.00 0.00 0.00 2.10
11 12 7.870509 TGCTTCTAAATTATGACATGCTTCT 57.129 32.000 0.00 0.00 0.00 2.85
12 13 8.133627 ACATGCTTCTAAATTATGACATGCTTC 58.866 33.333 0.00 0.00 37.71 3.86
13 14 8.004087 ACATGCTTCTAAATTATGACATGCTT 57.996 30.769 0.00 0.00 37.71 3.91
14 15 7.283807 TGACATGCTTCTAAATTATGACATGCT 59.716 33.333 0.00 0.00 37.71 3.79
16 17 9.394477 CATGACATGCTTCTAAATTATGACATG 57.606 33.333 1.71 0.00 41.53 3.21
18 19 8.510243 ACATGACATGCTTCTAAATTATGACA 57.490 30.769 15.49 0.00 0.00 3.58
19 20 9.443283 GAACATGACATGCTTCTAAATTATGAC 57.557 33.333 15.49 0.00 0.00 3.06
20 21 9.399797 AGAACATGACATGCTTCTAAATTATGA 57.600 29.630 21.58 0.00 32.67 2.15
22 23 9.399797 TCAGAACATGACATGCTTCTAAATTAT 57.600 29.630 22.06 3.77 32.94 1.28
24 25 7.692460 TCAGAACATGACATGCTTCTAAATT 57.308 32.000 22.06 7.74 32.94 1.82
26 27 7.692460 AATCAGAACATGACATGCTTCTAAA 57.308 32.000 22.06 16.85 41.91 1.85
27 28 8.791327 TTAATCAGAACATGACATGCTTCTAA 57.209 30.769 22.06 14.69 41.91 2.10
118 1244 1.405872 AGTGGTTACTGGTCACGTCA 58.594 50.000 0.00 0.00 35.34 4.35
163 1289 3.012274 TCTTCCTATTTGGCAAATGGGGA 59.988 43.478 38.63 33.84 46.25 4.81
446 1591 4.974645 TTCCTTATGTCCACTGTTCTGT 57.025 40.909 0.00 0.00 0.00 3.41
476 1626 2.742372 GCAATGTGGCTCGTCGGT 60.742 61.111 0.00 0.00 0.00 4.69
638 1914 1.279271 AGAAGATTACAAGCACGCCCT 59.721 47.619 0.00 0.00 0.00 5.19
753 2030 2.612212 GACGCCTGTTCTTTCAAAGTCA 59.388 45.455 0.00 0.00 0.00 3.41
865 2478 1.490910 CTGATTAACCACCCCTCCCTC 59.509 57.143 0.00 0.00 0.00 4.30
1257 2928 1.534235 AAGTGTCCCTCTCAGCCGT 60.534 57.895 0.00 0.00 0.00 5.68
1785 3457 8.691661 ATGTCTAAGTGTTGTAGGTTGAAAAT 57.308 30.769 0.00 0.00 0.00 1.82
1866 3538 6.691255 ATGGTAAAGGTACAAGGTAGTGAA 57.309 37.500 0.00 0.00 31.21 3.18
1958 3774 4.039488 ACGGAACCAGATAGTGTGTTGTTA 59.961 41.667 0.00 0.00 0.00 2.41
2051 3867 6.296374 CCAAATATCCCAAAACCAGTGGAATT 60.296 38.462 18.40 7.69 38.54 2.17
2300 4116 7.070074 TGGTTGAAATTAAGGTTTAAGAAGGCA 59.930 33.333 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.