Multiple sequence alignment - TraesCS5A01G507000

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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 TraesCS5A01G507000 chr5A 100.000 3466 0 0 1 3466 671625455 671621990 0.000000e+00 6401.0
1 TraesCS5A01G507000 chr5A 98.161 3481 21 18 1 3466 671754601 671751149 0.000000e+00 6034.0
2 TraesCS5A01G507000 chr5A 97.701 3480 23 11 1 3464 671822590 671819152 0.000000e+00 5930.0
3 TraesCS5A01G507000 chr5A 86.396 713 89 6 1573 2281 641725397 641726105 0.000000e+00 773.0
4 TraesCS5A01G507000 chr5A 89.024 82 7 2 3387 3466 14248707 14248626 2.200000e-17 100.0
5 TraesCS5A01G507000 chr5A 84.884 86 11 2 3381 3464 341145220 341145305 6.160000e-13 86.1
6 TraesCS5A01G507000 chr5A 89.394 66 7 0 3261 3326 473059829 473059764 2.220000e-12 84.2
7 TraesCS5A01G507000 chr4D 93.388 2193 98 27 469 2629 490331463 490329286 0.000000e+00 3203.0
8 TraesCS5A01G507000 chr4D 93.902 2050 89 23 605 2629 490975477 490977515 0.000000e+00 3061.0
9 TraesCS5A01G507000 chr4D 93.347 481 29 3 1 478 490346608 490346128 0.000000e+00 708.0
10 TraesCS5A01G507000 chr4B 93.272 1858 77 26 640 2472 629963561 629961727 0.000000e+00 2695.0
11 TraesCS5A01G507000 chr4B 90.846 579 42 6 67 643 629964883 629964314 0.000000e+00 765.0
12 TraesCS5A01G507000 chr5D 86.396 713 89 6 1573 2281 513926335 513927043 0.000000e+00 773.0
13 TraesCS5A01G507000 chr5D 89.720 107 8 3 2739 2842 506073664 506073558 2.170000e-27 134.0
14 TraesCS5A01G507000 chr5D 90.909 66 6 0 2682 2747 104489971 104489906 4.760000e-14 89.8
15 TraesCS5A01G507000 chr5D 87.500 80 4 5 2688 2765 258648013 258647938 1.710000e-13 87.9
16 TraesCS5A01G507000 chr5B 86.255 713 90 7 1573 2281 644874555 644875263 0.000000e+00 767.0
17 TraesCS5A01G507000 chr5B 89.552 67 7 0 3260 3326 557498296 557498230 6.160000e-13 86.1
18 TraesCS5A01G507000 chr2A 91.509 106 7 1 2739 2844 194551871 194551974 1.000000e-30 145.0
19 TraesCS5A01G507000 chr2A 89.720 107 9 2 2739 2844 194860282 194860387 6.030000e-28 135.0
20 TraesCS5A01G507000 chr2A 94.828 58 3 0 2690 2747 705767368 705767311 1.320000e-14 91.6
21 TraesCS5A01G507000 chr2A 85.057 87 11 2 3381 3466 581150111 581150196 1.710000e-13 87.9
22 TraesCS5A01G507000 chr6A 92.784 97 7 0 2739 2835 17031905 17032001 1.300000e-29 141.0
23 TraesCS5A01G507000 chr6A 83.217 143 15 7 2699 2835 181896990 181896851 4.700000e-24 122.0
24 TraesCS5A01G507000 chr6A 89.231 65 6 1 3261 3325 482190268 482190205 2.870000e-11 80.5
25 TraesCS5A01G507000 chr3A 90.566 106 8 1 2739 2844 561038565 561038668 4.660000e-29 139.0
26 TraesCS5A01G507000 chr3A 96.296 54 2 0 2694 2747 185593043 185592990 4.760000e-14 89.8
27 TraesCS5A01G507000 chr6B 88.991 109 9 3 2739 2844 552507157 552507049 7.810000e-27 132.0
28 TraesCS5A01G507000 chr3D 87.059 85 7 4 3384 3466 23211600 23211682 3.680000e-15 93.5
29 TraesCS5A01G507000 chr3D 84.884 86 11 2 3381 3464 44963153 44963238 6.160000e-13 86.1
30 TraesCS5A01G507000 chr7A 94.828 58 2 1 2691 2747 710762028 710761971 4.760000e-14 89.8
31 TraesCS5A01G507000 chr1B 90.909 66 6 0 3260 3325 571703333 571703398 4.760000e-14 89.8
32 TraesCS5A01G507000 chr1A 86.047 86 9 3 3382 3466 516384018 516383935 4.760000e-14 89.8
33 TraesCS5A01G507000 chr1A 86.420 81 10 1 3384 3463 457944326 457944406 1.710000e-13 87.9
34 TraesCS5A01G507000 chr4A 92.063 63 3 2 2685 2747 591874601 591874541 1.710000e-13 87.9
35 TraesCS5A01G507000 chr6D 75.330 227 31 13 3260 3463 16607655 16607879 6.160000e-13 86.1
36 TraesCS5A01G507000 chr6D 92.593 54 3 1 3256 3309 80108789 80108841 3.710000e-10 76.8
37 TraesCS5A01G507000 chr1D 87.143 70 8 1 3257 3326 180888969 180889037 1.030000e-10 78.7


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 TraesCS5A01G507000 chr5A 671621990 671625455 3465 True 6401 6401 100.000 1 3466 1 chr5A.!!$R3 3465
1 TraesCS5A01G507000 chr5A 671751149 671754601 3452 True 6034 6034 98.161 1 3466 1 chr5A.!!$R4 3465
2 TraesCS5A01G507000 chr5A 671819152 671822590 3438 True 5930 5930 97.701 1 3464 1 chr5A.!!$R5 3463
3 TraesCS5A01G507000 chr5A 641725397 641726105 708 False 773 773 86.396 1573 2281 1 chr5A.!!$F2 708
4 TraesCS5A01G507000 chr4D 490329286 490331463 2177 True 3203 3203 93.388 469 2629 1 chr4D.!!$R1 2160
5 TraesCS5A01G507000 chr4D 490975477 490977515 2038 False 3061 3061 93.902 605 2629 1 chr4D.!!$F1 2024
6 TraesCS5A01G507000 chr4B 629961727 629964883 3156 True 1730 2695 92.059 67 2472 2 chr4B.!!$R1 2405
7 TraesCS5A01G507000 chr5D 513926335 513927043 708 False 773 773 86.396 1573 2281 1 chr5D.!!$F1 708
8 TraesCS5A01G507000 chr5B 644874555 644875263 708 False 767 767 86.255 1573 2281 1 chr5B.!!$F1 708

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
715 1479 2.928116 ACGAAGCTTATGCCTACGTTTC 59.072 45.455 0.0 0.0 38.63 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2849 3652 5.128205 ACAAAAAGGGTGTGTCCTAGTTAC 58.872 41.667 0.0 0.0 35.8 2.5 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
252 253 3.926821 TTGCGGGACTAAAATTTGGAC 57.073 42.857 0.0 0.00 0.00 4.02
354 356 6.183360 GTTAAGCTAACAAGCATTAGGCGTTA 60.183 38.462 0.0 0.00 42.16 3.18
612 618 5.290400 GTGCTACGAAACTAGGGAATGTAAC 59.710 44.000 0.0 0.00 0.00 2.50
626 632 7.849160 AGGGAATGTAACTTTAGGAGAGTAAC 58.151 38.462 0.0 0.00 0.00 2.50
715 1479 2.928116 ACGAAGCTTATGCCTACGTTTC 59.072 45.455 0.0 0.00 38.63 2.78
2817 3620 7.251704 ACATCAAGATTCGTGTGGATATTTC 57.748 36.000 0.0 0.00 0.00 2.17
2849 3652 4.690184 TCACTTTGTGCTTGATATGCAG 57.310 40.909 0.0 0.00 41.41 4.41
3220 4023 6.608002 AGGTAGTTCATAGACCTGGTTCTAAG 59.392 42.308 0.0 1.93 42.13 2.18
3368 4171 7.940178 AGACCCATTTATTCAAAACGTTTTC 57.060 32.000 22.9 7.74 0.00 2.29
3370 4173 6.822442 ACCCATTTATTCAAAACGTTTTCCT 58.178 32.000 22.9 12.69 0.00 3.36
3372 4175 7.771361 ACCCATTTATTCAAAACGTTTTCCTTT 59.229 29.630 22.9 10.89 0.00 3.11
3394 4212 2.773993 TCGTAGACCCATTTTCACCC 57.226 50.000 0.0 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
354 356 1.824230 ACAAACCACGCCATTATGCAT 59.176 42.857 3.79 3.79 0.00 3.96
612 618 9.319143 CAACCATGAATAGTTACTCTCCTAAAG 57.681 37.037 0.00 0.00 0.00 1.85
626 632 7.121168 ACAATGACACCTTACAACCATGAATAG 59.879 37.037 0.00 0.00 0.00 1.73
1193 1978 3.894257 CAGGATATCGTCATGGCGT 57.106 52.632 20.64 9.72 35.06 5.68
2849 3652 5.128205 ACAAAAAGGGTGTGTCCTAGTTAC 58.872 41.667 0.00 0.00 35.80 2.50
3372 4175 3.822167 GGGTGAAAATGGGTCTACGAAAA 59.178 43.478 0.00 0.00 0.00 2.29
3375 4178 2.262637 AGGGTGAAAATGGGTCTACGA 58.737 47.619 0.00 0.00 0.00 3.43
3376 4179 2.747446 CAAGGGTGAAAATGGGTCTACG 59.253 50.000 0.00 0.00 0.00 3.51
3377 4180 4.028993 TCAAGGGTGAAAATGGGTCTAC 57.971 45.455 0.00 0.00 0.00 2.59
3378 4181 4.733077 TTCAAGGGTGAAAATGGGTCTA 57.267 40.909 0.00 0.00 40.87 2.59
3379 4182 3.611025 TTCAAGGGTGAAAATGGGTCT 57.389 42.857 0.00 0.00 40.87 3.85
3381 4184 4.907269 AGAAATTCAAGGGTGAAAATGGGT 59.093 37.500 0.00 0.00 46.66 4.51
3382 4185 5.488262 AGAAATTCAAGGGTGAAAATGGG 57.512 39.130 0.00 0.00 46.66 4.00
3394 4212 8.451687 TGAATATTCAACGCAAGAAATTCAAG 57.548 30.769 15.82 0.00 34.07 3.02


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

AutoCloner maintained by Alex Coulton.