Multiple sequence alignment - TraesCS7A01G214800

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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 TraesCS7A01G214800 chr7A 100.000 2624 0 0 1 2624 180170045 180167422 0.000000e+00 4846.0
1 TraesCS7A01G214800 chr7A 91.874 2658 130 33 1 2616 179910474 179907861 0.000000e+00 3633.0
2 TraesCS7A01G214800 chr7A 96.589 1466 29 2 1 1445 180380086 180378621 0.000000e+00 2410.0
3 TraesCS7A01G214800 chr7A 94.370 1190 45 10 1445 2624 180375157 180373980 0.000000e+00 1807.0
4 TraesCS7A01G214800 chr7A 90.304 1186 93 11 1445 2620 179602219 179601046 0.000000e+00 1533.0
5 TraesCS7A01G214800 chr7A 93.923 757 38 1 790 1538 179602933 179602177 0.000000e+00 1136.0
6 TraesCS7A01G214800 chr7A 92.639 720 38 7 1 720 179603698 179602994 0.000000e+00 1022.0
7 TraesCS7A01G214800 chr7A 85.493 517 71 2 1460 1976 178912968 178912456 1.070000e-148 536.0
8 TraesCS7A01G214800 chr7A 78.321 655 85 38 1968 2605 178903923 178903309 1.150000e-98 370.0
9 TraesCS7A01G214800 chr7D 92.125 1562 77 12 1 1538 176580151 176578612 0.000000e+00 2161.0
10 TraesCS7A01G214800 chr7D 87.140 1182 103 26 1445 2620 176578654 176577516 0.000000e+00 1295.0
11 TraesCS7A01G214800 chr7D 90.761 736 53 9 1 726 176471536 176470806 0.000000e+00 968.0
12 TraesCS7A01G214800 chr7D 79.949 1177 161 29 1445 2592 176443504 176442374 0.000000e+00 797.0
13 TraesCS7A01G214800 chr7D 89.765 596 55 3 949 1538 176444057 176443462 0.000000e+00 758.0
14 TraesCS7A01G214800 chr7D 84.035 451 40 13 2 422 176444836 176444388 3.140000e-109 405.0
15 TraesCS7A01G214800 chr7D 78.947 304 15 17 696 950 176444390 176444087 7.520000e-36 161.0
16 TraesCS7A01G214800 chr7B 93.392 1256 72 6 962 2208 143055776 143054523 0.000000e+00 1849.0
17 TraesCS7A01G214800 chr7B 88.384 1188 94 18 1445 2620 142779649 142778494 0.000000e+00 1389.0
18 TraesCS7A01G214800 chr7B 89.525 926 58 17 40 948 142867687 142866784 0.000000e+00 1136.0
19 TraesCS7A01G214800 chr7B 89.502 924 57 17 43 948 143056729 143055828 0.000000e+00 1133.0
20 TraesCS7A01G214800 chr7B 90.956 774 56 9 1445 2208 142866198 142865429 0.000000e+00 1029.0
21 TraesCS7A01G214800 chr7B 95.147 577 28 0 962 1538 142866732 142866156 0.000000e+00 911.0
22 TraesCS7A01G214800 chr7B 89.091 715 48 12 253 948 142781432 142780729 0.000000e+00 861.0
23 TraesCS7A01G214800 chr7B 93.517 509 25 2 962 1462 142780677 142780169 0.000000e+00 750.0
24 TraesCS7A01G214800 chr7B 89.430 596 57 3 949 1538 142284088 142283493 0.000000e+00 747.0
25 TraesCS7A01G214800 chr7B 87.918 538 53 5 1445 1976 142283535 142283004 7.980000e-175 623.0
26 TraesCS7A01G214800 chr7B 85.859 297 39 2 2282 2575 142282770 142282474 1.960000e-81 313.0
27 TraesCS7A01G214800 chr7B 93.023 215 13 2 1 215 142781638 142781426 1.960000e-81 313.0
28 TraesCS7A01G214800 chr7B 79.402 301 16 18 696 950 142284418 142284118 1.250000e-38 171.0
29 TraesCS7A01G214800 chr7B 97.297 37 1 0 1 37 142870837 142870801 2.180000e-06 63.9
30 TraesCS7A01G214800 chr2B 90.050 201 19 1 417 616 121646959 121646759 2.590000e-65 259.0
31 TraesCS7A01G214800 chr2D 91.667 96 7 1 606 701 610576039 610576133 5.890000e-27 132.0


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 TraesCS7A01G214800 chr7A 180167422 180170045 2623 True 4846.000000 4846 100.000000 1 2624 1 chr7A.!!$R4 2623
1 TraesCS7A01G214800 chr7A 179907861 179910474 2613 True 3633.000000 3633 91.874000 1 2616 1 chr7A.!!$R3 2615
2 TraesCS7A01G214800 chr7A 180373980 180380086 6106 True 2108.500000 2410 95.479500 1 2624 2 chr7A.!!$R6 2623
3 TraesCS7A01G214800 chr7A 179601046 179603698 2652 True 1230.333333 1533 92.288667 1 2620 3 chr7A.!!$R5 2619
4 TraesCS7A01G214800 chr7A 178912456 178912968 512 True 536.000000 536 85.493000 1460 1976 1 chr7A.!!$R2 516
5 TraesCS7A01G214800 chr7A 178903309 178903923 614 True 370.000000 370 78.321000 1968 2605 1 chr7A.!!$R1 637
6 TraesCS7A01G214800 chr7D 176577516 176580151 2635 True 1728.000000 2161 89.632500 1 2620 2 chr7D.!!$R3 2619
7 TraesCS7A01G214800 chr7D 176470806 176471536 730 True 968.000000 968 90.761000 1 726 1 chr7D.!!$R1 725
8 TraesCS7A01G214800 chr7D 176442374 176444836 2462 True 530.250000 797 83.174000 2 2592 4 chr7D.!!$R2 2590
9 TraesCS7A01G214800 chr7B 143054523 143056729 2206 True 1491.000000 1849 91.447000 43 2208 2 chr7B.!!$R4 2165
10 TraesCS7A01G214800 chr7B 142778494 142781638 3144 True 828.250000 1389 91.003750 1 2620 4 chr7B.!!$R2 2619
11 TraesCS7A01G214800 chr7B 142865429 142870837 5408 True 784.975000 1136 93.231250 1 2208 4 chr7B.!!$R3 2207
12 TraesCS7A01G214800 chr7B 142282474 142284418 1944 True 463.500000 747 85.652250 696 2575 4 chr7B.!!$R1 1879

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
683 3850 0.519077 GCATTTGCTATAGCCTCCGC 59.481 55.0 21.84 14.97 41.18 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 9717 0.515127 TTTGCTAACCGACGCACATG 59.485 50.0 0.0 0.0 35.6 3.21 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
520 3670 1.679680 GCATGTCATAGTTGCCTGCAT 59.320 47.619 0.00 0.00 0.00 3.96
524 3674 4.220693 TGTCATAGTTGCCTGCATAAGT 57.779 40.909 0.00 0.00 0.00 2.24
683 3850 0.519077 GCATTTGCTATAGCCTCCGC 59.481 55.000 21.84 14.97 41.18 5.54
1005 4275 0.843984 GCCTAACCCTAGCCATGGAA 59.156 55.000 18.40 0.69 0.00 3.53
1199 4469 1.135373 GTCGGAGTTCATCAGCTTCGA 60.135 52.381 0.00 0.00 40.05 3.71
1388 4658 4.873129 CTACAGCCGCGCCGTGAT 62.873 66.667 0.00 0.00 0.00 3.06
1752 8990 2.111162 CGAGGAGAGCTCGTCCAAT 58.889 57.895 24.96 12.03 40.32 3.16
1895 9137 6.018262 GCATCCTGCGTAGTGTAATAATTTGA 60.018 38.462 0.00 0.00 31.71 2.69
1925 9184 1.733402 CGGCCATGGTTTGTGTGTGT 61.733 55.000 14.67 0.00 0.00 3.72
1949 9208 3.813443 ACTGCTTATCTAATGTGGGCTG 58.187 45.455 0.00 0.00 0.00 4.85
2085 9386 5.625568 ACTCATCATTGATGATCAGGTGA 57.374 39.130 25.49 12.77 46.16 4.02
2150 9456 9.261180 GTATTATTGTGATGCACACTGTAGTAT 57.739 33.333 16.70 8.24 44.47 2.12
2153 9459 7.719778 ATTGTGATGCACACTGTAGTATATG 57.280 36.000 16.70 0.00 44.47 1.78
2228 9590 6.087028 GTCATACGATCTCTCACGCTTAAATC 59.913 42.308 0.00 0.00 0.00 2.17
2238 9600 5.742453 TCTCACGCTTAAATCGAAGTCATAC 59.258 40.000 0.00 0.00 0.00 2.39
2239 9601 5.647589 TCACGCTTAAATCGAAGTCATACT 58.352 37.500 0.00 0.00 0.00 2.12
2240 9602 5.742453 TCACGCTTAAATCGAAGTCATACTC 59.258 40.000 0.00 0.00 0.00 2.59
2241 9603 5.744345 CACGCTTAAATCGAAGTCATACTCT 59.256 40.000 0.00 0.00 0.00 3.24
2242 9604 6.910972 CACGCTTAAATCGAAGTCATACTCTA 59.089 38.462 0.00 0.00 0.00 2.43
2243 9605 7.591795 CACGCTTAAATCGAAGTCATACTCTAT 59.408 37.037 0.00 0.00 0.00 1.98
2244 9606 8.136165 ACGCTTAAATCGAAGTCATACTCTATT 58.864 33.333 0.00 0.00 0.00 1.73
2245 9607 8.969267 CGCTTAAATCGAAGTCATACTCTATTT 58.031 33.333 0.00 0.00 0.00 1.40
2250 9612 9.959749 AAATCGAAGTCATACTCTATTTCTCTC 57.040 33.333 0.00 0.00 0.00 3.20
2251 9613 8.918202 ATCGAAGTCATACTCTATTTCTCTCT 57.082 34.615 0.00 0.00 0.00 3.10
2252 9614 8.373048 TCGAAGTCATACTCTATTTCTCTCTC 57.627 38.462 0.00 0.00 0.00 3.20
2253 9615 8.208224 TCGAAGTCATACTCTATTTCTCTCTCT 58.792 37.037 0.00 0.00 0.00 3.10
2254 9616 8.495949 CGAAGTCATACTCTATTTCTCTCTCTC 58.504 40.741 0.00 0.00 0.00 3.20
2255 9617 9.561069 GAAGTCATACTCTATTTCTCTCTCTCT 57.439 37.037 0.00 0.00 0.00 3.10
2256 9618 9.561069 AAGTCATACTCTATTTCTCTCTCTCTC 57.439 37.037 0.00 0.00 0.00 3.20
2257 9619 8.938883 AGTCATACTCTATTTCTCTCTCTCTCT 58.061 37.037 0.00 0.00 0.00 3.10
2329 9717 2.603110 CTGTCGCCACATGTACATACAC 59.397 50.000 8.32 0.00 39.30 2.90
2366 9754 4.022589 AGCAAAGTGGTCATGAATGAGTTG 60.023 41.667 0.00 1.20 37.51 3.16
2378 9766 3.055458 TGAATGAGTTGGGAGCGACATAA 60.055 43.478 0.00 0.00 0.00 1.90
2416 9805 2.390599 CGGTGGTGACATCTTGCGG 61.391 63.158 0.00 0.00 46.14 5.69
2425 9815 0.758734 ACATCTTGCGGGCATAGCTA 59.241 50.000 0.00 0.00 35.28 3.32
2552 9950 1.318576 ACTTCCCTTTCAGCAAACCG 58.681 50.000 0.00 0.00 0.00 4.44
2563 9961 1.105457 AGCAAACCGCACATGCATAT 58.895 45.000 0.00 0.00 46.13 1.78
2620 10018 4.022242 CAGCAATACTACAGGTACGGCTAT 60.022 45.833 0.00 0.00 39.51 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
683 3850 0.748450 CACATTAAGGGCATGGGCTG 59.252 55.000 0.00 0.00 40.87 4.85
1882 9124 6.408428 GGATCGACACGTCAAATTATTACAC 58.592 40.000 0.00 0.00 0.00 2.90
1895 9137 3.458163 ATGGCCGGATCGACACGT 61.458 61.111 5.05 0.00 0.00 4.49
1925 9184 4.408921 AGCCCACATTAGATAAGCAGTACA 59.591 41.667 0.00 0.00 0.00 2.90
1949 9208 6.041069 AGCAGTACATGAATTACTAGAGGACC 59.959 42.308 0.00 0.00 0.00 4.46
2093 9395 8.822855 GTCGGAAACCTTTTTGAAAATAAATGT 58.177 29.630 0.00 0.00 0.00 2.71
2150 9456 8.773645 CATACGAAGGTCTAATTTGCAATCATA 58.226 33.333 0.00 0.00 0.00 2.15
2153 9459 7.246674 TCATACGAAGGTCTAATTTGCAATC 57.753 36.000 0.00 0.00 0.00 2.67
2228 9590 8.378172 AGAGAGAGAAATAGAGTATGACTTCG 57.622 38.462 0.00 0.00 0.00 3.79
2329 9717 0.515127 TTTGCTAACCGACGCACATG 59.485 50.000 0.00 0.00 35.60 3.21
2366 9754 4.119442 TCAAAGTACTTATGTCGCTCCC 57.881 45.455 8.92 0.00 0.00 4.30
2416 9805 4.518249 ACACTTTCCTTTCTAGCTATGCC 58.482 43.478 0.00 0.00 0.00 4.40
2425 9815 4.080299 ACAAGGTCAGACACTTTCCTTTCT 60.080 41.667 2.17 0.00 36.52 2.52
2552 9950 0.824595 TCCCCAGCATATGCATGTGC 60.825 55.000 33.67 33.67 44.07 4.57
2563 9961 3.305950 CGTTGATTCATTTTTCCCCAGCA 60.306 43.478 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.