Multiple sequence alignment - TraesCS5D01G133000

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 TraesCS5D01G133000 chr5D 100.000 2495 0 0 1 2495 212253320 212250826 0.000000e+00 4608.0
1 TraesCS5D01G133000 chr5A 97.804 1548 31 3 135 1680 275261212 275259666 0.000000e+00 2667.0
2 TraesCS5D01G133000 chr5A 89.225 826 68 14 1678 2495 275259365 275258553 0.000000e+00 1013.0
3 TraesCS5D01G133000 chr5A 98.305 118 2 0 1 118 275261403 275261286 9.040000e-50 207.0
4 TraesCS5D01G133000 chr2D 84.985 686 89 12 1819 2495 82905256 82905936 0.000000e+00 684.0
5 TraesCS5D01G133000 chr2D 86.348 293 27 7 1818 2098 459816336 459816045 8.670000e-80 307.0
6 TraesCS5D01G133000 chr2D 100.000 28 0 0 130 157 62277712 62277739 4.000000e-03 52.8
7 TraesCS5D01G133000 chr6B 78.147 1112 201 22 404 1497 719386592 719387679 0.000000e+00 669.0
8 TraesCS5D01G133000 chr7B 77.527 1108 219 20 404 1496 154144525 154145617 7.520000e-180 640.0
9 TraesCS5D01G133000 chr7B 81.338 284 35 12 1819 2098 70826283 70826014 5.400000e-52 215.0
10 TraesCS5D01G133000 chr7A 78.182 990 189 18 519 1496 191660726 191661700 7.630000e-170 606.0
11 TraesCS5D01G133000 chr1A 85.922 412 53 4 2074 2484 505557571 505557978 3.810000e-118 435.0
12 TraesCS5D01G133000 chr1A 83.726 424 58 9 2080 2495 559523674 559524094 8.370000e-105 390.0
13 TraesCS5D01G133000 chr3D 85.476 420 56 5 2080 2495 553398314 553397896 1.370000e-117 433.0
14 TraesCS5D01G133000 chr3D 84.709 412 53 9 2086 2495 507776041 507775638 1.070000e-108 403.0
15 TraesCS5D01G133000 chr3D 82.332 283 26 10 1819 2098 553398590 553398329 8.980000e-55 224.0
16 TraesCS5D01G133000 chr5B 84.652 417 59 5 2080 2495 51865070 51864658 6.420000e-111 411.0
17 TraesCS5D01G133000 chr5B 82.118 425 68 6 2074 2495 660348156 660348575 8.490000e-95 357.0
18 TraesCS5D01G133000 chr5B 84.444 225 19 6 1827 2048 51627141 51626930 9.040000e-50 207.0
19 TraesCS5D01G133000 chr5B 93.525 139 8 1 1648 1786 226331474 226331337 3.250000e-49 206.0
20 TraesCS5D01G133000 chr5B 82.906 234 25 5 1818 2048 51627532 51627311 1.960000e-46 196.0
21 TraesCS5D01G133000 chr2B 84.412 417 60 5 2080 2495 404182230 404181818 2.990000e-109 405.0
22 TraesCS5D01G133000 chr2B 82.918 281 37 9 1822 2098 635201435 635201162 2.480000e-60 243.0
23 TraesCS5D01G133000 chr2B 85.606 132 18 1 1649 1779 512928436 512928305 1.200000e-28 137.0
24 TraesCS5D01G133000 chr1D 84.859 284 35 6 1819 2098 456131576 456131297 1.890000e-71 279.0


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 TraesCS5D01G133000 chr5D 212250826 212253320 2494 True 4608.000000 4608 100.000000 1 2495 1 chr5D.!!$R1 2494
1 TraesCS5D01G133000 chr5A 275258553 275261403 2850 True 1295.666667 2667 95.111333 1 2495 3 chr5A.!!$R1 2494
2 TraesCS5D01G133000 chr2D 82905256 82905936 680 False 684.000000 684 84.985000 1819 2495 1 chr2D.!!$F2 676
3 TraesCS5D01G133000 chr6B 719386592 719387679 1087 False 669.000000 669 78.147000 404 1497 1 chr6B.!!$F1 1093
4 TraesCS5D01G133000 chr7B 154144525 154145617 1092 False 640.000000 640 77.527000 404 1496 1 chr7B.!!$F1 1092
5 TraesCS5D01G133000 chr7A 191660726 191661700 974 False 606.000000 606 78.182000 519 1496 1 chr7A.!!$F1 977
6 TraesCS5D01G133000 chr3D 553397896 553398590 694 True 328.500000 433 83.904000 1819 2495 2 chr3D.!!$R2 676
7 TraesCS5D01G133000 chr5B 51626930 51627532 602 True 201.500000 207 83.675000 1818 2048 2 chr5B.!!$R3 230

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
474 539 1.208358 CGACACGCTGGAGTTCGTA 59.792 57.895 0.0 0.0 37.14 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2985 0.108615 GCTCTGGCTCGCTCAACTAA 60.109 55.0 0.0 0.0 35.22 2.24 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
70 71 3.308014 AAGGCTCGAGTCAGCTGCC 62.308 63.158 20.97 10.80 43.52 4.85
84 85 1.884464 CTGCCATGATCCCGACACG 60.884 63.158 0.00 0.00 0.00 4.49
127 188 7.008941 AGAACATATTACCCTACTACCGATGT 58.991 38.462 0.00 0.00 0.00 3.06
128 189 7.508296 AGAACATATTACCCTACTACCGATGTT 59.492 37.037 0.00 0.00 37.62 2.71
129 190 8.710749 AACATATTACCCTACTACCGATGTTA 57.289 34.615 0.00 0.00 34.23 2.41
130 191 8.890410 ACATATTACCCTACTACCGATGTTAT 57.110 34.615 0.00 0.00 0.00 1.89
133 194 3.152341 ACCCTACTACCGATGTTATCCG 58.848 50.000 0.00 0.00 0.00 4.18
141 202 1.257936 CCGATGTTATCCGTTTGAGCG 59.742 52.381 0.00 0.00 0.00 5.03
167 228 8.658499 ACAGTTATTTCCGGATACTGAATTAC 57.342 34.615 28.48 18.94 39.68 1.89
219 281 1.507141 CGCCGTCTGGAAACAAGCTT 61.507 55.000 0.00 0.00 42.06 3.74
358 420 4.001618 TCTTCAAACGACATGGTCATGA 57.998 40.909 16.77 0.00 41.20 3.07
376 438 1.305297 ACTCCAGCTCCCGACATCA 60.305 57.895 0.00 0.00 0.00 3.07
380 442 2.685017 AGCTCCCGACATCAGCCA 60.685 61.111 0.00 0.00 33.28 4.75
474 539 1.208358 CGACACGCTGGAGTTCGTA 59.792 57.895 0.00 0.00 37.14 3.43
792 866 1.515521 CGTTCCCCAGCTTCGCTTTT 61.516 55.000 0.00 0.00 36.40 2.27
1292 1369 3.270027 CAGCGGTGTCCTTCATATTCAA 58.730 45.455 6.41 0.00 0.00 2.69
1293 1370 3.689161 CAGCGGTGTCCTTCATATTCAAA 59.311 43.478 6.41 0.00 0.00 2.69
1508 1585 7.364522 TCAGTTGCTGATAGTTATGTTGAAC 57.635 36.000 0.00 0.00 35.39 3.18
1684 2065 1.921230 GCAAGAACTAGCTACTGCGAC 59.079 52.381 0.00 0.00 45.42 5.19
1730 2111 8.806429 TGGTTGATGTTGAAGATATGTATGTT 57.194 30.769 0.00 0.00 0.00 2.71
1756 2137 7.188468 TCCTTTTGATTTGCAAACTTTATGC 57.812 32.000 15.41 0.00 45.64 3.14
1768 2149 5.615325 GCAAACTTTATGCAAAATGTGAGGC 60.615 40.000 0.00 0.00 43.29 4.70
1786 2167 9.860898 ATGTGAGGCTTTTCTTTGTATAAAATC 57.139 29.630 0.00 0.00 0.00 2.17
1787 2168 9.077885 TGTGAGGCTTTTCTTTGTATAAAATCT 57.922 29.630 0.00 0.00 0.00 2.40
1859 2279 2.632377 CCTTGAATTGAAGCGCTCCTA 58.368 47.619 12.06 0.00 0.00 2.94
1918 2339 5.450066 GCGTAAGTGTGTGTTGTTTAGTTTC 59.550 40.000 0.00 0.00 41.68 2.78
2070 2601 5.644636 TGGGGATATTTGTAAAGTTCACGTC 59.355 40.000 0.00 0.00 0.00 4.34
2256 2955 1.896660 GCAGTGGGGTGAGCGAAAA 60.897 57.895 0.00 0.00 0.00 2.29
2285 2985 2.284995 GTGAGAGGGGCAGGGAGT 60.285 66.667 0.00 0.00 0.00 3.85
2299 3000 0.460459 GGGAGTTAGTTGAGCGAGCC 60.460 60.000 0.00 0.00 0.00 4.70
2332 3033 2.018644 GCCGACCCATGTGAATGTCAT 61.019 52.381 0.00 0.00 0.00 3.06
2362 3063 7.560368 ACAATTCCATGGTTTTAGTGTGAAAA 58.440 30.769 12.58 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.139989 GTATGCGTGTCGGGATCATG 58.860 55.000 0.00 0.00 0.00 3.07
84 85 6.896021 TGTTCTATACTCCTACCTGTATGC 57.104 41.667 0.00 0.00 32.42 3.14
127 188 2.736144 ACTGTCGCTCAAACGGATAA 57.264 45.000 0.00 0.00 0.00 1.75
128 189 2.736144 AACTGTCGCTCAAACGGATA 57.264 45.000 0.00 0.00 0.00 2.59
129 190 2.736144 TAACTGTCGCTCAAACGGAT 57.264 45.000 0.00 0.00 0.00 4.18
130 191 2.736144 ATAACTGTCGCTCAAACGGA 57.264 45.000 0.00 0.00 0.00 4.69
133 194 3.424433 CCGGAAATAACTGTCGCTCAAAC 60.424 47.826 0.00 0.00 0.00 2.93
141 202 7.787725 AATTCAGTATCCGGAAATAACTGTC 57.212 36.000 25.93 6.72 0.00 3.51
167 228 2.658285 GTTTGCAAGCAGTGTCATCAG 58.342 47.619 8.58 0.00 0.00 2.90
219 281 2.124193 CAAGCGGGATGGATGGCA 60.124 61.111 0.00 0.00 0.00 4.92
333 395 1.531149 ACCATGTCGTTTGAAGAAGCG 59.469 47.619 0.00 0.00 37.15 4.68
358 420 1.305297 TGATGTCGGGAGCTGGAGT 60.305 57.895 0.00 0.00 0.00 3.85
380 442 1.270305 CGACAGATGGCCACGGAATAT 60.270 52.381 8.16 0.00 0.00 1.28
447 509 1.006102 CAGCGTGTCGAGGGAAGTT 60.006 57.895 0.00 0.00 0.00 2.66
474 539 1.227734 CCCGAAACCGACAACCACT 60.228 57.895 0.00 0.00 0.00 4.00
538 603 2.775890 CTGGCACTGGATCCATGATAC 58.224 52.381 16.63 5.80 0.00 2.24
582 647 1.296715 GAAGATGGGGTCGTGCTGT 59.703 57.895 0.00 0.00 0.00 4.40
1508 1585 7.661847 ACTCTTCACTTATTTACCAACCAGAAG 59.338 37.037 0.00 0.00 0.00 2.85
1621 1699 0.179121 TACGCACGGCCTGAACTATG 60.179 55.000 0.00 0.00 0.00 2.23
1624 1702 2.048503 GTACGCACGGCCTGAACT 60.049 61.111 0.00 0.00 0.00 3.01
1650 1728 2.812011 GTTCTTGCCTAAACACATCCGT 59.188 45.455 0.00 0.00 0.00 4.69
1663 1741 1.135083 TCGCAGTAGCTAGTTCTTGCC 60.135 52.381 0.00 0.00 39.10 4.52
1684 2065 0.741221 GCCTCACCAACTTAGAGCCG 60.741 60.000 0.00 0.00 0.00 5.52
1730 2111 8.127954 GCATAAAGTTTGCAAATCAAAAGGAAA 58.872 29.630 16.21 0.00 45.35 3.13
1756 2137 7.951530 ATACAAAGAAAAGCCTCACATTTTG 57.048 32.000 0.00 0.00 0.00 2.44
1810 2191 7.068962 GCTTAGTATCTGTATAGATTCTCCCCC 59.931 44.444 11.11 0.00 40.79 5.40
1811 2192 7.837187 AGCTTAGTATCTGTATAGATTCTCCCC 59.163 40.741 11.11 3.07 40.79 4.81
1812 2193 8.817092 AGCTTAGTATCTGTATAGATTCTCCC 57.183 38.462 11.11 3.35 40.79 4.30
1813 2194 8.899771 GGAGCTTAGTATCTGTATAGATTCTCC 58.100 40.741 11.11 11.10 40.79 3.71
1814 2195 8.899771 GGGAGCTTAGTATCTGTATAGATTCTC 58.100 40.741 11.11 7.18 40.79 2.87
1815 2196 8.620177 AGGGAGCTTAGTATCTGTATAGATTCT 58.380 37.037 7.34 10.15 40.79 2.40
1816 2197 8.817092 AGGGAGCTTAGTATCTGTATAGATTC 57.183 38.462 7.34 2.70 40.79 2.52
1825 2206 6.586344 TCAATTCAAGGGAGCTTAGTATCTG 58.414 40.000 0.00 0.00 0.00 2.90
1859 2279 1.002134 CCCACAACCCTCGAAGCAT 60.002 57.895 0.00 0.00 0.00 3.79
2040 2471 9.936759 TGAACTTTACAAATATCCCCAAATTTC 57.063 29.630 0.00 0.00 0.00 2.17
2256 2955 3.756963 GCCCCTCTCACTCGTTTATTTTT 59.243 43.478 0.00 0.00 0.00 1.94
2276 2976 0.741221 CGCTCAACTAACTCCCTGCC 60.741 60.000 0.00 0.00 0.00 4.85
2285 2985 0.108615 GCTCTGGCTCGCTCAACTAA 60.109 55.000 0.00 0.00 35.22 2.24
2332 3033 8.788806 CACACTAAAACCATGGAATTGTTACTA 58.211 33.333 21.47 1.55 29.96 1.82


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

AutoCloner maintained by Alex Coulton.