Multiple sequence alignment - TraesCS5A01G315600

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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 TraesCS5A01G315600 chr5A 100.000 3178 0 0 1 3178 525918368 525921545 0.000000e+00 5869.0
1 TraesCS5A01G315600 chr5A 97.548 3181 72 5 2 3178 525829744 525832922 0.000000e+00 5437.0
2 TraesCS5A01G315600 chr5A 95.284 1675 64 8 2 1664 525724311 525725982 0.000000e+00 2641.0
3 TraesCS5A01G315600 chr5A 93.393 1120 64 7 1677 2789 525726248 525727364 0.000000e+00 1650.0
4 TraesCS5A01G315600 chr5A 88.322 1216 87 26 2 1192 526264940 526266125 0.000000e+00 1408.0
5 TraesCS5A01G315600 chr5A 82.229 332 38 14 2 313 525601032 525601362 1.880000e-67 267.0
6 TraesCS5A01G315600 chr5A 86.017 236 13 4 2877 3112 525727401 525727616 5.300000e-58 235.0
7 TraesCS5A01G315600 chr5D 93.909 1412 71 8 2 1400 413489739 413491148 0.000000e+00 2117.0
8 TraesCS5A01G315600 chr5D 94.161 1096 54 4 314 1400 413592674 413593768 0.000000e+00 1661.0
9 TraesCS5A01G315600 chr5D 87.965 914 70 22 2289 3178 413594568 413595465 0.000000e+00 1042.0
10 TraesCS5A01G315600 chr5D 87.678 633 47 18 2289 2899 413491975 413492598 0.000000e+00 708.0
11 TraesCS5A01G315600 chr5D 90.094 424 32 6 1360 1775 413593767 413594188 2.790000e-150 542.0
12 TraesCS5A01G315600 chr5D 79.349 799 124 20 897 1657 413286485 413287280 1.010000e-144 523.0
13 TraesCS5A01G315600 chr5D 91.716 338 26 2 1777 2112 413594242 413594579 4.800000e-128 468.0
14 TraesCS5A01G315600 chr5D 92.593 324 20 4 1360 1682 413491147 413491467 2.230000e-126 462.0
15 TraesCS5A01G315600 chr5D 90.882 340 26 4 1775 2112 413491650 413491986 4.830000e-123 451.0
16 TraesCS5A01G315600 chr5D 94.862 253 10 3 2 251 413592423 413592675 2.970000e-105 392.0
17 TraesCS5A01G315600 chr5D 88.448 277 23 3 2903 3178 413492681 413492949 3.060000e-85 326.0
18 TraesCS5A01G315600 chr5D 83.200 250 22 15 2 233 413285248 413285495 8.930000e-51 211.0
19 TraesCS5A01G315600 chr5B 88.545 1196 101 18 935 2112 498722815 498723992 0.000000e+00 1417.0
20 TraesCS5A01G315600 chr5B 87.353 767 84 8 1171 1929 498511900 498512661 0.000000e+00 867.0
21 TraesCS5A01G315600 chr5B 94.033 419 15 7 2 411 498511424 498511841 7.480000e-176 627.0
22 TraesCS5A01G315600 chr5B 88.998 409 34 6 2774 3178 498779251 498779652 2.200000e-136 496.0
23 TraesCS5A01G315600 chr5B 82.932 457 48 10 2648 3101 498698277 498698706 4.970000e-103 385.0
24 TraesCS5A01G315600 chr5B 81.321 530 49 20 2278 2777 498723969 498724478 4.970000e-103 385.0
25 TraesCS5A01G315600 chr5B 94.944 178 6 2 2 176 498722615 498722792 3.120000e-70 276.0
26 TraesCS5A01G315600 chr5B 88.442 199 16 3 2980 3178 498512660 498512851 1.910000e-57 233.0
27 TraesCS5A01G315600 chr7D 88.213 263 22 5 1858 2112 447078139 447078400 3.980000e-79 305.0
28 TraesCS5A01G315600 chr7D 75.829 211 35 6 2302 2497 30762397 30762606 3.380000e-15 93.5
29 TraesCS5A01G315600 chr3A 86.038 265 28 6 1856 2112 153928197 153927934 3.120000e-70 276.0
30 TraesCS5A01G315600 chr3A 87.736 106 9 3 2188 2290 175168557 175168453 1.550000e-23 121.0
31 TraesCS5A01G315600 chr1B 85.878 262 31 5 1856 2112 469025293 469025553 1.120000e-69 274.0
32 TraesCS5A01G315600 chr1B 85.792 183 16 5 2114 2291 643457042 643457219 5.410000e-43 185.0
33 TraesCS5A01G315600 chr6B 84.906 265 28 7 1856 2112 501111921 501112181 1.130000e-64 257.0


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 TraesCS5A01G315600 chr5A 525918368 525921545 3177 False 5869.000000 5869 100.000000 1 3178 1 chr5A.!!$F3 3177
1 TraesCS5A01G315600 chr5A 525829744 525832922 3178 False 5437.000000 5437 97.548000 2 3178 1 chr5A.!!$F2 3176
2 TraesCS5A01G315600 chr5A 525724311 525727616 3305 False 1508.666667 2641 91.564667 2 3112 3 chr5A.!!$F5 3110
3 TraesCS5A01G315600 chr5A 526264940 526266125 1185 False 1408.000000 1408 88.322000 2 1192 1 chr5A.!!$F4 1190
4 TraesCS5A01G315600 chr5D 413592423 413595465 3042 False 821.000000 1661 91.759600 2 3178 5 chr5D.!!$F3 3176
5 TraesCS5A01G315600 chr5D 413489739 413492949 3210 False 812.800000 2117 90.702000 2 3178 5 chr5D.!!$F2 3176
6 TraesCS5A01G315600 chr5D 413285248 413287280 2032 False 367.000000 523 81.274500 2 1657 2 chr5D.!!$F1 1655
7 TraesCS5A01G315600 chr5B 498722615 498724478 1863 False 692.666667 1417 88.270000 2 2777 3 chr5B.!!$F4 2775
8 TraesCS5A01G315600 chr5B 498511424 498512851 1427 False 575.666667 867 89.942667 2 3178 3 chr5B.!!$F3 3176


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
753 1205 4.142881 GCCTTCTTGAGACATAAAACCGTC 60.143 45.833 0.00 0.0 0.0 4.79 F
1217 1733 4.096003 GCTGAAGCGCCCCTACCA 62.096 66.667 2.29 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 2787 1.078709 CACCTCAACACTGCCATACG 58.921 55.0 0.0 0.0 0.00 3.06 R
2591 3590 2.755655 GAGACAGGATGAAACCTCTCGA 59.244 50.0 0.0 0.0 39.69 4.04 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
535 751 9.213777 TGGATTCTATATCAAAGTTGACTAGGT 57.786 33.333 0.00 0.0 40.49 3.08
713 1165 8.611654 AAAAACTTCGGCAACTTAGTATTAGA 57.388 30.769 0.00 0.0 0.00 2.10
753 1205 4.142881 GCCTTCTTGAGACATAAAACCGTC 60.143 45.833 0.00 0.0 0.00 4.79
1217 1733 4.096003 GCTGAAGCGCCCCTACCA 62.096 66.667 2.29 0.0 0.00 3.25
1351 1867 4.351938 CGCTCGGTGTCGGTTGGA 62.352 66.667 0.00 0.0 36.95 3.53
1450 2005 5.273944 GTGTTGAAGAGAATGTTTGGACAC 58.726 41.667 0.00 0.0 38.91 3.67
1526 2093 4.322057 AATTGGGTGAGCTAGATTTGGT 57.678 40.909 0.00 0.0 0.00 3.67
1665 2240 4.757657 TGTCCATGTAACACGCACTAATTT 59.242 37.500 0.00 0.0 0.00 1.82
1811 2787 1.308069 ATGTGGTGCCTCATTCGTGC 61.308 55.000 0.38 0.0 0.00 5.34
1957 2933 8.934023 TTCAGGAAAGTTCAATTTAGGTATGT 57.066 30.769 0.00 0.0 0.00 2.29
2188 3166 4.501915 CGTGGGTAACTAGTGTTGGAGAAA 60.502 45.833 0.00 0.0 37.59 2.52
2425 3411 1.037493 CCGGACCCATCGAGATACAA 58.963 55.000 0.00 0.0 0.00 2.41
2486 3485 2.047179 GTCCCACCGAAGAGCACC 60.047 66.667 0.00 0.0 0.00 5.01
2591 3590 2.158900 GGTCATCATCGTTCAGTCCCAT 60.159 50.000 0.00 0.0 0.00 4.00
2661 3688 3.552604 ATTGGTGCACGTATTCAACAC 57.447 42.857 11.45 0.0 28.35 3.32
2668 3695 2.032030 GCACGTATTCAACACACAAGCT 60.032 45.455 0.00 0.0 0.00 3.74
3031 4139 3.427573 GGCTAACCTAACCAAACATGGT 58.572 45.455 0.00 0.0 45.55 3.55
3101 4209 8.375506 TGTGAGTTTCATAGTTTGAACTCCTAT 58.624 33.333 15.88 0.0 43.99 2.57
3130 4238 9.859152 TCATGGACCATATTACATGAAATAACA 57.141 29.630 6.67 0.0 44.60 2.41
3174 4282 4.979335 TCCCGAATGATTGCACCATATTA 58.021 39.130 1.63 0.0 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.778834 TTCAGAAATGTGACGTATACCCTA 57.221 37.500 0.00 0.00 0.00 3.53
535 751 9.153721 CATTTTAGAATTGCAGGCATAGAAAAA 57.846 29.630 0.00 0.51 0.00 1.94
640 924 2.041620 AGGTGGAAATGTATGTGGTGCT 59.958 45.455 0.00 0.00 0.00 4.40
1164 1677 0.251634 GGAGCCAGAAGGAGGTGAAG 59.748 60.000 0.00 0.00 36.89 3.02
1217 1733 1.814394 CACACAGCAATAGTGGCACAT 59.186 47.619 21.41 8.51 44.52 3.21
1351 1867 1.167851 CACAACCTCATGACGCCATT 58.832 50.000 0.00 0.00 0.00 3.16
1550 2119 7.396907 ACCATGGATCATTGTTTATGTTCTTCA 59.603 33.333 21.47 0.00 34.66 3.02
1811 2787 1.078709 CACCTCAACACTGCCATACG 58.921 55.000 0.00 0.00 0.00 3.06
1819 2795 1.523711 CGTGCACCACCTCAACACT 60.524 57.895 12.15 0.00 0.00 3.55
1821 2797 2.203139 CCGTGCACCACCTCAACA 60.203 61.111 12.15 0.00 0.00 3.33
1957 2933 3.758023 GGTCCACATTCACATCACATTGA 59.242 43.478 0.00 0.00 0.00 2.57
2145 3123 5.918011 CCACGTTGCACTTAACATAAAACAT 59.082 36.000 0.00 0.00 0.00 2.71
2323 3301 4.524328 GGGTGTGATTGAGAATTTTGGAGT 59.476 41.667 0.00 0.00 0.00 3.85
2425 3411 3.066203 CCGAGGCGCTATGGTTTAAAAAT 59.934 43.478 7.64 0.00 0.00 1.82
2591 3590 2.755655 GAGACAGGATGAAACCTCTCGA 59.244 50.000 0.00 0.00 39.69 4.04
3031 4139 3.436243 CATTAACTTTAGGGGTTGGCCA 58.564 45.455 0.00 0.00 36.17 5.36
3130 4238 6.038271 GGGAAATCAAATAACGTGCTAGTGAT 59.962 38.462 0.00 0.00 0.00 3.06



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

AutoCloner maintained by Alex Coulton.