Multiple sequence alignment - TraesCS6B01G157800

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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 TraesCS6B01G157800 chr6B 100.000 3227 0 0 1 3227 159989890 159986664 0.000000e+00 5960.0
1 TraesCS6B01G157800 chr6B 88.429 2394 243 19 5 2380 160683195 160680818 0.000000e+00 2856.0
2 TraesCS6B01G157800 chr6B 87.963 2243 227 27 3 2229 160904974 160902759 0.000000e+00 2606.0
3 TraesCS6B01G157800 chr6B 86.866 2246 259 23 3 2228 160663259 160661030 0.000000e+00 2481.0
4 TraesCS6B01G157800 chr6B 86.685 2238 274 12 12 2234 160717020 160714792 0.000000e+00 2460.0
5 TraesCS6B01G157800 chr6B 80.159 126 15 6 2384 2506 160714241 160714123 5.740000e-13 86.1
6 TraesCS6B01G157800 chr6A 97.533 3243 60 7 1 3227 101562729 101559491 0.000000e+00 5528.0
7 TraesCS6B01G157800 chr6A 88.146 2244 228 22 3 2229 101865449 101863227 0.000000e+00 2636.0
8 TraesCS6B01G157800 chr6A 87.344 2244 251 20 3 2229 101548242 101546015 0.000000e+00 2540.0
9 TraesCS6B01G157800 chr6A 85.751 2358 297 20 3 2346 101554833 101552501 0.000000e+00 2457.0
10 TraesCS6B01G157800 chr6D 96.639 3243 65 10 1 3227 84231912 84228698 0.000000e+00 5345.0
11 TraesCS6B01G157800 chr6D 87.528 2245 246 21 3 2229 84218204 84215976 0.000000e+00 2564.0
12 TraesCS6B01G157800 chr6D 86.813 2237 273 10 12 2234 84631062 84628834 0.000000e+00 2477.0
13 TraesCS6B01G157800 chr6D 86.364 2244 274 22 3 2229 84474105 84471877 0.000000e+00 2420.0
14 TraesCS6B01G157800 chr6D 85.115 2358 299 27 3 2346 84224475 84222156 0.000000e+00 2362.0


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 TraesCS6B01G157800 chr6B 159986664 159989890 3226 True 5960.00 5960 100.0000 1 3227 1 chr6B.!!$R1 3226
1 TraesCS6B01G157800 chr6B 160680818 160683195 2377 True 2856.00 2856 88.4290 5 2380 1 chr6B.!!$R3 2375
2 TraesCS6B01G157800 chr6B 160902759 160904974 2215 True 2606.00 2606 87.9630 3 2229 1 chr6B.!!$R4 2226
3 TraesCS6B01G157800 chr6B 160661030 160663259 2229 True 2481.00 2481 86.8660 3 2228 1 chr6B.!!$R2 2225
4 TraesCS6B01G157800 chr6B 160714123 160717020 2897 True 1273.05 2460 83.4220 12 2506 2 chr6B.!!$R5 2494
5 TraesCS6B01G157800 chr6A 101559491 101562729 3238 True 5528.00 5528 97.5330 1 3227 1 chr6A.!!$R3 3226
6 TraesCS6B01G157800 chr6A 101863227 101865449 2222 True 2636.00 2636 88.1460 3 2229 1 chr6A.!!$R4 2226
7 TraesCS6B01G157800 chr6A 101546015 101548242 2227 True 2540.00 2540 87.3440 3 2229 1 chr6A.!!$R1 2226
8 TraesCS6B01G157800 chr6A 101552501 101554833 2332 True 2457.00 2457 85.7510 3 2346 1 chr6A.!!$R2 2343
9 TraesCS6B01G157800 chr6D 84228698 84231912 3214 True 5345.00 5345 96.6390 1 3227 1 chr6D.!!$R1 3226
10 TraesCS6B01G157800 chr6D 84628834 84631062 2228 True 2477.00 2477 86.8130 12 2234 1 chr6D.!!$R3 2222
11 TraesCS6B01G157800 chr6D 84215976 84224475 8499 True 2463.00 2564 86.3215 3 2346 2 chr6D.!!$R4 2343
12 TraesCS6B01G157800 chr6D 84471877 84474105 2228 True 2420.00 2420 86.3640 3 2229 1 chr6D.!!$R2 2226

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
165 169 0.907704 TTCTTAGCCTCTCCCGCCAA 60.908 55.0 0.0 0.0 0.0 4.52 F
672 676 1.217882 CCGTCTTCTCTTTGCGTTGT 58.782 50.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 8342 1.898574 CGCACAGCTTTGGGTTCCT 60.899 57.895 8.67 0.0 0.0 3.36 R
2631 9376 0.251916 TCGTCGCCAAATTCCTCCAT 59.748 50.000 0.00 0.0 0.0 3.41 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
41 42 4.804597 AGATGATAGCTAGTACCACCACA 58.195 43.478 0.00 0.00 0.00 4.17
165 169 0.907704 TTCTTAGCCTCTCCCGCCAA 60.908 55.000 0.00 0.00 0.00 4.52
672 676 1.217882 CCGTCTTCTCTTTGCGTTGT 58.782 50.000 0.00 0.00 0.00 3.32
811 822 3.152341 CTGCCTGTTGAAATCTTCCACT 58.848 45.455 0.00 0.00 0.00 4.00
1225 1238 3.448093 TGTCAGCCAACCATTTCCATA 57.552 42.857 0.00 0.00 0.00 2.74
1258 1271 4.141528 CCCTGAGAATAGGCAATCTGAAGT 60.142 45.833 0.00 0.00 36.47 3.01
1403 1417 2.629137 TGCCACAAGATGAAAGCATTGT 59.371 40.909 0.00 0.00 34.11 2.71
1491 1505 3.127721 GGTTATCAAAGCTCACAAGGCTC 59.872 47.826 0.00 0.00 39.30 4.70
1657 1671 2.875094 ATCAGATAAGCCTGCCATCC 57.125 50.000 0.00 0.00 34.28 3.51
1732 1746 5.455525 GCATCAAAACTTCAATACCGCATAC 59.544 40.000 0.00 0.00 0.00 2.39
1764 1778 1.270785 TGCAAAGTGCTGAATCTCGGA 60.271 47.619 1.43 0.00 45.31 4.55
1836 1850 4.319177 CACTCCTTTACCTGAACTTGAGG 58.681 47.826 0.00 0.00 36.57 3.86
2050 8342 9.840427 GCACATTTCAAGCTTCTAGTTTTAATA 57.160 29.630 0.00 0.00 0.00 0.98
2250 8548 2.622436 GCTAAGCCCACTTCAGTGTAG 58.378 52.381 6.22 2.79 44.21 2.74
2459 9204 1.070376 GTCGTGTTTTACAAGGTCGCC 60.070 52.381 0.00 0.00 0.00 5.54
2533 9278 2.746362 GAGAAGGTTCAGGCTGTGAATG 59.254 50.000 15.27 0.00 46.99 2.67
2541 9286 3.548770 TCAGGCTGTGAATGATGGATTC 58.451 45.455 15.27 0.00 40.99 2.52
2804 9552 3.706373 CCGGCAGGCTACCACACT 61.706 66.667 4.31 0.00 0.00 3.55
3081 9830 4.124351 CTGCATGGGCGTGCCAAG 62.124 66.667 13.76 2.71 44.43 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.304110 CTGTTGCTTGAAGAATGCATGTT 58.696 39.130 0.00 0.00 36.55 2.71
672 676 2.362077 GAGGTCAAGCAAAGCCAAAGAA 59.638 45.455 0.00 0.00 0.00 2.52
985 996 2.098607 CAGACATGTTATTGCTGCCCAG 59.901 50.000 0.00 0.00 0.00 4.45
1225 1238 4.739793 CCTATTCTCAGGGAGATCTCACT 58.260 47.826 22.28 22.28 45.87 3.41
1258 1271 5.503927 ACTAAGTGATACGAAGGACAGGTA 58.496 41.667 0.00 0.00 0.00 3.08
1403 1417 6.055588 AGAAACTGAAGATTCTGAAAACCGA 58.944 36.000 2.38 0.00 36.10 4.69
1657 1671 2.185004 ACGAGACTTGGGTCCAAATG 57.815 50.000 3.87 0.00 43.05 2.32
1732 1746 2.734670 CACTTTGCACCAATCACTGTG 58.265 47.619 0.17 0.17 35.58 3.66
1836 1850 5.407407 TCTCTCCATAGAAGTTGTTGGAC 57.593 43.478 0.00 0.00 34.62 4.02
2050 8342 1.898574 CGCACAGCTTTGGGTTCCT 60.899 57.895 8.67 0.00 0.00 3.36
2250 8548 3.812053 GACCATTGCATACTGGATCAGAC 59.188 47.826 15.23 0.07 36.35 3.51
2459 9204 1.660607 CAAAGTCGTCGGGTCATGATG 59.339 52.381 0.00 0.00 0.00 3.07
2533 9278 0.533755 CAGGGTCGCCTGAATCCATC 60.534 60.000 3.13 0.00 39.96 3.51
2541 9286 1.949847 ATCTCGTTCAGGGTCGCCTG 61.950 60.000 2.85 2.85 39.01 4.85
2631 9376 0.251916 TCGTCGCCAAATTCCTCCAT 59.748 50.000 0.00 0.00 0.00 3.41
2804 9552 1.687146 ATGAGGCGAGGAAGGAGCA 60.687 57.895 0.00 0.00 0.00 4.26
3081 9830 0.108138 CTCCCATGAACTCGTCCCAC 60.108 60.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.