Multiple sequence alignment - TraesCS5D01G100300

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 TraesCS5D01G100300 chr5D 100.000 2555 0 0 1 2555 112839152 112841706 0.000000e+00 4719.0
1 TraesCS5D01G100300 chr5D 97.710 1878 27 3 1 1877 109533320 109535182 0.000000e+00 3216.0
2 TraesCS5D01G100300 chr5D 92.788 416 30 0 1154 1569 109578059 109577644 1.010000e-168 603.0
3 TraesCS5D01G100300 chr5D 97.561 41 1 0 1877 1917 109535233 109535273 1.270000e-08 71.3
4 TraesCS5D01G100300 chr3D 96.557 639 18 4 1919 2555 10697938 10697302 0.000000e+00 1055.0
5 TraesCS5D01G100300 chr3D 87.500 56 5 2 1915 1968 582541064 582541009 2.120000e-06 63.9
6 TraesCS5D01G100300 chr2D 96.759 617 10 3 1939 2555 520642650 520642044 0.000000e+00 1020.0
7 TraesCS5D01G100300 chr2D 97.826 46 1 0 1919 1964 391384845 391384890 2.110000e-11 80.5
8 TraesCS5D01G100300 chr2D 100.000 30 0 0 1355 1384 584798262 584798291 3.550000e-04 56.5
9 TraesCS5D01G100300 chr5A 88.256 843 64 15 1057 1877 118253457 118254286 0.000000e+00 976.0
10 TraesCS5D01G100300 chr5A 85.714 56 6 2 1915 1968 456625967 456626022 9.870000e-05 58.4
11 TraesCS5D01G100300 chr7B 90.767 639 42 9 1919 2555 126760630 126761253 0.000000e+00 837.0
12 TraesCS5D01G100300 chr2A 89.308 636 42 17 1922 2555 158518608 158517997 0.000000e+00 774.0
13 TraesCS5D01G100300 chr2A 100.000 30 0 0 1355 1384 718934347 718934376 3.550000e-04 56.5
14 TraesCS5D01G100300 chr4A 89.739 536 39 11 1146 1673 699100518 699101045 0.000000e+00 671.0
15 TraesCS5D01G100300 chr6B 87.459 606 38 17 1952 2555 710358811 710358242 0.000000e+00 664.0
16 TraesCS5D01G100300 chr7A 87.226 548 46 13 1146 1676 30383340 30382800 1.010000e-168 603.0
17 TraesCS5D01G100300 chr7A 88.341 446 41 3 1146 1583 30413736 30413294 2.250000e-145 525.0
18 TraesCS5D01G100300 chr5B 80.213 657 85 25 1919 2555 262432164 262431533 3.880000e-123 451.0
19 TraesCS5D01G100300 chr4B 80.346 636 82 15 1919 2544 568737641 568738243 2.330000e-120 442.0
20 TraesCS5D01G100300 chr3A 80.249 643 74 24 1919 2555 515915976 515916571 3.900000e-118 435.0
21 TraesCS5D01G100300 chr7D 87.087 333 28 11 1353 1676 30062635 30062309 1.870000e-96 363.0
22 TraesCS5D01G100300 chr4D 86.068 323 40 5 1909 2227 504557449 504557128 2.430000e-90 342.0
23 TraesCS5D01G100300 chr3B 85.933 327 36 8 1919 2241 810508168 810508488 8.750000e-90 340.0
24 TraesCS5D01G100300 chr1D 84.356 326 45 5 1919 2241 304630198 304629876 5.310000e-82 315.0
25 TraesCS5D01G100300 chr1B 88.136 236 26 2 2301 2536 250427226 250427459 1.940000e-71 279.0
26 TraesCS5D01G100300 chr6D 88.889 54 4 2 1916 1968 464648955 464649007 5.900000e-07 65.8
27 TraesCS5D01G100300 chr6D 94.872 39 2 0 229 267 445458739 445458701 7.630000e-06 62.1


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 TraesCS5D01G100300 chr5D 112839152 112841706 2554 False 4719.00 4719 100.0000 1 2555 1 chr5D.!!$F1 2554
1 TraesCS5D01G100300 chr5D 109533320 109535273 1953 False 1643.65 3216 97.6355 1 1917 2 chr5D.!!$F2 1916
2 TraesCS5D01G100300 chr3D 10697302 10697938 636 True 1055.00 1055 96.5570 1919 2555 1 chr3D.!!$R1 636
3 TraesCS5D01G100300 chr2D 520642044 520642650 606 True 1020.00 1020 96.7590 1939 2555 1 chr2D.!!$R1 616
4 TraesCS5D01G100300 chr5A 118253457 118254286 829 False 976.00 976 88.2560 1057 1877 1 chr5A.!!$F1 820
5 TraesCS5D01G100300 chr7B 126760630 126761253 623 False 837.00 837 90.7670 1919 2555 1 chr7B.!!$F1 636
6 TraesCS5D01G100300 chr2A 158517997 158518608 611 True 774.00 774 89.3080 1922 2555 1 chr2A.!!$R1 633
7 TraesCS5D01G100300 chr4A 699100518 699101045 527 False 671.00 671 89.7390 1146 1673 1 chr4A.!!$F1 527
8 TraesCS5D01G100300 chr6B 710358242 710358811 569 True 664.00 664 87.4590 1952 2555 1 chr6B.!!$R1 603
9 TraesCS5D01G100300 chr7A 30382800 30383340 540 True 603.00 603 87.2260 1146 1676 1 chr7A.!!$R1 530
10 TraesCS5D01G100300 chr5B 262431533 262432164 631 True 451.00 451 80.2130 1919 2555 1 chr5B.!!$R1 636
11 TraesCS5D01G100300 chr4B 568737641 568738243 602 False 442.00 442 80.3460 1919 2544 1 chr4B.!!$F1 625
12 TraesCS5D01G100300 chr3A 515915976 515916571 595 False 435.00 435 80.2490 1919 2555 1 chr3A.!!$F1 636

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
681 682 0.470766 GAGGGTGGGTGTGTTGTACA 59.529 55.0 0.0 0.0 36.82 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1881 4.44088 AGAGATTACAGCTGCAATCAGAC 58.559 43.478 31.74 23.52 42.95 3.51 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
208 209 3.550431 ACCCGCCGAGATCCATGG 61.550 66.667 4.97 4.97 0.00 3.66
215 216 4.996434 GAGATCCATGGCCGCCCG 62.996 72.222 6.96 0.00 0.00 6.13
267 268 4.033776 CCCCCAAGCTCCTTCGCA 62.034 66.667 0.00 0.00 0.00 5.10
360 361 1.153823 ATCTTCCGAACTGTCGCCG 60.154 57.895 0.00 0.00 46.28 6.46
669 670 3.518992 TTAAACCAAAGAGGAGGGTGG 57.481 47.619 0.00 0.00 41.22 4.61
681 682 0.470766 GAGGGTGGGTGTGTTGTACA 59.529 55.000 0.00 0.00 36.82 2.90
965 966 2.203126 CGCCAGAATCCTCCAGCC 60.203 66.667 0.00 0.00 0.00 4.85
1039 1040 4.039357 CCGGCGTCGAGTGTGTCT 62.039 66.667 12.93 0.00 39.00 3.41
1132 1133 0.460987 CGAGGGAGACAAGGATGCAC 60.461 60.000 0.00 0.00 0.00 4.57
1455 1482 1.153667 GACGAGGCTGAGCAAGGAG 60.154 63.158 6.82 0.00 0.00 3.69
1557 1584 3.054802 CAGTTAGGAGCTGGGTCTGAAAT 60.055 47.826 0.00 0.00 0.00 2.17
1681 1719 1.346395 TCTTTGTACTGATGCCCGTGT 59.654 47.619 0.00 0.00 0.00 4.49
1843 1881 2.138320 TCTGTTGCTCAAGCTTCTTCG 58.862 47.619 0.00 0.00 42.66 3.79
1906 1995 8.909923 TCGTGATAATCTACTGAAACTATTCCA 58.090 33.333 0.00 0.00 34.49 3.53
2128 2236 3.594775 CCGTGCTTGCTTGCCACA 61.595 61.111 0.00 0.00 0.00 4.17
2137 2245 2.492773 GCTTGCCACACTTGCCACT 61.493 57.895 0.00 0.00 0.00 4.00
2340 2458 1.865970 TGTTGTTAACTTGTACCGCCG 59.134 47.619 7.22 0.00 0.00 6.46
2352 2470 0.317799 TACCGCCGTGTCTAGCAAAA 59.682 50.000 0.00 0.00 0.00 2.44
2515 2636 2.034812 AGCAAAAATAAACGCCGGTTCA 59.965 40.909 1.90 0.00 34.62 3.18
2545 2668 4.717233 ATCATGCCGCTTCAAACAAATA 57.283 36.364 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.222847 GCGGAGACACGGGATCCC 62.223 72.222 22.12 22.12 0.00 3.85
84 85 0.460459 GCTGGGCTCTAGTTTCGGTC 60.460 60.000 0.00 0.00 0.00 4.79
85 86 1.597461 GCTGGGCTCTAGTTTCGGT 59.403 57.895 0.00 0.00 0.00 4.69
86 87 1.519455 CGCTGGGCTCTAGTTTCGG 60.519 63.158 0.00 0.00 0.00 4.30
89 90 2.125512 CGCGCTGGGCTCTAGTTT 60.126 61.111 14.94 0.00 40.44 2.66
267 268 2.450476 GTGGGAGATTTTGTGGCTCAT 58.550 47.619 0.00 0.00 0.00 2.90
326 327 0.923358 AGATGACGAGGAGGAGACCT 59.077 55.000 0.00 0.00 43.64 3.85
327 328 1.679153 GAAGATGACGAGGAGGAGACC 59.321 57.143 0.00 0.00 0.00 3.85
328 329 1.679153 GGAAGATGACGAGGAGGAGAC 59.321 57.143 0.00 0.00 0.00 3.36
329 330 1.747552 CGGAAGATGACGAGGAGGAGA 60.748 57.143 0.00 0.00 0.00 3.71
330 331 0.665835 CGGAAGATGACGAGGAGGAG 59.334 60.000 0.00 0.00 0.00 3.69
331 332 0.255033 TCGGAAGATGACGAGGAGGA 59.745 55.000 0.00 0.00 34.67 3.71
332 333 1.103803 TTCGGAAGATGACGAGGAGG 58.896 55.000 0.00 0.00 40.51 4.30
333 334 1.746220 AGTTCGGAAGATGACGAGGAG 59.254 52.381 0.00 0.00 40.51 3.69
334 335 1.472878 CAGTTCGGAAGATGACGAGGA 59.527 52.381 0.00 0.00 40.51 3.71
335 336 1.202582 ACAGTTCGGAAGATGACGAGG 59.797 52.381 9.24 0.00 40.51 4.63
336 337 2.520979 GACAGTTCGGAAGATGACGAG 58.479 52.381 9.24 0.00 40.51 4.18
337 338 1.135774 CGACAGTTCGGAAGATGACGA 60.136 52.381 16.77 0.00 39.41 4.20
338 339 1.260206 CGACAGTTCGGAAGATGACG 58.740 55.000 9.24 10.30 41.89 4.35
339 340 0.992802 GCGACAGTTCGGAAGATGAC 59.007 55.000 9.24 3.48 45.98 3.06
470 471 1.379977 CTGGAGGAGCCGGAGTGTA 60.380 63.158 5.05 0.00 46.81 2.90
555 556 0.377554 AGATGTCTCGTCTAACGGCG 59.622 55.000 4.80 4.80 42.81 6.46
681 682 2.086869 GTGCCATGTCAACAGCATACT 58.913 47.619 1.11 0.00 37.60 2.12
965 966 5.023533 TGGATGGTTTATCGAAGGAAGAG 57.976 43.478 0.00 0.00 36.62 2.85
1039 1040 2.439837 CCTTTCTTTTGGCAGGGCA 58.560 52.632 0.00 0.00 0.00 5.36
1455 1482 3.607370 GAACACCTCCTCCCGTGCC 62.607 68.421 0.00 0.00 33.09 5.01
1843 1881 4.440880 AGAGATTACAGCTGCAATCAGAC 58.559 43.478 31.74 23.52 42.95 3.51
1906 1995 7.164230 GCCTATCAGCGCCTAATATATATCT 57.836 40.000 2.29 0.00 0.00 1.98
2352 2470 5.334802 GCACTTGAGGTTTTTGTTGCTTTTT 60.335 36.000 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.