Multiple sequence alignment - TraesCS2B01G387400

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 TraesCS2B01G387400 chr2B 100.000 2450 0 0 1 2450 550642977 550640528 0.000000e+00 4525
1 TraesCS2B01G387400 chr2B 92.323 495 36 1 1 495 298275968 298276460 0.000000e+00 702
2 TraesCS2B01G387400 chr3B 96.822 2454 57 10 1 2450 409840482 409838046 0.000000e+00 4080
3 TraesCS2B01G387400 chr3B 94.199 2448 133 8 1 2444 565179965 565182407 0.000000e+00 3725
4 TraesCS2B01G387400 chr3B 93.117 2470 139 13 1 2444 398773030 398775494 0.000000e+00 3591
5 TraesCS2B01G387400 chr3B 88.202 2475 242 29 1 2443 120083003 120080547 0.000000e+00 2907
6 TraesCS2B01G387400 chr3B 88.268 2344 219 35 1 2313 74830740 74828422 0.000000e+00 2754
7 TraesCS2B01G387400 chr3B 86.698 1684 166 30 788 2444 393193799 393195451 0.000000e+00 1816
8 TraesCS2B01G387400 chr3B 89.011 1183 97 16 1 1151 376502241 376503422 0.000000e+00 1434
9 TraesCS2B01G387400 chr3B 92.929 495 35 0 1 495 40495222 40495716 0.000000e+00 721
10 TraesCS2B01G387400 chr3B 92.784 97 5 2 2350 2444 291336929 291337025 3.290000e-29 139
11 TraesCS2B01G387400 chr5B 95.383 2469 85 10 4 2450 316555857 316553396 0.000000e+00 3901
12 TraesCS2B01G387400 chrUn 92.886 2474 150 11 1 2450 59444603 59442132 0.000000e+00 3570
13 TraesCS2B01G387400 chrUn 91.679 1959 135 19 495 2450 79019530 79017597 0.000000e+00 2689
14 TraesCS2B01G387400 chr4B 90.950 2453 180 28 11 2444 534533205 534535634 0.000000e+00 3262
15 TraesCS2B01G387400 chr6B 89.968 2472 207 16 3 2444 144614275 144616735 0.000000e+00 3153
16 TraesCS2B01G387400 chr7B 92.547 1959 135 8 495 2450 476087354 476085404 0.000000e+00 2798
17 TraesCS2B01G387400 chr2A 86.414 1266 140 17 1 1241 100908425 100907167 0.000000e+00 1356


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 TraesCS2B01G387400 chr2B 550640528 550642977 2449 True 4525 4525 100.000 1 2450 1 chr2B.!!$R1 2449
1 TraesCS2B01G387400 chr3B 409838046 409840482 2436 True 4080 4080 96.822 1 2450 1 chr3B.!!$R3 2449
2 TraesCS2B01G387400 chr3B 565179965 565182407 2442 False 3725 3725 94.199 1 2444 1 chr3B.!!$F6 2443
3 TraesCS2B01G387400 chr3B 398773030 398775494 2464 False 3591 3591 93.117 1 2444 1 chr3B.!!$F5 2443
4 TraesCS2B01G387400 chr3B 120080547 120083003 2456 True 2907 2907 88.202 1 2443 1 chr3B.!!$R2 2442
5 TraesCS2B01G387400 chr3B 74828422 74830740 2318 True 2754 2754 88.268 1 2313 1 chr3B.!!$R1 2312
6 TraesCS2B01G387400 chr3B 393193799 393195451 1652 False 1816 1816 86.698 788 2444 1 chr3B.!!$F4 1656
7 TraesCS2B01G387400 chr3B 376502241 376503422 1181 False 1434 1434 89.011 1 1151 1 chr3B.!!$F3 1150
8 TraesCS2B01G387400 chr5B 316553396 316555857 2461 True 3901 3901 95.383 4 2450 1 chr5B.!!$R1 2446
9 TraesCS2B01G387400 chrUn 59442132 59444603 2471 True 3570 3570 92.886 1 2450 1 chrUn.!!$R1 2449
10 TraesCS2B01G387400 chrUn 79017597 79019530 1933 True 2689 2689 91.679 495 2450 1 chrUn.!!$R2 1955
11 TraesCS2B01G387400 chr4B 534533205 534535634 2429 False 3262 3262 90.950 11 2444 1 chr4B.!!$F1 2433
12 TraesCS2B01G387400 chr6B 144614275 144616735 2460 False 3153 3153 89.968 3 2444 1 chr6B.!!$F1 2441
13 TraesCS2B01G387400 chr7B 476085404 476087354 1950 True 2798 2798 92.547 495 2450 1 chr7B.!!$R1 1955
14 TraesCS2B01G387400 chr2A 100907167 100908425 1258 True 1356 1356 86.414 1 1241 1 chr2A.!!$R1 1240

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
973 1006 0.933097 CATACCAGAGCGTGATGTGC 59.067 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2327 2.443632 TCACCAAAGGAACATACCACCA 59.556 45.455 0.0 0.0 0.0 4.17 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
284 285 1.959710 TTACTCACATGGGTGGCCTA 58.040 50.000 3.32 0.00 45.32 3.93
327 328 2.290577 GGAGCAACAACCCTGAGATCTT 60.291 50.000 0.00 0.00 0.00 2.40
379 380 6.078664 GGGATTTAGGTATGAAGAGGAGAGA 58.921 44.000 0.00 0.00 0.00 3.10
410 411 4.713553 TGCTCCACAACAGTCTTATTCAA 58.286 39.130 0.00 0.00 0.00 2.69
664 697 8.527567 AGAAGTAAAGAAGATTGAGAAGAACG 57.472 34.615 0.00 0.00 0.00 3.95
875 908 4.214971 CCCAAGTGATCAAGTTGAAGACTG 59.785 45.833 10.14 9.04 41.10 3.51
973 1006 0.933097 CATACCAGAGCGTGATGTGC 59.067 55.000 0.00 0.00 0.00 4.57
1457 1490 1.135094 GCATGGGGATGAGGAGAAGA 58.865 55.000 0.00 0.00 0.00 2.87
1484 1522 3.513119 AGCACACATGAAGAGAGAAGCTA 59.487 43.478 0.00 0.00 0.00 3.32
1524 1562 2.304470 GGAAGCAAAAGGAGAGGAGTCT 59.696 50.000 0.00 0.00 34.86 3.24
1576 1616 5.775701 AGCGAGACCTACATCATATAAACCT 59.224 40.000 0.00 0.00 0.00 3.50
2212 2267 1.607148 GTTCCTTTGGGGAGACAAACG 59.393 52.381 0.00 0.00 46.01 3.60
2213 2268 1.133363 TCCTTTGGGGAGACAAACGA 58.867 50.000 0.00 0.00 39.58 3.85
2214 2269 1.491332 TCCTTTGGGGAGACAAACGAA 59.509 47.619 0.00 0.00 39.58 3.85
2215 2270 1.607148 CCTTTGGGGAGACAAACGAAC 59.393 52.381 0.00 0.00 35.57 3.95
2216 2271 2.572290 CTTTGGGGAGACAAACGAACT 58.428 47.619 0.00 0.00 35.57 3.01
2217 2272 3.495453 CCTTTGGGGAGACAAACGAACTA 60.495 47.826 0.00 0.00 35.57 2.24
2266 2327 4.202326 GGTGTATACCATGTTCTCGGGATT 60.202 45.833 3.35 0.00 46.71 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 4.443978 AATATGGCATGTAGGAGCAACT 57.556 40.909 10.98 0.0 0.00 3.16
255 256 5.010516 CACCCATGTGAGTAATTGTTTTGGA 59.989 40.000 0.00 0.0 45.76 3.53
284 285 7.390718 GCTCCTATATGACATATTCGGGTTTTT 59.609 37.037 13.09 0.0 0.00 1.94
327 328 7.384115 GCATATGATTACTAGAAGCAAACGGTA 59.616 37.037 6.97 0.0 0.00 4.02
379 380 3.141398 CTGTTGTGGAGCATAGTTGTGT 58.859 45.455 0.00 0.0 0.00 3.72
410 411 5.482175 GGTGCTGAGGTATATGAATAGGAGT 59.518 44.000 0.00 0.0 0.00 3.85
664 697 2.295253 ATAGTACTGCCAGCGTTGAC 57.705 50.000 5.39 0.0 0.00 3.18
875 908 7.817418 ACTTCTTCAGGAGTAGTAGATGATC 57.183 40.000 0.00 0.0 34.62 2.92
973 1006 3.010138 TCAAGAGGATTGGGTAAACCTGG 59.990 47.826 0.00 0.0 38.99 4.45
1295 1328 5.715439 AATACCCTCCAAGTCATCAATCA 57.285 39.130 0.00 0.0 0.00 2.57
1457 1490 3.326006 TCTCTCTTCATGTGTGCTCCTTT 59.674 43.478 0.00 0.0 0.00 3.11
1484 1522 1.350071 CCTATCCTCATGCCTGCTCT 58.650 55.000 0.00 0.0 0.00 4.09
1524 1562 1.550072 TCTCACATCCTCGTGCATTGA 59.450 47.619 0.00 0.0 36.80 2.57
1576 1616 1.545428 GGGTCATGAAACAGCTCACCA 60.545 52.381 0.00 0.0 0.00 4.17
1766 1807 6.018832 GCTTTCACTAATTTCAGCAAAGCAAA 60.019 34.615 14.67 0.0 40.82 3.68
2266 2327 2.443632 TCACCAAAGGAACATACCACCA 59.556 45.455 0.00 0.0 0.00 4.17


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

AutoCloner maintained by Alex Coulton.