Multiple sequence alignment - TraesCS2D01G535200

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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 TraesCS2D01G535200 chr2D 100.000 2438 0 0 1 2438 618286614 618289051 0.000000e+00 4503.0
1 TraesCS2D01G535200 chr2D 82.706 1249 205 10 727 1968 5748847 5747603 0.000000e+00 1099.0
2 TraesCS2D01G535200 chr2D 90.588 85 8 0 312 396 481141194 481141110 1.980000e-21 113.0
3 TraesCS2D01G535200 chr2A 96.132 2068 64 11 382 2438 749103009 749105071 0.000000e+00 3362.0
4 TraesCS2D01G535200 chr2A 82.767 1265 206 10 727 1982 4292548 4293809 0.000000e+00 1118.0
5 TraesCS2D01G535200 chr2A 91.040 346 17 4 1 346 749102676 749103007 2.860000e-124 455.0
6 TraesCS2D01G535200 chr2B 95.739 1502 42 10 649 2133 754927337 754928833 0.000000e+00 2399.0
7 TraesCS2D01G535200 chr2B 81.709 1252 212 16 727 1968 5629618 5628374 0.000000e+00 1027.0
8 TraesCS2D01G535200 chr2B 88.050 159 13 4 2140 2298 754931259 754931411 1.490000e-42 183.0
9 TraesCS2D01G535200 chr2B 89.412 85 9 0 312 396 457697640 457697556 9.220000e-20 108.0
10 TraesCS2D01G535200 chr6B 81.481 216 17 9 389 603 162550692 162550499 3.250000e-34 156.0
11 TraesCS2D01G535200 chr5B 83.133 166 19 6 396 559 18070370 18070528 2.530000e-30 143.0
12 TraesCS2D01G535200 chr5B 77.049 305 25 16 1 298 18065677 18065943 1.520000e-27 134.0
13 TraesCS2D01G535200 chr3A 90.110 91 7 2 138 228 549909424 549909512 1.530000e-22 117.0
14 TraesCS2D01G535200 chr3A 88.764 89 10 0 308 396 127266682 127266594 2.560000e-20 110.0
15 TraesCS2D01G535200 chr6D 89.130 92 8 1 312 401 382702952 382702861 1.980000e-21 113.0
16 TraesCS2D01G535200 chr6D 89.412 85 9 0 312 396 60049615 60049531 9.220000e-20 108.0
17 TraesCS2D01G535200 chr3B 90.588 85 8 0 305 389 621334391 621334475 1.980000e-21 113.0
18 TraesCS2D01G535200 chr7A 93.333 75 5 0 312 386 728022274 728022348 7.130000e-21 111.0
19 TraesCS2D01G535200 chr3D 89.412 85 9 0 312 396 23206099 23206183 9.220000e-20 108.0
20 TraesCS2D01G535200 chr3D 88.506 87 10 0 312 398 26166864 26166778 3.320000e-19 106.0
21 TraesCS2D01G535200 chr1D 84.043 94 8 7 72 159 104527853 104527945 1.550000e-12 84.2
22 TraesCS2D01G535200 chr7D 81.111 90 13 3 72 159 72117041 72116954 4.350000e-08 69.4


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 TraesCS2D01G535200 chr2D 618286614 618289051 2437 False 4503.0 4503 100.0000 1 2438 1 chr2D.!!$F1 2437
1 TraesCS2D01G535200 chr2D 5747603 5748847 1244 True 1099.0 1099 82.7060 727 1968 1 chr2D.!!$R1 1241
2 TraesCS2D01G535200 chr2A 749102676 749105071 2395 False 1908.5 3362 93.5860 1 2438 2 chr2A.!!$F2 2437
3 TraesCS2D01G535200 chr2A 4292548 4293809 1261 False 1118.0 1118 82.7670 727 1982 1 chr2A.!!$F1 1255
4 TraesCS2D01G535200 chr2B 754927337 754931411 4074 False 1291.0 2399 91.8945 649 2298 2 chr2B.!!$F1 1649
5 TraesCS2D01G535200 chr2B 5628374 5629618 1244 True 1027.0 1027 81.7090 727 1968 1 chr2B.!!$R1 1241

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
302 303 0.89694 CAGACACTGGGCAATGGCTT 60.897 55.0 6.78 0.0 40.87 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1665 1.006832 CCAGGTTCGACATTAAGCCG 58.993 55.0 0.0 0.0 0.0 5.52 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
75 76 8.001292 GCATTATTAGCTAATATTCCCCCATCT 58.999 37.037 23.50 0.37 0.00 2.90
179 180 8.732531 GGAGTAATAGGTACATAGCTTAGACAG 58.267 40.741 0.00 0.00 34.88 3.51
215 216 5.881923 TTAGAAGGCTAATACCAATCCGT 57.118 39.130 0.00 0.00 31.81 4.69
216 217 6.982160 TTAGAAGGCTAATACCAATCCGTA 57.018 37.500 0.00 0.00 31.81 4.02
217 218 5.211174 AGAAGGCTAATACCAATCCGTAC 57.789 43.478 0.00 0.00 0.00 3.67
218 219 4.652421 AGAAGGCTAATACCAATCCGTACA 59.348 41.667 0.00 0.00 0.00 2.90
219 220 4.332428 AGGCTAATACCAATCCGTACAC 57.668 45.455 0.00 0.00 0.00 2.90
220 221 3.707611 AGGCTAATACCAATCCGTACACA 59.292 43.478 0.00 0.00 0.00 3.72
221 222 4.347000 AGGCTAATACCAATCCGTACACAT 59.653 41.667 0.00 0.00 0.00 3.21
222 223 5.061179 GGCTAATACCAATCCGTACACATT 58.939 41.667 0.00 0.00 0.00 2.71
223 224 5.529800 GGCTAATACCAATCCGTACACATTT 59.470 40.000 0.00 0.00 0.00 2.32
224 225 6.427150 GCTAATACCAATCCGTACACATTTG 58.573 40.000 0.00 0.00 0.00 2.32
225 226 6.259167 GCTAATACCAATCCGTACACATTTGA 59.741 38.462 0.00 0.00 0.00 2.69
226 227 7.201661 GCTAATACCAATCCGTACACATTTGAA 60.202 37.037 0.00 0.00 0.00 2.69
227 228 7.455641 AATACCAATCCGTACACATTTGAAA 57.544 32.000 0.00 0.00 0.00 2.69
244 245 9.868277 ACATTTGAAAGTACACATTTGAAAAGA 57.132 25.926 0.00 0.00 28.94 2.52
268 269 1.076332 CTTTAACCTTCCAGCGTCCG 58.924 55.000 0.00 0.00 0.00 4.79
301 302 1.303888 CAGACACTGGGCAATGGCT 60.304 57.895 6.78 0.00 40.87 4.75
302 303 0.896940 CAGACACTGGGCAATGGCTT 60.897 55.000 6.78 0.00 40.87 4.35
306 307 2.298729 GACACTGGGCAATGGCTTTAAA 59.701 45.455 6.78 0.00 40.87 1.52
320 321 8.749354 CAATGGCTTTAAAGTAATACTCCCTTT 58.251 33.333 16.38 7.94 33.32 3.11
323 324 7.392393 TGGCTTTAAAGTAATACTCCCTTTGTC 59.608 37.037 16.38 0.00 31.33 3.18
324 325 7.148120 GGCTTTAAAGTAATACTCCCTTTGTCC 60.148 40.741 16.38 0.00 31.33 4.02
339 340 6.331572 TCCCTTTGTCCCATAATATAAGAGCA 59.668 38.462 0.00 0.00 0.00 4.26
406 407 9.483489 TGGGACAGATAGAGTAATAAAGTAACA 57.517 33.333 0.00 0.00 0.00 2.41
443 444 5.444983 TGTGATTACAAACATAACACGTGC 58.555 37.500 17.22 0.00 32.88 5.34
454 455 1.144969 AACACGTGCTGAACCATACG 58.855 50.000 17.22 0.00 41.86 3.06
499 500 1.268743 GCGAGCAGATAAACCCAATGC 60.269 52.381 0.00 0.00 37.15 3.56
954 963 1.014564 CCTTGCCGAAGAAGTCCGTC 61.015 60.000 0.00 0.00 0.00 4.79
1656 1665 1.782028 GCACGGTGGTGTTGAACTCC 61.782 60.000 10.60 9.36 46.13 3.85
1926 1935 2.189257 CCGACGATGATTGGGCCA 59.811 61.111 0.00 0.00 0.00 5.36
2006 2027 4.344865 GCTTCCTGGCCGGGTTGA 62.345 66.667 30.31 16.04 0.00 3.18
2050 2071 2.531522 ATTTGCTGGGTTTGCTCAAC 57.468 45.000 0.00 0.00 34.18 3.18
2175 4626 9.786105 CAAATTTAAAATGTTTCCAAAAGCACT 57.214 25.926 0.00 0.00 0.00 4.40
2312 4763 6.090358 TGAAGAAAGCTTAACGATCTAAACGG 59.910 38.462 0.00 0.00 33.61 4.44
2330 4781 8.819974 TCTAAACGGTCTTACAAAAGTTTACAG 58.180 33.333 0.00 0.00 34.29 2.74
2331 4782 5.413969 ACGGTCTTACAAAAGTTTACAGC 57.586 39.130 0.00 0.00 34.13 4.40
2388 4839 4.044426 GCGTGATAATGGCTTTTTCCATC 58.956 43.478 0.00 0.00 45.64 3.51
2398 4849 5.630121 TGGCTTTTTCCATCTTCTAACAGA 58.370 37.500 0.00 0.00 0.00 3.41
2400 4851 5.940470 GGCTTTTTCCATCTTCTAACAGAGA 59.060 40.000 0.00 0.00 0.00 3.10
2406 4857 7.487822 TTCCATCTTCTAACAGAGAGTCAAT 57.512 36.000 0.00 0.00 34.93 2.57
2417 4868 3.513119 CAGAGAGTCAATCCTCCTTGTGA 59.487 47.826 0.00 0.00 31.53 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.134815 GGGAATATTAGCTAATAATGCATGCG 58.865 38.462 25.90 0.00 35.63 4.73
132 133 6.156429 ACTCCCTCGGTCTCAAAATAAGTATT 59.844 38.462 0.00 0.00 0.00 1.89
149 150 5.254901 AGCTATGTACCTATTACTCCCTCG 58.745 45.833 0.00 0.00 0.00 4.63
179 180 5.735766 AGCCTTCTAATACTTGTGAGTTCC 58.264 41.667 0.00 0.00 37.33 3.62
211 212 5.358090 TGTGTACTTTCAAATGTGTACGGA 58.642 37.500 0.00 0.00 38.35 4.69
214 215 9.509855 TTCAAATGTGTACTTTCAAATGTGTAC 57.490 29.630 0.00 0.00 36.69 2.90
216 217 8.994429 TTTCAAATGTGTACTTTCAAATGTGT 57.006 26.923 0.00 0.00 0.00 3.72
217 218 9.904647 CTTTTCAAATGTGTACTTTCAAATGTG 57.095 29.630 0.00 0.00 0.00 3.21
218 219 9.868277 TCTTTTCAAATGTGTACTTTCAAATGT 57.132 25.926 0.00 0.00 0.00 2.71
244 245 4.382793 GGACGCTGGAAGGTTAAAGATAGT 60.383 45.833 0.00 0.00 0.00 2.12
283 284 0.896940 AAGCCATTGCCCAGTGTCTG 60.897 55.000 0.00 0.00 38.69 3.51
301 302 7.757611 TGGGACAAAGGGAGTATTACTTTAAA 58.242 34.615 0.00 0.00 33.47 1.52
302 303 7.332433 TGGGACAAAGGGAGTATTACTTTAA 57.668 36.000 0.00 0.00 33.47 1.52
380 381 9.483489 TGTTACTTTATTACTCTATCTGTCCCA 57.517 33.333 0.00 0.00 0.00 4.37
406 407 2.341846 ATCACAGTCACCGGTGTTTT 57.658 45.000 32.74 17.15 37.90 2.43
443 444 3.623060 CCATCCTGTTTCGTATGGTTCAG 59.377 47.826 0.00 0.00 35.23 3.02
454 455 0.719465 CGTACGTGCCATCCTGTTTC 59.281 55.000 7.22 0.00 0.00 2.78
499 500 1.746615 CAGGGCCTTGATCCACACG 60.747 63.158 9.80 0.00 0.00 4.49
588 593 4.133820 TGGGTCAGTGTGTAAGTCATTTG 58.866 43.478 0.00 0.00 0.00 2.32
591 596 3.391296 ACTTGGGTCAGTGTGTAAGTCAT 59.609 43.478 0.00 0.00 0.00 3.06
592 597 2.769663 ACTTGGGTCAGTGTGTAAGTCA 59.230 45.455 0.00 0.00 0.00 3.41
659 665 2.025887 GGTCCTGGAATTGTGTGGAGAT 60.026 50.000 0.00 0.00 0.00 2.75
885 894 3.681129 TGGAAGGGCCAGTTTGGA 58.319 55.556 6.18 0.00 43.33 3.53
1656 1665 1.006832 CCAGGTTCGACATTAAGCCG 58.993 55.000 0.00 0.00 0.00 5.52
1926 1935 2.196382 CTCGTCGTGTGTCGGTGGAT 62.196 60.000 0.00 0.00 40.32 3.41
2301 4752 6.701432 ACTTTTGTAAGACCGTTTAGATCG 57.299 37.500 0.00 0.00 35.30 3.69
2312 4763 4.512571 TCCCGCTGTAAACTTTTGTAAGAC 59.487 41.667 0.00 0.00 35.30 3.01
2330 4781 4.809958 GTCCTTTTTCTCTAATACTCCCGC 59.190 45.833 0.00 0.00 0.00 6.13
2331 4782 6.223351 AGTCCTTTTTCTCTAATACTCCCG 57.777 41.667 0.00 0.00 0.00 5.14
2387 4838 5.654650 GGAGGATTGACTCTCTGTTAGAAGA 59.345 44.000 0.00 0.00 37.63 2.87
2388 4839 5.656416 AGGAGGATTGACTCTCTGTTAGAAG 59.344 44.000 0.00 0.00 37.63 2.85
2398 4849 3.515562 AGTCACAAGGAGGATTGACTCT 58.484 45.455 0.00 0.00 44.26 3.24
2406 4857 3.808834 TCAGTCTAGTCACAAGGAGGA 57.191 47.619 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.