Multiple sequence alignment - TraesCS2B01G601200

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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 TraesCS2B01G601200 chr2B 100.000 2201 0 0 1 2201 784243547 784241347 0.000000e+00 4065
1 TraesCS2B01G601200 chr2B 96.416 279 10 0 1923 2201 748468283 748468005 5.540000e-126 460
2 TraesCS2B01G601200 chr3B 96.784 1928 56 4 1 1924 201569462 201571387 0.000000e+00 3212
3 TraesCS2B01G601200 chr3B 96.421 1928 60 5 1 1924 201544842 201542920 0.000000e+00 3169
4 TraesCS2B01G601200 chr2A 96.784 1928 56 4 1 1924 726901130 726903055 0.000000e+00 3212
5 TraesCS2B01G601200 chr2A 96.057 279 11 0 1923 2201 726903147 726903425 2.580000e-124 455
6 TraesCS2B01G601200 chr5D 96.630 1929 57 6 1 1924 503259452 503261377 0.000000e+00 3195
7 TraesCS2B01G601200 chr5D 96.421 1928 62 5 1 1924 503250595 503248671 0.000000e+00 3171
8 TraesCS2B01G601200 chr5D 95.699 279 12 0 1923 2201 503248579 503248301 1.200000e-122 449
9 TraesCS2B01G601200 chr5D 95.341 279 13 0 1923 2201 503261469 503261747 5.580000e-121 444
10 TraesCS2B01G601200 chr3D 96.627 1927 60 4 1 1924 589258203 589260127 0.000000e+00 3193
11 TraesCS2B01G601200 chr3D 95.699 279 12 0 1923 2201 589260219 589260497 1.200000e-122 449
12 TraesCS2B01G601200 chr7B 96.369 1928 63 4 1 1924 662732238 662730314 0.000000e+00 3166
13 TraesCS2B01G601200 chr6B 96.317 1928 65 5 1 1924 450085127 450083202 0.000000e+00 3162
14 TraesCS2B01G601200 chr1D 96.317 1928 65 4 1 1924 254530931 254529006 0.000000e+00 3162
15 TraesCS2B01G601200 chr1D 96.057 279 11 0 1923 2201 254528914 254528636 2.580000e-124 455
16 TraesCS2B01G601200 chr7D 96.057 279 11 0 1923 2201 231544318 231544040 2.580000e-124 455
17 TraesCS2B01G601200 chr3A 96.057 279 11 0 1923 2201 66001825 66002103 2.580000e-124 455
18 TraesCS2B01G601200 chrUn 96.000 275 11 0 1923 2197 414709425 414709151 4.310000e-122 448


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 TraesCS2B01G601200 chr2B 784241347 784243547 2200 True 4065.0 4065 100.0000 1 2201 1 chr2B.!!$R2 2200
1 TraesCS2B01G601200 chr3B 201569462 201571387 1925 False 3212.0 3212 96.7840 1 1924 1 chr3B.!!$F1 1923
2 TraesCS2B01G601200 chr3B 201542920 201544842 1922 True 3169.0 3169 96.4210 1 1924 1 chr3B.!!$R1 1923
3 TraesCS2B01G601200 chr2A 726901130 726903425 2295 False 1833.5 3212 96.4205 1 2201 2 chr2A.!!$F1 2200
4 TraesCS2B01G601200 chr5D 503259452 503261747 2295 False 1819.5 3195 95.9855 1 2201 2 chr5D.!!$F1 2200
5 TraesCS2B01G601200 chr5D 503248301 503250595 2294 True 1810.0 3171 96.0600 1 2201 2 chr5D.!!$R1 2200
6 TraesCS2B01G601200 chr3D 589258203 589260497 2294 False 1821.0 3193 96.1630 1 2201 2 chr3D.!!$F1 2200
7 TraesCS2B01G601200 chr7B 662730314 662732238 1924 True 3166.0 3166 96.3690 1 1924 1 chr7B.!!$R1 1923
8 TraesCS2B01G601200 chr6B 450083202 450085127 1925 True 3162.0 3162 96.3170 1 1924 1 chr6B.!!$R1 1923
9 TraesCS2B01G601200 chr1D 254528636 254530931 2295 True 1808.5 3162 96.1870 1 2201 2 chr1D.!!$R1 2200

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
324 325 0.105658 CTGGATCTCTTCCCGGGGTA 60.106 60.0 23.5 8.5 44.77 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 1376 0.544357 TCCCCAAGAGTCCACATCGT 60.544 55.0 0.0 0.0 0.0 3.73 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
35 36 4.961440 TGACCCTTAGGAGTAGGTAACT 57.039 45.455 0.00 0.00 44.36 2.24
160 161 1.400737 AGCTTTACGTCCGCTATCCT 58.599 50.000 0.00 0.00 31.12 3.24
323 324 1.383248 CTGGATCTCTTCCCGGGGT 60.383 63.158 23.50 0.00 44.77 4.95
324 325 0.105658 CTGGATCTCTTCCCGGGGTA 60.106 60.000 23.50 8.50 44.77 3.69
325 326 0.398098 TGGATCTCTTCCCGGGGTAC 60.398 60.000 23.50 5.45 44.77 3.34
573 574 2.423088 CCTCCCCTACAGTATCGTCACT 60.423 54.545 0.00 0.00 0.00 3.41
574 575 3.181447 CCTCCCCTACAGTATCGTCACTA 60.181 52.174 0.00 0.00 0.00 2.74
614 615 3.943671 AATTCGGGATGGATTGGTGTA 57.056 42.857 0.00 0.00 0.00 2.90
641 642 1.134560 CTACGCCTAGGACACCAGAAC 59.865 57.143 14.75 0.00 0.00 3.01
755 756 2.685522 GCCCTCCCTCTCTATCTATCCG 60.686 59.091 0.00 0.00 0.00 4.18
771 772 0.617535 TCCGAGAGATGGAAGGGCAA 60.618 55.000 0.00 0.00 30.98 4.52
776 781 3.683847 CGAGAGATGGAAGGGCAAAGATT 60.684 47.826 0.00 0.00 0.00 2.40
777 782 4.276642 GAGAGATGGAAGGGCAAAGATTT 58.723 43.478 0.00 0.00 0.00 2.17
778 783 4.681484 AGAGATGGAAGGGCAAAGATTTT 58.319 39.130 0.00 0.00 0.00 1.82
884 890 4.204012 AGGAACAAGGTTCAAATCGTTCA 58.796 39.130 10.86 0.00 35.56 3.18
926 932 2.353889 GCATACATCACTGCACTTCCAG 59.646 50.000 0.00 0.00 38.28 3.86
954 960 5.116180 CACCTATTTAAATGGCTCGTCTCA 58.884 41.667 11.05 0.00 0.00 3.27
1106 1112 7.661847 GTGGGCTTACTACTTATATGCTTTCAT 59.338 37.037 0.00 0.00 36.73 2.57
1167 1173 2.176889 AGGCACGATAACTGGTACACT 58.823 47.619 0.00 0.00 0.00 3.55
1194 1200 1.305046 GTCCTTCCCGGTCCTCTCA 60.305 63.158 0.00 0.00 0.00 3.27
1214 1220 5.675421 TCTCATACTAGGGAAAGGTCCTCTA 59.325 44.000 0.00 0.00 44.28 2.43
1277 1283 1.363744 GACATTCTGAACCCAGCTCG 58.636 55.000 0.00 0.00 40.20 5.03
1370 1376 4.792087 GGTGCCAAACCTTCTCGA 57.208 55.556 0.00 0.00 46.55 4.04
1398 1404 1.836802 GACTCTTGGGGAAGATCAGCT 59.163 52.381 0.00 0.00 0.00 4.24
1434 1440 5.416947 AGTAACTTTTATCCGTTGAGCGAT 58.583 37.500 0.00 0.00 44.77 4.58
1439 1446 1.399744 TATCCGTTGAGCGATGGCCT 61.400 55.000 3.32 0.00 44.77 5.19
1484 1491 1.542492 AAGGCCGACTTTCGTCTCTA 58.458 50.000 0.00 0.00 38.40 2.43
1518 1525 2.479566 CTTGCAGTCAAGCTCCCTTA 57.520 50.000 0.00 0.00 42.66 2.69
1565 1572 1.079621 TCTGGCCCGAGGAAACCTA 59.920 57.895 0.00 0.00 31.76 3.08
1572 1579 0.108329 CCGAGGAAACCTATGCACGT 60.108 55.000 0.00 0.00 31.76 4.49
1574 1581 1.653151 GAGGAAACCTATGCACGTCC 58.347 55.000 0.00 0.00 31.76 4.79
1612 1619 1.690352 GCCTACGCCCCATAGAAACTA 59.310 52.381 0.00 0.00 0.00 2.24
1855 1867 0.251832 TTTCACCGAGCCTCTCTCCT 60.252 55.000 0.00 0.00 38.62 3.69
1878 1890 0.172578 CAGTGCCCAGATCGTTACGA 59.827 55.000 10.62 10.62 41.13 3.43
1905 1917 2.580815 GGGTCGGAACTTACCCGG 59.419 66.667 0.00 0.00 45.73 5.73
1972 2077 1.825090 TACGACTTTGCGGAGACCTA 58.175 50.000 0.00 0.00 35.12 3.08
1998 2103 2.344872 GTAAACAGTCGCCCGGGT 59.655 61.111 24.63 0.00 0.00 5.28
2050 2155 1.838077 CACCCCTTCTCCCGAAGTTAT 59.162 52.381 1.92 0.00 44.12 1.89
2063 2168 3.951680 CCGAAGTTATGGGGCTATTTTGT 59.048 43.478 0.00 0.00 0.00 2.83
2130 2235 0.838608 TACCCACCTGTGTCGGTTTT 59.161 50.000 3.98 0.00 34.29 2.43
2157 2262 2.296190 CAGGTACCCTTTTGTTGAAGGC 59.704 50.000 8.74 0.00 43.97 4.35
2197 2302 5.012046 TGGGAGTATGGCATCAGTTACATAG 59.988 44.000 1.65 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.587797 AGAAACAAGGATAGCGAACGA 57.412 42.857 0.00 0.0 0.00 3.85
160 161 5.163163 CCTGAGGGTAGGAAAATCATGATCA 60.163 44.000 9.06 0.0 40.42 2.92
231 232 1.294138 GTGTCGGGGGTTCGAATCA 59.706 57.895 11.19 0.0 41.05 2.57
323 324 6.395780 TCTTAACCTGAAATGAATGGGGTA 57.604 37.500 0.00 0.0 0.00 3.69
324 325 5.269554 TCTTAACCTGAAATGAATGGGGT 57.730 39.130 0.00 0.0 0.00 4.95
325 326 5.951747 TCTTCTTAACCTGAAATGAATGGGG 59.048 40.000 0.00 0.0 0.00 4.96
329 330 7.413446 TCCCATCTTCTTAACCTGAAATGAAT 58.587 34.615 0.00 0.0 0.00 2.57
492 493 6.819397 AAGCTTAACACCTCTTATTTGACC 57.181 37.500 0.00 0.0 0.00 4.02
573 574 7.385752 CGAATTTGGTGGTTAAACTCTACTGTA 59.614 37.037 0.00 0.0 0.00 2.74
574 575 6.204108 CGAATTTGGTGGTTAAACTCTACTGT 59.796 38.462 0.00 0.0 0.00 3.55
614 615 1.284198 TGTCCTAGGCGTAGAGGAACT 59.716 52.381 14.94 0.0 43.52 3.01
641 642 4.036027 CCTTTCCTCATTCATGGTTCGATG 59.964 45.833 0.00 0.0 0.00 3.84
755 756 3.574354 ATCTTTGCCCTTCCATCTCTC 57.426 47.619 0.00 0.0 0.00 3.20
884 890 1.765314 AGCTGAGGCATCCTAACGAAT 59.235 47.619 0.00 0.0 41.70 3.34
926 932 5.123344 ACGAGCCATTTAAATAGGTGTCAAC 59.877 40.000 3.00 0.0 0.00 3.18
954 960 4.228824 TGGAAATAGGATAAGGTAGCGGT 58.771 43.478 0.00 0.0 0.00 5.68
1106 1112 2.145397 AGTGCGGAGAGGATAACTGA 57.855 50.000 0.00 0.0 0.00 3.41
1194 1200 6.043358 GCATTTAGAGGACCTTTCCCTAGTAT 59.957 42.308 0.00 0.0 44.10 2.12
1214 1220 1.165270 GTGTGGGCGTTAGAGCATTT 58.835 50.000 0.00 0.0 39.27 2.32
1293 1299 1.106944 CAAGGGTTGGGTTGTTCGCT 61.107 55.000 0.00 0.0 0.00 4.93
1370 1376 0.544357 TCCCCAAGAGTCCACATCGT 60.544 55.000 0.00 0.0 0.00 3.73
1434 1440 1.070786 GTGACGAGTGGAAAGGCCA 59.929 57.895 5.01 0.0 46.96 5.36
1449 1456 1.100510 CCTTAGTGATCCGACGGTGA 58.899 55.000 14.79 0.0 0.00 4.02
1484 1491 1.957562 CAAGACTCACCCGTCGAGT 59.042 57.895 0.00 0.0 46.32 4.18
1572 1579 1.562475 CCTCCCAAAAGATAACGGGGA 59.438 52.381 0.00 0.0 45.34 4.81
1574 1581 1.389555 GCCTCCCAAAAGATAACGGG 58.610 55.000 0.00 0.0 40.32 5.28
1581 1588 1.298667 GCGTAGGCCTCCCAAAAGA 59.701 57.895 9.68 0.0 0.00 2.52
1612 1619 3.370104 CAAGGGACAGTCTCAGGTAGAT 58.630 50.000 2.43 0.0 36.36 1.98
1855 1867 1.557099 AACGATCTGGGCACTGTCTA 58.443 50.000 0.00 0.0 0.00 2.59
1972 2077 3.243602 GGGCGACTGTTTACCAAAAACAT 60.244 43.478 3.97 0.0 39.16 2.71
2003 2108 2.996734 AAAATGGGGCCGCAGTGG 60.997 61.111 27.76 0.0 42.50 4.00
2016 2121 4.539235 GGTGCCCCCTCACAAAAT 57.461 55.556 0.00 0.0 38.66 1.82
2050 2155 2.617021 GGAACTCGACAAAATAGCCCCA 60.617 50.000 0.00 0.0 0.00 4.96
2063 2168 4.653868 ACAACTCTCTCTAAGGAACTCGA 58.346 43.478 0.00 0.0 38.49 4.04
2089 2194 2.490535 GGTAGAGAATACCTAGGGGCGT 60.491 54.545 14.81 0.0 34.82 5.68
2157 2262 1.298859 CCCAGGAAAAGCTCGAACGG 61.299 60.000 0.00 0.0 0.00 4.44


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

AutoCloner maintained by Alex Coulton.