Multiple sequence alignment - TraesCS2D01G244800

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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 TraesCS2D01G244800 chr2D 100.000 2237 0 0 1 2237 276942514 276944750 0.000000e+00 4132
1 TraesCS2D01G244800 chr2A 92.635 2254 141 9 1 2237 313900718 313902963 0.000000e+00 3219
2 TraesCS2D01G244800 chr2A 93.614 1613 82 8 1 1595 305826871 305825262 0.000000e+00 2388
3 TraesCS2D01G244800 chr2A 93.270 1263 70 2 1 1248 628571074 628572336 0.000000e+00 1847
4 TraesCS2D01G244800 chr2A 93.117 1264 70 4 1 1248 374484942 374486204 0.000000e+00 1836
5 TraesCS2D01G244800 chr2A 92.959 1264 67 5 1 1248 161528138 161529395 0.000000e+00 1821
6 TraesCS2D01G244800 chr2A 92.041 980 61 4 633 1595 756945365 756944386 0.000000e+00 1362
7 TraesCS2D01G244800 chr5B 94.169 1612 75 6 1 1595 411794778 411796387 0.000000e+00 2438
8 TraesCS2D01G244800 chr4B 90.763 1613 130 6 1 1595 256158621 256157010 0.000000e+00 2135
9 TraesCS2D01G244800 chr2B 93.829 1264 61 4 1 1248 424683749 424682487 0.000000e+00 1886
10 TraesCS2D01G244800 chr2B 84.399 391 54 5 1604 1989 261045098 261044710 5.830000e-101 377
11 TraesCS2D01G244800 chr2B 87.189 281 34 2 1596 1876 697514166 697514444 3.580000e-83 318
12 TraesCS2D01G244800 chr1B 93.513 1264 65 4 1 1248 95493309 95494571 0.000000e+00 1864
13 TraesCS2D01G244800 chr1A 93.354 1264 68 3 1 1248 409610502 409611765 0.000000e+00 1855
14 TraesCS2D01G244800 chr7A 92.755 980 54 4 633 1595 2870254 2871233 0.000000e+00 1400
15 TraesCS2D01G244800 chr7A 91.939 980 62 4 633 1595 85878818 85877839 0.000000e+00 1356
16 TraesCS2D01G244800 chr6A 92.041 980 61 4 633 1595 604391783 604392762 0.000000e+00 1362
17 TraesCS2D01G244800 chr4A 91.939 980 62 4 633 1595 684408419 684409398 0.000000e+00 1356
18 TraesCS2D01G244800 chr3A 91.735 980 64 4 633 1595 26421876 26420897 0.000000e+00 1345
19 TraesCS2D01G244800 chr5D 89.752 644 64 2 1596 2237 223377814 223377171 0.000000e+00 822
20 TraesCS2D01G244800 chr6D 84.769 650 71 17 1592 2236 184531946 184532572 5.240000e-176 627
21 TraesCS2D01G244800 chr6B 83.645 642 78 15 1590 2225 383728978 383728358 1.490000e-161 579
22 TraesCS2D01G244800 chr1D 75.753 631 114 27 1605 2222 165126383 165126987 4.700000e-72 281
23 TraesCS2D01G244800 chrUn 82.828 297 47 3 1595 1889 69002281 69001987 1.700000e-66 263
24 TraesCS2D01G244800 chr4D 86.364 154 20 1 1605 1758 504376642 504376794 1.370000e-37 167
25 TraesCS2D01G244800 chr7D 83.333 168 27 1 1592 1759 115442327 115442161 1.070000e-33 154


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 TraesCS2D01G244800 chr2D 276942514 276944750 2236 False 4132 4132 100.000 1 2237 1 chr2D.!!$F1 2236
1 TraesCS2D01G244800 chr2A 313900718 313902963 2245 False 3219 3219 92.635 1 2237 1 chr2A.!!$F2 2236
2 TraesCS2D01G244800 chr2A 305825262 305826871 1609 True 2388 2388 93.614 1 1595 1 chr2A.!!$R1 1594
3 TraesCS2D01G244800 chr2A 628571074 628572336 1262 False 1847 1847 93.270 1 1248 1 chr2A.!!$F4 1247
4 TraesCS2D01G244800 chr2A 374484942 374486204 1262 False 1836 1836 93.117 1 1248 1 chr2A.!!$F3 1247
5 TraesCS2D01G244800 chr2A 161528138 161529395 1257 False 1821 1821 92.959 1 1248 1 chr2A.!!$F1 1247
6 TraesCS2D01G244800 chr2A 756944386 756945365 979 True 1362 1362 92.041 633 1595 1 chr2A.!!$R2 962
7 TraesCS2D01G244800 chr5B 411794778 411796387 1609 False 2438 2438 94.169 1 1595 1 chr5B.!!$F1 1594
8 TraesCS2D01G244800 chr4B 256157010 256158621 1611 True 2135 2135 90.763 1 1595 1 chr4B.!!$R1 1594
9 TraesCS2D01G244800 chr2B 424682487 424683749 1262 True 1886 1886 93.829 1 1248 1 chr2B.!!$R2 1247
10 TraesCS2D01G244800 chr1B 95493309 95494571 1262 False 1864 1864 93.513 1 1248 1 chr1B.!!$F1 1247
11 TraesCS2D01G244800 chr1A 409610502 409611765 1263 False 1855 1855 93.354 1 1248 1 chr1A.!!$F1 1247
12 TraesCS2D01G244800 chr7A 2870254 2871233 979 False 1400 1400 92.755 633 1595 1 chr7A.!!$F1 962
13 TraesCS2D01G244800 chr7A 85877839 85878818 979 True 1356 1356 91.939 633 1595 1 chr7A.!!$R1 962
14 TraesCS2D01G244800 chr6A 604391783 604392762 979 False 1362 1362 92.041 633 1595 1 chr6A.!!$F1 962
15 TraesCS2D01G244800 chr4A 684408419 684409398 979 False 1356 1356 91.939 633 1595 1 chr4A.!!$F1 962
16 TraesCS2D01G244800 chr3A 26420897 26421876 979 True 1345 1345 91.735 633 1595 1 chr3A.!!$R1 962
17 TraesCS2D01G244800 chr5D 223377171 223377814 643 True 822 822 89.752 1596 2237 1 chr5D.!!$R1 641
18 TraesCS2D01G244800 chr6D 184531946 184532572 626 False 627 627 84.769 1592 2236 1 chr6D.!!$F1 644
19 TraesCS2D01G244800 chr6B 383728358 383728978 620 True 579 579 83.645 1590 2225 1 chr6B.!!$R1 635
20 TraesCS2D01G244800 chr1D 165126383 165126987 604 False 281 281 75.753 1605 2222 1 chr1D.!!$F1 617

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
420 421 0.03889 TTTCATGGGATGACCGCCAA 59.961 50.0 0.0 0.0 44.64 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2137 0.546747 ATGTGAACCGGGAAGAGGGA 60.547 55.0 6.32 0.0 0.0 4.2 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
21 22 1.834263 AGCATCACCTCCTACAAGGAC 59.166 52.381 0.00 0.00 40.06 3.85
204 205 4.379290 GCAAGCCTTGAGAAAGATCTTGTC 60.379 45.833 9.17 9.71 35.54 3.18
214 215 5.784177 AGAAAGATCTTGTCGACTTGCTTA 58.216 37.500 17.92 0.00 29.15 3.09
216 217 6.706270 AGAAAGATCTTGTCGACTTGCTTAAA 59.294 34.615 17.92 0.00 29.15 1.52
397 398 4.702131 TCAAAGAGATAAGGAAGCAAAGCC 59.298 41.667 0.00 0.00 0.00 4.35
420 421 0.038890 TTTCATGGGATGACCGCCAA 59.961 50.000 0.00 0.00 44.64 4.52
573 574 6.881602 CACCCTAAAGCTAGAAAGTTCAAGAT 59.118 38.462 0.00 0.00 0.00 2.40
654 655 8.913487 ACTTCATTCATATGCTCATGTCATTA 57.087 30.769 0.00 0.00 0.00 1.90
785 789 2.040145 TGCTCAACCCAATCACATCTCA 59.960 45.455 0.00 0.00 0.00 3.27
804 808 3.431415 TCAAGAATCTTGGAGGAGTCGA 58.569 45.455 21.35 0.00 35.76 4.20
843 847 2.996249 TCAGCTGATGGTGAGAATCC 57.004 50.000 13.74 0.00 44.58 3.01
1022 1039 6.678900 GCAATGATGGAGAAGTACATGGAAAC 60.679 42.308 0.00 0.00 0.00 2.78
1076 1093 1.538047 CCAAGGGTTGTGGATGAGTG 58.462 55.000 0.00 0.00 38.54 3.51
1096 1113 5.251764 AGTGCTCTATCAAAAACTGCATCT 58.748 37.500 0.00 0.00 0.00 2.90
1127 1145 6.009589 TGAAAACAATGGACATCACACCTAT 58.990 36.000 0.00 0.00 0.00 2.57
1135 1153 6.867519 TGGACATCACACCTATAGAAGAAA 57.132 37.500 0.00 0.00 0.00 2.52
1141 1159 7.497249 ACATCACACCTATAGAAGAAATCAAGC 59.503 37.037 0.00 0.00 0.00 4.01
1385 1404 6.702329 CCTTGTTCATCTAGTAACCTGAAGT 58.298 40.000 0.00 0.00 0.00 3.01
1425 1444 6.331369 TCACATCAAAAGGTCCATTTCTTC 57.669 37.500 0.00 0.00 0.00 2.87
1440 1459 6.207417 TCCATTTCTTCTTCTGGTTGTTGATC 59.793 38.462 0.00 0.00 0.00 2.92
1441 1460 5.673337 TTTCTTCTTCTGGTTGTTGATCG 57.327 39.130 0.00 0.00 0.00 3.69
1529 1549 0.671781 GCCTCTCATCGTGTTGCTGT 60.672 55.000 0.00 0.00 0.00 4.40
1673 1693 5.156608 TCATCATCCATTCGAGTATGCAT 57.843 39.130 3.79 3.79 0.00 3.96
1723 1743 2.288025 GCCACGTAGGAAGGGGACA 61.288 63.158 8.04 0.00 41.22 4.02
1856 1876 1.308216 CCTGTTCATCCCCTCCCCT 60.308 63.158 0.00 0.00 0.00 4.79
1878 1901 4.798682 GCTCTTCCCCTCCCCCGA 62.799 72.222 0.00 0.00 0.00 5.14
1883 1906 3.494080 TTCCCCTCCCCCGAGTTGT 62.494 63.158 0.00 0.00 33.93 3.32
1935 1959 0.923358 TTTCCCCACACCAACACTCT 59.077 50.000 0.00 0.00 0.00 3.24
2035 2059 2.031012 TCGCTGGTGTTCAGGCAG 59.969 61.111 0.00 0.00 43.54 4.85
2036 2060 2.031012 CGCTGGTGTTCAGGCAGA 59.969 61.111 0.00 0.00 43.54 4.26
2038 2062 1.227943 GCTGGTGTTCAGGCAGACA 60.228 57.895 0.00 0.00 43.54 3.41
2109 2137 1.561542 CTACTGGTCCCAATCTGCCTT 59.438 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.233431 CCTCTCCTCCTCTTTGTCACAG 59.767 54.545 0.00 0.00 0.00 3.66
214 215 4.910195 TGTTCAGGTGTATCATGCTCTTT 58.090 39.130 0.00 0.00 0.00 2.52
216 217 4.767578 ATGTTCAGGTGTATCATGCTCT 57.232 40.909 0.00 0.00 0.00 4.09
397 398 1.721487 GGTCATCCCATGAAACGCG 59.279 57.895 3.53 3.53 41.69 6.01
420 421 2.369860 TGGATCCGCTAGAATCTTGCAT 59.630 45.455 16.09 3.68 32.19 3.96
573 574 5.221441 GCTTCAAAAAGAGGGAAGGCTTTTA 60.221 40.000 0.00 0.00 41.88 1.52
785 789 3.165875 TGTCGACTCCTCCAAGATTCTT 58.834 45.455 17.92 0.00 0.00 2.52
804 808 5.182760 GCTGATGTTTCTCCTTGATTCTTGT 59.817 40.000 0.00 0.00 0.00 3.16
843 847 0.035630 CTGCACCCTTTCTCCTCCAG 60.036 60.000 0.00 0.00 0.00 3.86
1022 1039 3.197790 CCACATGCTTCGCCCTCG 61.198 66.667 0.00 0.00 0.00 4.63
1076 1093 7.574496 CAGATAGATGCAGTTTTTGATAGAGC 58.426 38.462 0.00 0.00 0.00 4.09
1096 1113 5.945191 TGATGTCCATTGTTTTCAGCAGATA 59.055 36.000 0.00 0.00 0.00 1.98
1127 1145 5.160607 TCGGAAAGGCTTGATTTCTTCTA 57.839 39.130 0.00 0.00 36.96 2.10
1141 1159 3.526534 GGATCTTGAAGACTCGGAAAGG 58.473 50.000 0.00 0.00 0.00 3.11
1224 1242 6.338146 TGAGTACCTGAGTTATTCCATTTCG 58.662 40.000 0.00 0.00 0.00 3.46
1385 1404 6.295249 TGATGTGAACTAGTTGAACCATCAA 58.705 36.000 19.19 8.63 43.18 2.57
1425 1444 8.286800 TGTTTTATTACGATCAACAACCAGAAG 58.713 33.333 0.00 0.00 0.00 2.85
1480 1500 8.245195 ACAACCATAGTTAAAAGGAACAACAT 57.755 30.769 0.00 0.00 33.27 2.71
1529 1549 7.500892 TGGAGTCTTTGCTTAGTTATCAAACAA 59.499 33.333 0.00 0.00 38.12 2.83
1587 1607 5.220989 GGGCGTTATCATTAGGGAAAACTTC 60.221 44.000 0.00 0.00 0.00 3.01
1673 1693 4.583907 TCTGCCAAATTGTGTCAAGATTCA 59.416 37.500 0.00 0.00 0.00 2.57
1723 1743 3.359695 ACTGTTAAACACCCACACACT 57.640 42.857 0.00 0.00 0.00 3.55
1856 1876 1.613630 GGGAGGGGAAGAGCAGACA 60.614 63.158 0.00 0.00 0.00 3.41
1878 1901 2.751816 GCAAGGTGGGGAAACTACAACT 60.752 50.000 0.00 0.00 36.92 3.16
1883 1906 0.774491 AGGGCAAGGTGGGGAAACTA 60.774 55.000 0.00 0.00 0.00 2.24
1935 1959 2.011947 CTTGCCATTGCTCTCGAATGA 58.988 47.619 0.00 0.00 38.71 2.57
2035 2059 1.875813 CCAGCGACGATGCTCTGTC 60.876 63.158 7.77 0.00 45.23 3.51
2036 2060 2.182791 CCAGCGACGATGCTCTGT 59.817 61.111 7.77 0.00 45.23 3.41
2038 2062 2.804167 CTCCAGCGACGATGCTCT 59.196 61.111 7.77 0.00 45.23 4.09
2109 2137 0.546747 ATGTGAACCGGGAAGAGGGA 60.547 55.000 6.32 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.