Multiple sequence alignment - TraesCS5D01G096500

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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 TraesCS5D01G096500 chr5D 100.000 2513 0 0 1 2513 106939216 106941728 0.000000e+00 4641.0
1 TraesCS5D01G096500 chr5D 98.018 1917 18 9 1 1913 107011555 107013455 0.000000e+00 3312.0
2 TraesCS5D01G096500 chr5D 87.028 848 81 12 827 1660 104825941 104826773 0.000000e+00 929.0
3 TraesCS5D01G096500 chr5D 86.910 848 82 12 827 1660 104580051 104579219 0.000000e+00 924.0
4 TraesCS5D01G096500 chr5D 92.788 624 34 6 1893 2513 107013876 107014491 0.000000e+00 893.0
5 TraesCS5D01G096500 chr5D 91.316 380 21 4 1769 2146 107030629 107030998 2.230000e-140 508.0
6 TraesCS5D01G096500 chr5D 93.787 338 20 1 2177 2513 107030999 107031336 8.020000e-140 507.0
7 TraesCS5D01G096500 chr5A 92.020 1842 90 28 423 2246 136643564 136645366 0.000000e+00 2534.0
8 TraesCS5D01G096500 chr5A 93.865 163 9 1 1 162 136641825 136641987 6.940000e-61 244.0
9 TraesCS5D01G096500 chr5A 95.604 91 3 1 160 249 136642251 136642341 7.240000e-31 145.0
10 TraesCS5D01G096500 chr5A 88.060 67 8 0 183 249 136642324 136642390 2.070000e-11 80.5
11 TraesCS5D01G096500 chr5B 95.626 1006 31 5 921 1925 115870899 115871892 0.000000e+00 1602.0
12 TraesCS5D01G096500 chr5B 93.664 584 34 2 1930 2513 115886039 115886619 0.000000e+00 870.0
13 TraesCS5D01G096500 chr5B 90.091 656 14 11 265 888 115870269 115870905 0.000000e+00 804.0
14 TraesCS5D01G096500 chr5B 89.855 483 36 3 827 1298 114446393 114446873 2.140000e-170 608.0
15 TraesCS5D01G096500 chr5B 85.246 427 46 12 1293 1718 114452344 114452754 8.310000e-115 424.0
16 TraesCS5D01G096500 chr5B 98.222 225 4 0 22 246 115869927 115870151 6.520000e-106 394.0
17 TraesCS5D01G096500 chr2D 88.947 190 15 6 63 249 637604145 637604331 1.940000e-56 230.0
18 TraesCS5D01G096500 chr2B 76.640 381 77 12 2127 2501 697466570 697466944 1.520000e-47 200.0
19 TraesCS5D01G096500 chr2B 82.000 150 17 8 63 210 463359908 463359767 4.390000e-23 119.0
20 TraesCS5D01G096500 chr3A 83.871 186 23 5 70 249 507118597 507118781 1.200000e-38 171.0
21 TraesCS5D01G096500 chr3A 93.333 45 3 0 2127 2171 375740703 375740747 1.610000e-07 67.6
22 TraesCS5D01G096500 chr4B 76.176 340 64 14 2127 2460 673115774 673116102 2.000000e-36 163.0
23 TraesCS5D01G096500 chr4B 97.500 40 1 0 2390 2429 486625509 486625470 4.490000e-08 69.4
24 TraesCS5D01G096500 chr7A 79.186 221 36 9 2120 2335 458124971 458125186 7.240000e-31 145.0
25 TraesCS5D01G096500 chr6D 86.420 81 8 3 2127 2205 123121045 123121124 4.450000e-13 86.1
26 TraesCS5D01G096500 chr2A 86.842 76 7 3 135 210 762413653 762413581 5.760000e-12 82.4
27 TraesCS5D01G096500 chr7B 95.556 45 2 0 2127 2171 552907388 552907344 3.470000e-09 73.1
28 TraesCS5D01G096500 chr7B 95.349 43 2 0 2127 2169 552873210 552873168 4.490000e-08 69.4
29 TraesCS5D01G096500 chr3D 85.294 68 10 0 182 249 384565964 384566031 1.250000e-08 71.3


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 TraesCS5D01G096500 chr5D 106939216 106941728 2512 False 4641.000000 4641 100.000000 1 2513 1 chr5D.!!$F2 2512
1 TraesCS5D01G096500 chr5D 107011555 107014491 2936 False 2102.500000 3312 95.403000 1 2513 2 chr5D.!!$F3 2512
2 TraesCS5D01G096500 chr5D 104825941 104826773 832 False 929.000000 929 87.028000 827 1660 1 chr5D.!!$F1 833
3 TraesCS5D01G096500 chr5D 104579219 104580051 832 True 924.000000 924 86.910000 827 1660 1 chr5D.!!$R1 833
4 TraesCS5D01G096500 chr5D 107030629 107031336 707 False 507.500000 508 92.551500 1769 2513 2 chr5D.!!$F4 744
5 TraesCS5D01G096500 chr5A 136641825 136645366 3541 False 750.875000 2534 92.387250 1 2246 4 chr5A.!!$F1 2245
6 TraesCS5D01G096500 chr5B 115869927 115871892 1965 False 933.333333 1602 94.646333 22 1925 3 chr5B.!!$F4 1903
7 TraesCS5D01G096500 chr5B 115886039 115886619 580 False 870.000000 870 93.664000 1930 2513 1 chr5B.!!$F3 583

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
628 2001 5.374921 TCTCCCTTCGTACGATCTAGATTT 58.625 41.667 20.27 0.0 0.00 2.17 F
1316 2706 1.633915 AAGCTGAGGAGGATGCCCTG 61.634 60.000 0.00 0.0 44.53 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 2890 0.179936 GGCTGCCTCAATCAGTAGCT 59.820 55.0 12.43 0.0 33.16 3.32 R
2224 4069 1.448985 TTTGATAGAGCACGGTTGGC 58.551 50.0 0.00 0.0 0.00 4.52 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
628 2001 5.374921 TCTCCCTTCGTACGATCTAGATTT 58.625 41.667 20.27 0.00 0.00 2.17
675 2048 5.855925 CGATTGGATCTACATCTCTCTTTCG 59.144 44.000 0.00 0.00 0.00 3.46
1316 2706 1.633915 AAGCTGAGGAGGATGCCCTG 61.634 60.000 0.00 0.00 44.53 4.45
1449 2839 3.673484 GCAAAAGCCGAGGCAGCA 61.673 61.111 17.18 0.00 44.88 4.41
1565 2962 2.967599 TGTGATCTGAAGACGATGGG 57.032 50.000 0.00 0.00 0.00 4.00
1770 3171 3.547746 TGTGTAACCTGACCCTTTGTTC 58.452 45.455 0.00 0.00 34.36 3.18
1811 3212 1.718396 TTCTCTTCTGCTCACATGCG 58.282 50.000 0.00 0.00 35.36 4.73
1812 3213 0.108472 TCTCTTCTGCTCACATGCGG 60.108 55.000 0.00 0.00 40.46 5.69
1813 3214 1.078918 TCTTCTGCTCACATGCGGG 60.079 57.895 0.00 0.00 39.62 6.13
1814 3215 2.747460 TTCTGCTCACATGCGGGC 60.747 61.111 0.00 0.00 39.62 6.13
1815 3216 3.258228 TTCTGCTCACATGCGGGCT 62.258 57.895 7.19 0.00 39.62 5.19
1816 3217 3.506096 CTGCTCACATGCGGGCTG 61.506 66.667 7.19 2.29 35.80 4.85
1879 3280 3.549625 CGCGTCCTTGTATACTTCTACCC 60.550 52.174 4.17 0.00 0.00 3.69
2076 3921 4.493547 CCAACAAAACTGCTTGACTTTCA 58.506 39.130 0.00 0.00 0.00 2.69
2127 3972 8.302515 TCTAAATACTCTTTCCCTCGTATGTT 57.697 34.615 0.00 0.00 0.00 2.71
2156 4001 1.060122 CGAAACCCGTAGAACAATCGC 59.940 52.381 0.00 0.00 0.00 4.58
2175 4020 9.784680 ACAATCGCTCTACGGTATATATTAAAG 57.215 33.333 0.00 0.00 43.89 1.85
2231 4077 4.306600 AGAAAGCAAAAATTAGCCAACCG 58.693 39.130 0.00 0.00 0.00 4.44
2327 4173 6.397272 TCAAACTTGAACTTGATTTTGTGCT 58.603 32.000 0.00 0.00 33.55 4.40
2369 4215 9.962783 CATTTTTCAATAATCCTCTCCAAGATC 57.037 33.333 0.00 0.00 0.00 2.75
2383 4229 6.552932 TCTCCAAGATCGAATAGAATAGGGA 58.447 40.000 0.00 0.00 0.00 4.20
2441 4287 2.524306 TGTTCCAACACCCCATGATTC 58.476 47.619 0.00 0.00 33.17 2.52
2462 4308 7.779326 TGATTCAGATTTCCATAGCAATTGGTA 59.221 33.333 18.95 18.95 35.64 3.25
2463 4309 7.953005 TTCAGATTTCCATAGCAATTGGTAA 57.047 32.000 20.35 6.83 35.64 2.85
2475 4321 3.371595 GCAATTGGTAAGGGGAGAGCTTA 60.372 47.826 7.72 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.518493 ACAAATATCATCATGGATTGGTTGC 58.482 36.000 0.00 0.00 0.00 4.17
462 1821 6.144402 CGTTTTGATCTGGAAGGTTTGATTTG 59.856 38.462 0.00 0.00 0.00 2.32
628 2001 1.801302 AACGACCTGGAGGAGAGGGA 61.801 60.000 0.00 0.00 38.94 4.20
675 2048 1.821216 TCCTGAAATTTCCTGTCGCC 58.179 50.000 15.48 0.00 0.00 5.54
1316 2706 0.543749 ATGGAAGGAGTGGTAGCAGC 59.456 55.000 0.00 0.00 0.00 5.25
1449 2839 1.078214 CCCATCACCACATGTCGCT 60.078 57.895 0.00 0.00 0.00 4.93
1477 2867 4.070552 GAGTCTCCGCCGCTTGGT 62.071 66.667 0.00 0.00 34.16 3.67
1500 2890 0.179936 GGCTGCCTCAATCAGTAGCT 59.820 55.000 12.43 0.00 33.16 3.32
1565 2962 0.321996 AGAAAGTCCTTGGCCGAGTC 59.678 55.000 19.14 9.20 0.00 3.36
1660 3060 9.354673 CATCTTAGCCTTAATCTCCCAAAATAA 57.645 33.333 0.00 0.00 0.00 1.40
1661 3061 7.944554 CCATCTTAGCCTTAATCTCCCAAAATA 59.055 37.037 0.00 0.00 0.00 1.40
1742 3143 5.836024 AGGGTCAGGTTACACAGATTAAA 57.164 39.130 0.00 0.00 0.00 1.52
1770 3171 2.276740 GGTTGCCCATCCCCAGAG 59.723 66.667 0.00 0.00 0.00 3.35
1811 3212 3.127533 CAGTTACAGCCGCAGCCC 61.128 66.667 0.00 0.00 41.25 5.19
1812 3213 3.804193 GCAGTTACAGCCGCAGCC 61.804 66.667 0.00 0.00 41.25 4.85
1813 3214 4.152625 CGCAGTTACAGCCGCAGC 62.153 66.667 0.00 0.00 40.32 5.25
1814 3215 4.152625 GCGCAGTTACAGCCGCAG 62.153 66.667 0.30 0.00 33.78 5.18
1879 3280 8.523523 TTGCATGTCATTTCACTGATAAAAAG 57.476 30.769 0.00 0.00 0.00 2.27
1889 3290 4.093514 CACGAGATTGCATGTCATTTCAC 58.906 43.478 0.00 0.00 0.00 3.18
2127 3972 3.539604 TCTACGGGTTTCGGTTCAAAAA 58.460 40.909 0.00 0.00 44.45 1.94
2224 4069 1.448985 TTTGATAGAGCACGGTTGGC 58.551 50.000 0.00 0.00 0.00 4.52
2231 4077 5.841957 AATGATGGGTTTTGATAGAGCAC 57.158 39.130 0.00 0.00 0.00 4.40
2273 4119 2.996249 TCCAGCTGGATTGATCAGTC 57.004 50.000 32.00 9.63 39.78 3.51
2298 4144 3.297134 TCAAGTTCAAGTTTGAGGCCT 57.703 42.857 3.86 3.86 38.61 5.19
2327 4173 4.640771 AAAATGACCTCCAGCTTCTACA 57.359 40.909 0.00 0.00 0.00 2.74
2369 4215 7.163001 TCAGATCACATCCCTATTCTATTCG 57.837 40.000 0.00 0.00 0.00 3.34
2383 4229 6.323225 GGAATGGGAAAATCTTCAGATCACAT 59.677 38.462 0.00 0.00 32.75 3.21
2441 4287 6.239120 CCCTTACCAATTGCTATGGAAATCTG 60.239 42.308 12.26 0.00 40.56 2.90
2475 4321 3.245658 TGAGGAGGTTACACTTCTAGCCT 60.246 47.826 0.00 0.00 30.36 4.58


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

AutoCloner maintained by Alex Coulton.