Multiple sequence alignment - TraesCS1D01G014000

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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 TraesCS1D01G014000 chr1D 100.000 2336 0 0 1 2336 6914347 6916682 0.000000e+00 4314.0
1 TraesCS1D01G014000 chr1D 89.632 1495 129 17 6 1490 407671359 407669881 0.000000e+00 1879.0
2 TraesCS1D01G014000 chr1D 87.231 1535 173 17 3 1529 6713416 6711897 0.000000e+00 1727.0
3 TraesCS1D01G014000 chr1B 96.104 2336 78 9 1 2334 8818737 8816413 0.000000e+00 3797.0
4 TraesCS1D01G014000 chr1B 97.561 41 1 0 2281 2321 548190075 548190035 1.160000e-08 71.3
5 TraesCS1D01G014000 chr1A 90.268 1490 118 18 1 1464 8343231 8344719 0.000000e+00 1923.0
6 TraesCS1D01G014000 chr1A 86.880 1532 174 18 3 1523 8143308 8141793 0.000000e+00 1690.0
7 TraesCS1D01G014000 chr1A 86.349 1531 185 19 4 1523 7835866 7837383 0.000000e+00 1648.0
8 TraesCS1D01G014000 chr4B 86.450 1535 181 18 3 1529 36634666 36633151 0.000000e+00 1657.0
9 TraesCS1D01G014000 chr2A 87.855 1375 156 7 1 1367 611304019 611305390 0.000000e+00 1604.0
10 TraesCS1D01G014000 chr2B 87.837 1373 152 10 1 1367 548625181 548626544 0.000000e+00 1596.0
11 TraesCS1D01G014000 chr5B 78.972 214 38 6 1602 1810 13773306 13773095 3.130000e-29 139.0
12 TraesCS1D01G014000 chr5A 82.639 144 23 2 1669 1810 12191297 12191154 2.440000e-25 126.0


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 TraesCS1D01G014000 chr1D 6914347 6916682 2335 False 4314 4314 100.000 1 2336 1 chr1D.!!$F1 2335
1 TraesCS1D01G014000 chr1D 407669881 407671359 1478 True 1879 1879 89.632 6 1490 1 chr1D.!!$R2 1484
2 TraesCS1D01G014000 chr1D 6711897 6713416 1519 True 1727 1727 87.231 3 1529 1 chr1D.!!$R1 1526
3 TraesCS1D01G014000 chr1B 8816413 8818737 2324 True 3797 3797 96.104 1 2334 1 chr1B.!!$R1 2333
4 TraesCS1D01G014000 chr1A 8343231 8344719 1488 False 1923 1923 90.268 1 1464 1 chr1A.!!$F2 1463
5 TraesCS1D01G014000 chr1A 8141793 8143308 1515 True 1690 1690 86.880 3 1523 1 chr1A.!!$R1 1520
6 TraesCS1D01G014000 chr1A 7835866 7837383 1517 False 1648 1648 86.349 4 1523 1 chr1A.!!$F1 1519
7 TraesCS1D01G014000 chr4B 36633151 36634666 1515 True 1657 1657 86.450 3 1529 1 chr4B.!!$R1 1526
8 TraesCS1D01G014000 chr2A 611304019 611305390 1371 False 1604 1604 87.855 1 1367 1 chr2A.!!$F1 1366
9 TraesCS1D01G014000 chr2B 548625181 548626544 1363 False 1596 1596 87.837 1 1367 1 chr2B.!!$F1 1366

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
137 138 1.376683 TCTGGAACGGGGAATTGCG 60.377 57.895 0.0 0.0 33.92 4.85 F
328 329 4.202377 TGGTTGTTACTGAATCGGAGGAAA 60.202 41.667 0.0 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1057 1063 0.795085 CTGTTGCTGCTGCTAGTGTC 59.205 55.0 17.0 0.0 40.48 3.67 R
1570 1612 0.995024 AAGTTCCCATCCCAGGTCTG 59.005 55.0 0.0 0.0 0.00 3.51 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
137 138 1.376683 TCTGGAACGGGGAATTGCG 60.377 57.895 0.00 0.00 33.92 4.85
232 233 7.330262 AGATTTCTTGCCAAGTTTGAGAAAAA 58.670 30.769 4.04 0.00 39.10 1.94
328 329 4.202377 TGGTTGTTACTGAATCGGAGGAAA 60.202 41.667 0.00 0.00 0.00 3.13
367 368 6.426328 GTGGTCTGCTTCCATTATTCTATGAG 59.574 42.308 0.00 0.00 37.30 2.90
492 493 6.495872 TCTGTATACAAGGGAGTGTTAAGTGT 59.504 38.462 7.06 0.00 32.75 3.55
1057 1063 6.668541 ATTCTTCACCTGAAACATCATACG 57.331 37.500 0.00 0.00 33.07 3.06
1305 1320 2.158475 GGAGATTGATGTGCCCCCAATA 60.158 50.000 0.00 0.00 31.40 1.90
1639 1681 9.515020 TTTTTCTAACTGCTCACAATAAAACTG 57.485 29.630 0.00 0.00 0.00 3.16
1645 1687 4.609947 TGCTCACAATAAAACTGCAACAG 58.390 39.130 0.00 0.00 37.52 3.16
1675 1717 4.391216 CAGTTCTGCAAGTAGGAAGATGTG 59.609 45.833 0.00 0.00 33.76 3.21
1719 1761 2.634982 TGATCAAGCAAAACATCGGC 57.365 45.000 0.00 0.00 0.00 5.54
1770 1812 4.574421 TCCGTGTGATTTGTATAATGCTGG 59.426 41.667 0.00 0.00 0.00 4.85
1863 1905 1.936547 CCGAAGTGCATTCTAGGCTTC 59.063 52.381 0.00 0.00 35.61 3.86
1902 1944 9.758651 ATAAACTATTTTTCTTTTCCACACCAC 57.241 29.630 0.00 0.00 0.00 4.16
1909 1951 3.417101 TCTTTTCCACACCACGCATATT 58.583 40.909 0.00 0.00 0.00 1.28
1912 1954 5.650266 TCTTTTCCACACCACGCATATTAAT 59.350 36.000 0.00 0.00 0.00 1.40
1914 1956 5.994887 TTCCACACCACGCATATTAATAC 57.005 39.130 0.00 0.00 0.00 1.89
1921 1963 7.011016 CACACCACGCATATTAATACTTTCTCA 59.989 37.037 0.00 0.00 0.00 3.27
1947 1989 4.082125 GGAAAATGTGGAACTGATCACCT 58.918 43.478 0.00 0.00 38.04 4.00
2022 2064 8.536175 TCAACTTGGAAGGTTATTTGTTTTTCT 58.464 29.630 0.00 0.00 0.00 2.52
2023 2065 8.603181 CAACTTGGAAGGTTATTTGTTTTTCTG 58.397 33.333 0.00 0.00 0.00 3.02
2091 2133 6.400727 CGGTTTTCGCTATATAGTTACATGCC 60.401 42.308 11.38 5.68 0.00 4.40
2099 2141 6.237942 GCTATATAGTTACATGCCTGCGAATG 60.238 42.308 11.38 0.00 0.00 2.67
2175 2217 2.092753 CACTCTGGCCATGATACCAACT 60.093 50.000 5.51 0.00 34.96 3.16
2176 2218 2.578021 ACTCTGGCCATGATACCAACTT 59.422 45.455 5.51 0.00 34.96 2.66
2246 2288 6.591935 TCTGTTTGGTTGTTATCTCTTCAGT 58.408 36.000 0.00 0.00 0.00 3.41
2268 2310 6.087291 CAGTTTCATTTTTCTGCGATTCTCAC 59.913 38.462 0.00 0.00 0.00 3.51
2284 2326 9.077674 GCGATTCTCACGATACATTTATTATCT 57.922 33.333 0.00 0.00 0.00 1.98
2319 2361 1.163554 GAAGCTGCTTCCTTGGACTG 58.836 55.000 27.74 0.00 34.71 3.51
2324 2366 0.768221 TGCTTCCTTGGACTGGACCT 60.768 55.000 0.00 0.00 32.65 3.85
2327 2369 1.208293 CTTCCTTGGACTGGACCTAGC 59.792 57.143 0.00 0.00 32.91 3.42
2334 2376 1.619977 GGACTGGACCTAGCCAAGAGA 60.620 57.143 0.00 0.00 37.52 3.10
2335 2377 2.393646 GACTGGACCTAGCCAAGAGAT 58.606 52.381 0.00 0.00 37.52 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 6.411630 TGCCGTTGTTCATATTTACACTAC 57.588 37.500 0.00 0.00 0.00 2.73
328 329 3.243839 GCAGACCACACCACATGAATTTT 60.244 43.478 0.00 0.00 0.00 1.82
367 368 1.200020 CCGCCAACACTTCCTTGATTC 59.800 52.381 0.00 0.00 0.00 2.52
492 493 6.020971 TCACTGCTACAATAGTCTTCGAAA 57.979 37.500 0.00 0.00 0.00 3.46
1057 1063 0.795085 CTGTTGCTGCTGCTAGTGTC 59.205 55.000 17.00 0.00 40.48 3.67
1169 1184 1.471684 CAGCCTCTTCCAAGTTGATGC 59.528 52.381 3.87 0.00 0.00 3.91
1369 1384 6.616774 ACAAAGACTAGTACTATCGGCTAC 57.383 41.667 2.33 0.00 0.00 3.58
1425 1457 5.441500 CCTTCCTTTATTCCTTTCTCTCCC 58.558 45.833 0.00 0.00 0.00 4.30
1432 1464 4.420206 AGCTTGCCTTCCTTTATTCCTTT 58.580 39.130 0.00 0.00 0.00 3.11
1570 1612 0.995024 AAGTTCCCATCCCAGGTCTG 59.005 55.000 0.00 0.00 0.00 3.51
1619 1661 6.183360 TGTTGCAGTTTTATTGTGAGCAGTTA 60.183 34.615 0.00 0.00 0.00 2.24
1675 1717 5.359194 TCAACCCATATCTTTCAGACCTC 57.641 43.478 0.00 0.00 0.00 3.85
1719 1761 6.266168 TGAAAATACCTGGCAATTGTACAG 57.734 37.500 19.24 19.24 0.00 2.74
1793 1835 6.421501 TGTCATTTCAGCACAACATTGAAATC 59.578 34.615 8.30 1.53 45.03 2.17
1883 1925 3.118956 TGCGTGGTGTGGAAAAGAAAAAT 60.119 39.130 0.00 0.00 0.00 1.82
1912 1954 7.831691 TCCACATTTTCCAAATGAGAAAGTA 57.168 32.000 14.66 0.00 34.84 2.24
1914 1956 7.170320 CAGTTCCACATTTTCCAAATGAGAAAG 59.830 37.037 14.66 9.47 34.84 2.62
1921 1963 6.458210 GTGATCAGTTCCACATTTTCCAAAT 58.542 36.000 0.00 0.00 33.72 2.32
1975 2017 7.170998 AGTTGACCAAGTAGACGAAATTTACTG 59.829 37.037 0.00 0.00 0.00 2.74
1986 2028 4.065789 CCTTCCAAGTTGACCAAGTAGAC 58.934 47.826 3.87 0.00 0.00 2.59
2022 2064 7.882791 TCTGCACAAGAAATTTCTACCTTATCA 59.117 33.333 20.76 11.19 36.28 2.15
2023 2065 8.268850 TCTGCACAAGAAATTTCTACCTTATC 57.731 34.615 20.76 7.66 36.28 1.75
2131 2173 5.587388 CACCATATCTTTGTGCCTGAAAT 57.413 39.130 0.00 0.00 0.00 2.17
2284 2326 4.637534 GCAGCTTCCTCATTCAACTGAATA 59.362 41.667 4.66 0.00 42.41 1.75
2289 2331 2.875094 AGCAGCTTCCTCATTCAACT 57.125 45.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.