Multiple sequence alignment - TraesCS4D01G155100

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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 TraesCS4D01G155100 chr4D 100.000 2213 0 0 1 2213 207068217 207066005 0.000000e+00 4087
1 TraesCS4D01G155100 chr2D 94.739 2224 100 10 2 2213 638424514 638426732 0.000000e+00 3443
2 TraesCS4D01G155100 chr2D 95.376 173 7 1 244 416 112182002 112182173 7.780000e-70 274
3 TraesCS4D01G155100 chr1D 94.557 2223 106 11 2 2213 254435043 254437261 0.000000e+00 3421
4 TraesCS4D01G155100 chr1D 93.348 2225 122 16 2 2213 51871928 51869717 0.000000e+00 3265
5 TraesCS4D01G155100 chr5D 94.474 2226 105 11 2 2213 503291880 503294101 0.000000e+00 3413
6 TraesCS4D01G155100 chr5D 94.065 2224 100 12 2 2213 6176907 6174704 0.000000e+00 3347
7 TraesCS4D01G155100 chr5D 94.815 1890 80 10 2 1877 512410194 512412079 0.000000e+00 2931
8 TraesCS4D01G155100 chr5D 94.815 1890 79 11 2 1877 512417131 512419015 0.000000e+00 2929
9 TraesCS4D01G155100 chr5D 91.411 489 39 3 1726 2213 12935856 12936342 0.000000e+00 667
10 TraesCS4D01G155100 chr4B 93.579 2227 124 10 2 2213 308679759 308677537 0.000000e+00 3302
11 TraesCS4D01G155100 chr1B 94.603 1890 86 11 336 2213 633708037 633709922 0.000000e+00 2911
12 TraesCS4D01G155100 chr2B 95.090 387 19 0 61 447 90714308 90713922 5.220000e-171 610
13 TraesCS4D01G155100 chr3B 95.618 251 11 0 180 430 460131979 460132229 9.520000e-109 403
14 TraesCS4D01G155100 chr7D 93.985 266 14 1 1950 2213 231596557 231596822 3.420000e-108 401
15 TraesCS4D01G155100 chr3A 91.795 195 16 0 136 330 614191799 614191605 2.800000e-69 272
16 TraesCS4D01G155100 chr3A 98.246 57 1 0 2 58 421091101 421091045 1.400000e-17 100


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 TraesCS4D01G155100 chr4D 207066005 207068217 2212 True 4087 4087 100.000 1 2213 1 chr4D.!!$R1 2212
1 TraesCS4D01G155100 chr2D 638424514 638426732 2218 False 3443 3443 94.739 2 2213 1 chr2D.!!$F2 2211
2 TraesCS4D01G155100 chr1D 254435043 254437261 2218 False 3421 3421 94.557 2 2213 1 chr1D.!!$F1 2211
3 TraesCS4D01G155100 chr1D 51869717 51871928 2211 True 3265 3265 93.348 2 2213 1 chr1D.!!$R1 2211
4 TraesCS4D01G155100 chr5D 503291880 503294101 2221 False 3413 3413 94.474 2 2213 1 chr5D.!!$F2 2211
5 TraesCS4D01G155100 chr5D 6174704 6176907 2203 True 3347 3347 94.065 2 2213 1 chr5D.!!$R1 2211
6 TraesCS4D01G155100 chr5D 512410194 512412079 1885 False 2931 2931 94.815 2 1877 1 chr5D.!!$F3 1875
7 TraesCS4D01G155100 chr5D 512417131 512419015 1884 False 2929 2929 94.815 2 1877 1 chr5D.!!$F4 1875
8 TraesCS4D01G155100 chr4B 308677537 308679759 2222 True 3302 3302 93.579 2 2213 1 chr4B.!!$R1 2211
9 TraesCS4D01G155100 chr1B 633708037 633709922 1885 False 2911 2911 94.603 336 2213 1 chr1B.!!$F1 1877

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
523 525 0.179034 AGCCGAGCCATTCATTCCTC 60.179 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1976 0.031917 TAGAGGGGCGTATCCAACCA 60.032 55.0 0.0 0.0 36.21 3.67 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
28 29 1.488705 ATCCGCTCAAGGACCCACAA 61.489 55.000 0.00 0.00 44.07 3.33
123 124 2.271800 CTTCGTGCTCCATGGTTAGAC 58.728 52.381 12.58 3.92 0.00 2.59
209 210 6.208988 AGAACGACACTCAGCAGAATATAA 57.791 37.500 0.00 0.00 0.00 0.98
217 218 4.716784 ACTCAGCAGAATATAAGACCCACA 59.283 41.667 0.00 0.00 0.00 4.17
251 252 1.540267 TTAAATTCTGTGGGTGGCGG 58.460 50.000 0.00 0.00 0.00 6.13
288 289 8.964476 TCAATTCAGTTAATTATGTCTCTCCC 57.036 34.615 0.00 0.00 35.54 4.30
290 291 9.177608 CAATTCAGTTAATTATGTCTCTCCCAA 57.822 33.333 0.00 0.00 35.54 4.12
416 417 3.621268 GGAATCGATCGTGATTTGGAACA 59.379 43.478 15.94 0.00 38.65 3.18
424 425 5.356882 TCGTGATTTGGAACATGTTCTTC 57.643 39.130 31.81 23.31 39.30 2.87
451 452 9.588096 ACATGAACCCTCTTAACTAAGATTTTT 57.412 29.630 0.00 0.00 41.12 1.94
523 525 0.179034 AGCCGAGCCATTCATTCCTC 60.179 55.000 0.00 0.00 0.00 3.71
547 550 8.760980 TCTTATGAAAGAAAGAAAAGGGACAA 57.239 30.769 0.00 0.00 38.81 3.18
694 701 8.326765 TCCACAGCCTAATCCTTATTTTACTA 57.673 34.615 0.00 0.00 0.00 1.82
870 882 3.048600 TCTTCTCACCCCCATATCCAAG 58.951 50.000 0.00 0.00 0.00 3.61
875 887 4.165372 TCTCACCCCCATATCCAAGTAAAC 59.835 45.833 0.00 0.00 0.00 2.01
880 892 4.277476 CCCCATATCCAAGTAAACAAGCA 58.723 43.478 0.00 0.00 0.00 3.91
991 1012 6.103205 AGTGGGGGATCAAATATGTAGTCAAT 59.897 38.462 0.00 0.00 0.00 2.57
1020 1041 4.298626 TGATGGTAGCTTGGAGGATTAGT 58.701 43.478 0.00 0.00 0.00 2.24
1112 1133 4.288626 TGTACCCCTTGTATTTGCTTCTCT 59.711 41.667 0.00 0.00 0.00 3.10
1348 1372 8.700051 TGCTAGCTCTTCTCTTTCAGTATTATT 58.300 33.333 17.23 0.00 0.00 1.40
1381 1405 7.773489 TTCCCATTAGAATGTTCATTGACAA 57.227 32.000 2.63 0.00 34.60 3.18
1448 1474 2.199117 TGGTCGACCCAGACATAGC 58.801 57.895 31.19 3.09 42.62 2.97
1462 1488 1.001760 ATAGCAGGTCGACCCAGGT 59.998 57.895 30.82 28.07 36.42 4.00
1699 1726 1.180029 CCTTCCTTTGCATCCCACTG 58.820 55.000 0.00 0.00 0.00 3.66
1722 1750 3.914551 AAGAGGGCGCTCCAGAGGT 62.915 63.158 25.68 4.64 38.24 3.85
1815 1845 3.579742 AAAGGGAAGGGAGAGGTAGAA 57.420 47.619 0.00 0.00 0.00 2.10
1836 1866 7.519032 AGAATGTCCCTTTCGTTTCATTTTA 57.481 32.000 0.00 0.00 0.00 1.52
1965 1997 1.411041 GTTGGATACGCCCCTCTACT 58.589 55.000 0.00 0.00 42.51 2.57
1973 2005 5.997129 GGATACGCCCCTCTACTATATCTAC 59.003 48.000 0.00 0.00 0.00 2.59
1975 2007 5.252586 ACGCCCCTCTACTATATCTACAA 57.747 43.478 0.00 0.00 0.00 2.41
2079 2111 2.233922 GCTACCAAACTGCTCTACTCCA 59.766 50.000 0.00 0.00 0.00 3.86
2081 2113 1.348036 ACCAAACTGCTCTACTCCACC 59.652 52.381 0.00 0.00 0.00 4.61
2082 2114 1.625818 CCAAACTGCTCTACTCCACCT 59.374 52.381 0.00 0.00 0.00 4.00
2196 2228 1.005450 GGGTAGCTGGAATCAAACCCA 59.995 52.381 11.48 0.00 44.94 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.683011 CCTTGAGCGGATCCCACATTT 60.683 52.381 6.06 0.00 0.00 2.32
28 29 9.269453 GGAACGCATTAGATATTTACCTAAACT 57.731 33.333 0.00 0.00 0.00 2.66
68 69 5.643777 CGCATAGTTTCCCCTCCAAATATAG 59.356 44.000 0.00 0.00 0.00 1.31
72 73 2.025321 ACGCATAGTTTCCCCTCCAAAT 60.025 45.455 0.00 0.00 0.00 2.32
169 170 3.749088 CGTTCTTGCCAAGGTTGTATGTA 59.251 43.478 4.30 0.00 0.00 2.29
209 210 0.984995 GCCTAAAGGAGTGTGGGTCT 59.015 55.000 0.00 0.00 37.39 3.85
217 218 7.391833 CACAGAATTTAAAGAGCCTAAAGGAGT 59.608 37.037 0.00 0.00 37.39 3.85
268 269 8.383175 ACTTTTGGGAGAGACATAATTAACTGA 58.617 33.333 0.00 0.00 0.00 3.41
424 425 8.567285 AAATCTTAGTTAAGAGGGTTCATGTG 57.433 34.615 7.57 0.00 44.67 3.21
479 481 6.904626 AGATGGAATAACTAAGCCAGAACAT 58.095 36.000 0.00 0.00 33.26 2.71
490 492 3.510360 GGCTCGGCTAGATGGAATAACTA 59.490 47.826 0.00 0.00 0.00 2.24
491 493 2.300437 GGCTCGGCTAGATGGAATAACT 59.700 50.000 0.00 0.00 0.00 2.24
523 525 9.816354 TTTTGTCCCTTTTCTTTCTTTCATAAG 57.184 29.630 0.00 0.00 0.00 1.73
569 576 9.460019 CCTCTCTCTCCTTTTTCTTATTGAATT 57.540 33.333 0.00 0.00 34.24 2.17
580 587 4.097418 TCGAATCCCTCTCTCTCCTTTTT 58.903 43.478 0.00 0.00 0.00 1.94
694 701 8.871629 TTATATGGTTGTGTTCCATTTGTAGT 57.128 30.769 2.79 0.00 42.24 2.73
793 805 6.842437 AGCGGATCTTGTATCTGTGTATAT 57.158 37.500 0.00 0.00 0.00 0.86
962 983 7.287810 ACTACATATTTGATCCCCCACTTAAC 58.712 38.462 0.00 0.00 0.00 2.01
991 1012 6.489603 TCCTCCAAGCTACCATCAAATAAAA 58.510 36.000 0.00 0.00 0.00 1.52
1033 1054 5.055812 TGCAAAAACAGCTAATTGGAAAGG 58.944 37.500 0.00 0.00 0.00 3.11
1151 1172 9.331466 AGACTAGTCCAATCCATAATGATGTAT 57.669 33.333 19.38 0.00 0.00 2.29
1280 1304 9.031360 TGCGTTTTAATACATCTCACTATTCTC 57.969 33.333 0.00 0.00 0.00 2.87
1448 1474 0.686441 TATCCACCTGGGTCGACCTG 60.686 60.000 32.52 22.39 41.11 4.00
1659 1686 6.460103 AGGGTAAGATAGTAAGGGATACGA 57.540 41.667 0.00 0.00 39.62 3.43
1717 1745 4.279145 TGGCGAGTTCTATTTCTACCTCT 58.721 43.478 0.00 0.00 0.00 3.69
1722 1750 6.265649 AGCTCTATTGGCGAGTTCTATTTCTA 59.734 38.462 0.00 0.00 34.52 2.10
1766 1794 3.701040 AGTTTGCCTGTTGTTTGTCTCAT 59.299 39.130 0.00 0.00 0.00 2.90
1789 1819 4.737578 ACCTCTCCCTTCCCTTTAAAAAC 58.262 43.478 0.00 0.00 0.00 2.43
1815 1845 9.554395 AAAATTAAAATGAAACGAAAGGGACAT 57.446 25.926 0.00 0.00 0.00 3.06
1836 1866 2.919602 TCTCCCTACCCTGCAGAAAATT 59.080 45.455 17.39 0.00 0.00 1.82
1944 1976 0.031917 TAGAGGGGCGTATCCAACCA 60.032 55.000 0.00 0.00 36.21 3.67
2005 2037 1.673033 CGATTCCCGTCTCTGCACTTT 60.673 52.381 0.00 0.00 0.00 2.66
2012 2044 2.200052 GGGTTCGATTCCCGTCTCT 58.800 57.895 9.87 0.00 39.75 3.10
2079 2111 2.372172 CCAGTTTCTGGTACTCCAAGGT 59.628 50.000 7.55 0.00 45.82 3.50
2124 2156 5.738619 TTTGTCTAGACATGTTAGAGGCA 57.261 39.130 25.68 4.47 41.52 4.75
2183 2215 2.577606 ACGATGTGGGTTTGATTCCA 57.422 45.000 0.00 0.00 0.00 3.53
2190 2222 2.159382 CCAAGCTAACGATGTGGGTTT 58.841 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.