Multiple sequence alignment - TraesCS1A01G387100

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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 TraesCS1A01G387100 chr1A 100.000 2838 0 0 630 3467 555824911 555827748 0.000000e+00 5241
1 TraesCS1A01G387100 chr1A 100.000 363 0 0 1 363 555824282 555824644 0.000000e+00 671
2 TraesCS1A01G387100 chr1D 96.590 2698 69 7 779 3467 463863726 463866409 0.000000e+00 4451
3 TraesCS1A01G387100 chr1D 90.934 364 7 7 1 338 463862876 463863239 1.880000e-127 466
4 TraesCS1A01G387100 chr7B 92.311 2146 139 10 779 2919 671258188 671256064 0.000000e+00 3025
5 TraesCS1A01G387100 chr7B 85.801 493 47 6 2430 2919 671001329 671000857 5.170000e-138 501
6 TraesCS1A01G387100 chr7B 85.628 494 47 8 2430 2919 671066248 671065775 6.680000e-137 497
7 TraesCS1A01G387100 chr7B 85.425 494 48 8 2430 2919 671184073 671183600 3.110000e-135 492
8 TraesCS1A01G387100 chr7A 92.206 2117 140 10 779 2892 683096839 683098933 0.000000e+00 2972
9 TraesCS1A01G387100 chr7D 91.970 2117 146 7 779 2890 591854655 591856752 0.000000e+00 2946
10 TraesCS1A01G387100 chr1B 95.983 1394 55 1 779 2172 639034078 639035470 0.000000e+00 2263
11 TraesCS1A01G387100 chr1B 96.486 1309 28 5 2171 3467 639043609 639044911 0.000000e+00 2146
12 TraesCS1A01G387100 chr1B 81.350 311 17 9 25 311 639033166 639033459 7.540000e-52 215
13 TraesCS1A01G387100 chrUn 85.628 494 47 8 2430 2919 147236760 147236287 6.680000e-137 497
14 TraesCS1A01G387100 chrUn 85.425 494 48 8 2430 2919 147306238 147305765 3.110000e-135 492
15 TraesCS1A01G387100 chrUn 85.253 495 48 8 2430 2919 147154943 147154469 1.450000e-133 486
16 TraesCS1A01G387100 chr2A 83.188 345 53 1 2920 3259 629925153 629924809 9.340000e-81 311


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 TraesCS1A01G387100 chr1A 555824282 555827748 3466 False 2956.0 5241 100.0000 1 3467 2 chr1A.!!$F1 3466
1 TraesCS1A01G387100 chr1D 463862876 463866409 3533 False 2458.5 4451 93.7620 1 3467 2 chr1D.!!$F1 3466
2 TraesCS1A01G387100 chr7B 671256064 671258188 2124 True 3025.0 3025 92.3110 779 2919 1 chr7B.!!$R4 2140
3 TraesCS1A01G387100 chr7A 683096839 683098933 2094 False 2972.0 2972 92.2060 779 2892 1 chr7A.!!$F1 2113
4 TraesCS1A01G387100 chr7D 591854655 591856752 2097 False 2946.0 2946 91.9700 779 2890 1 chr7D.!!$F1 2111
5 TraesCS1A01G387100 chr1B 639043609 639044911 1302 False 2146.0 2146 96.4860 2171 3467 1 chr1B.!!$F1 1296
6 TraesCS1A01G387100 chr1B 639033166 639035470 2304 False 1239.0 2263 88.6665 25 2172 2 chr1B.!!$F2 2147

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
352 762 1.996187 GGTTCCACTCCCTCCTCCC 60.996 68.421 0.0 0.0 0.0 4.30 F
1455 1908 0.798776 GTGGGCATGAGTTCGAGTTG 59.201 55.000 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1934 0.251341 CCAACCCTTGAACTCCTGGG 60.251 60.0 0.00 0.00 44.89 4.45 R
2526 2982 1.136690 CAAGCACTGCAGCATTGTTG 58.863 50.0 15.27 12.21 36.85 3.33 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
248 272 2.262915 GCTCTCTCCACCACCACG 59.737 66.667 0.00 0.00 0.00 4.94
352 762 1.996187 GGTTCCACTCCCTCCTCCC 60.996 68.421 0.00 0.00 0.00 4.30
353 763 2.038975 TTCCACTCCCTCCTCCCG 59.961 66.667 0.00 0.00 0.00 5.14
357 767 4.467107 ACTCCCTCCTCCCGCTCC 62.467 72.222 0.00 0.00 0.00 4.70
360 770 4.150454 CCCTCCTCCCGCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
361 771 2.520741 CCTCCTCCCGCTCCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
821 1274 3.701604 ATGTCCGTCGCCTTCTCGC 62.702 63.158 0.00 0.00 0.00 5.03
1008 1461 2.641815 GGATAGAGAGGTGATGGCCATT 59.358 50.000 21.84 2.81 0.00 3.16
1025 1478 1.903877 ATTCGGGAGGAGGTGCACAG 61.904 60.000 20.43 0.00 0.00 3.66
1026 1479 2.997315 CGGGAGGAGGTGCACAGA 60.997 66.667 20.43 0.00 0.00 3.41
1054 1507 4.475345 TCCTAGAGTCAAGGATAAGAGCC 58.525 47.826 0.00 0.00 38.24 4.70
1192 1645 2.361737 GGGGCTTGGAGGTGAAGC 60.362 66.667 0.00 0.00 44.32 3.86
1215 1668 2.224281 TGACAGGTTTGGTAGCTCAGTG 60.224 50.000 0.00 0.00 30.51 3.66
1455 1908 0.798776 GTGGGCATGAGTTCGAGTTG 59.201 55.000 0.00 0.00 0.00 3.16
1481 1934 3.861840 TCCGAATTGAGGATGAAGTGTC 58.138 45.455 0.00 0.00 31.86 3.67
1590 2043 4.039973 ACATCCGGTGACTTCTTTTCACTA 59.960 41.667 0.00 0.00 42.63 2.74
1694 2147 4.864334 GAGGGGCCACGGCATGAG 62.864 72.222 10.83 0.00 44.11 2.90
1714 2167 3.894427 GAGTGAGGATGAGGAGATGCTAA 59.106 47.826 0.00 0.00 0.00 3.09
1782 2235 5.279206 GGACTTGACAGAGTTGAAGATGAGA 60.279 44.000 0.00 0.00 0.00 3.27
1884 2337 4.464069 AAAGCTACTCATCTGTCTGGAC 57.536 45.455 0.00 0.00 0.00 4.02
1896 2349 3.638627 TCTGTCTGGACGATGCAGATATT 59.361 43.478 11.11 0.00 46.33 1.28
1986 2439 6.428159 AGATGGTCAAGATTGTTGTGAGTTAC 59.572 38.462 0.00 0.00 0.00 2.50
2172 2625 3.713003 TCTCTCTGATCCAAAGCCTGTA 58.287 45.455 0.00 0.00 0.00 2.74
2227 2680 1.276421 CAGTCGATGACACCTCCCTTT 59.724 52.381 0.00 0.00 34.60 3.11
2526 2982 3.438087 ACACACAGCTCACATAAAGATGC 59.562 43.478 0.00 0.00 36.43 3.91
2527 2983 3.437741 CACACAGCTCACATAAAGATGCA 59.562 43.478 0.00 0.00 36.43 3.96
2528 2984 4.074259 ACACAGCTCACATAAAGATGCAA 58.926 39.130 0.00 0.00 36.43 4.08
2533 2992 5.515270 CAGCTCACATAAAGATGCAACAATG 59.485 40.000 0.00 0.00 36.43 2.82
2773 3246 3.018856 GTTCAGGAATGATGTGGCATGA 58.981 45.455 0.00 0.00 0.00 3.07
2825 3300 9.988815 ACTTCATATCAATGTTACTCAGGTATC 57.011 33.333 0.00 0.00 34.50 2.24
2880 3355 5.280945 TGCTAATTGTTTTCAACTCACTGC 58.719 37.500 0.00 0.00 42.94 4.40
2947 3424 4.569162 GCAATACAACTAGTATGCGACCAA 59.431 41.667 0.00 0.00 42.56 3.67
3069 3546 3.193691 CGGCTTAGATGTATCTGGGGTAG 59.806 52.174 4.67 0.00 37.76 3.18
3367 3856 5.337652 GGAGTAGAGTCAGCAAGTTGGTATT 60.338 44.000 7.35 0.00 0.00 1.89
3403 3892 2.364970 TGTTTCTGGCCATGACCAAAAG 59.635 45.455 5.51 0.00 39.86 2.27
3404 3893 2.627699 GTTTCTGGCCATGACCAAAAGA 59.372 45.455 5.51 0.00 39.86 2.52
3450 3939 7.834181 GGATACCAAGCAAACATACCCATATAT 59.166 37.037 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.158957 ACACACACAACCGAGAGACAAT 60.159 45.455 0.00 0.00 0.00 2.71
233 257 1.906824 GGTCGTGGTGGTGGAGAGA 60.907 63.158 0.00 0.00 0.00 3.10
338 382 4.787280 AGCGGGAGGAGGGAGTGG 62.787 72.222 0.00 0.00 0.00 4.00
339 383 3.151022 GAGCGGGAGGAGGGAGTG 61.151 72.222 0.00 0.00 0.00 3.51
340 384 4.467107 GGAGCGGGAGGAGGGAGT 62.467 72.222 0.00 0.00 0.00 3.85
804 1257 4.415332 GCGAGAAGGCGACGGACA 62.415 66.667 0.00 0.00 0.00 4.02
1008 1461 2.997315 CTGTGCACCTCCTCCCGA 60.997 66.667 15.69 0.00 0.00 5.14
1192 1645 3.070018 CTGAGCTACCAAACCTGTCAAG 58.930 50.000 0.00 0.00 0.00 3.02
1215 1668 1.516161 TCTCTGACATTGCACTGTGC 58.484 50.000 25.15 25.15 45.29 4.57
1225 1678 5.397672 CCAGGAATTCCATCTTCTCTGACAT 60.398 44.000 26.22 0.00 38.89 3.06
1455 1908 1.134098 TCATCCTCAATTCGGAAGCCC 60.134 52.381 0.00 0.00 33.55 5.19
1481 1934 0.251341 CCAACCCTTGAACTCCTGGG 60.251 60.000 0.00 0.00 44.89 4.45
1590 2043 4.386424 GGCAACTGATCCCTAACCCTATTT 60.386 45.833 0.00 0.00 0.00 1.40
1688 2141 2.037901 TCTCCTCATCCTCACTCATGC 58.962 52.381 0.00 0.00 0.00 4.06
1694 2147 3.386078 TGTTAGCATCTCCTCATCCTCAC 59.614 47.826 0.00 0.00 0.00 3.51
1714 2167 2.091885 GTCTCTCATCCTCCTCCTCTGT 60.092 54.545 0.00 0.00 0.00 3.41
1782 2235 3.641434 AGCTCTATTGGTGCATTGACT 57.359 42.857 0.00 0.00 36.95 3.41
1884 2337 7.854422 GCATACCATTTGATAATATCTGCATCG 59.146 37.037 1.66 0.00 0.00 3.84
1896 2349 4.206375 CCACACCAGCATACCATTTGATA 58.794 43.478 0.00 0.00 0.00 2.15
1986 2439 0.689623 AGCAGGAGAACCTCAAGTGG 59.310 55.000 0.00 0.00 45.94 4.00
2172 2625 3.458857 AGATCATTGTCAAGGCTCCATCT 59.541 43.478 0.00 0.00 0.00 2.90
2526 2982 1.136690 CAAGCACTGCAGCATTGTTG 58.863 50.000 15.27 12.21 36.85 3.33
2527 2983 3.580904 CAAGCACTGCAGCATTGTT 57.419 47.368 15.27 5.46 36.85 2.83
2825 3300 4.255833 ACAGAGCTGTTGAAAGAGAGAG 57.744 45.455 0.00 0.00 41.83 3.20
2947 3424 7.337167 AGATTGAATCAGTTTCTAGCATCACT 58.663 34.615 8.03 0.00 35.23 3.41
3069 3546 7.390718 ACAAGATCTTGGACAGTGTTTTATACC 59.609 37.037 33.11 0.00 44.45 2.73
3270 3758 9.313118 CCGAAATTTTAGCTAGCCAAATATTTT 57.687 29.630 18.34 13.74 0.00 1.82
3403 3892 2.231235 CACAACCAGCCCTACCAATTTC 59.769 50.000 0.00 0.00 0.00 2.17
3404 3893 2.247358 CACAACCAGCCCTACCAATTT 58.753 47.619 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.