Multiple sequence alignment - TraesCS6D01G115600

Loading Multiple Alignment...

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 TraesCS6D01G115600 chr6D 100.000 2291 0 0 1 2291 82093711 82091421 0.000000e+00 4231
1 TraesCS6D01G115600 chr6A 92.095 2353 98 28 1 2291 98606594 98604268 0.000000e+00 3234
2 TraesCS6D01G115600 chr6B 92.154 1848 72 25 503 2291 156932974 156931141 0.000000e+00 2542
3 TraesCS6D01G115600 chr6B 84.807 362 43 4 1 362 157008692 157008343 1.010000e-93 353
4 TraesCS6D01G115600 chr1B 84.106 755 84 25 719 1455 194358160 194357424 0.000000e+00 697
5 TraesCS6D01G115600 chr1D 83.947 760 81 29 719 1455 144678200 144677459 0.000000e+00 689
6 TraesCS6D01G115600 chr1A 81.722 755 93 28 719 1455 144552438 144553165 2.540000e-164 588


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 TraesCS6D01G115600 chr6D 82091421 82093711 2290 True 4231 4231 100.000 1 2291 1 chr6D.!!$R1 2290
1 TraesCS6D01G115600 chr6A 98604268 98606594 2326 True 3234 3234 92.095 1 2291 1 chr6A.!!$R1 2290
2 TraesCS6D01G115600 chr6B 156931141 156932974 1833 True 2542 2542 92.154 503 2291 1 chr6B.!!$R1 1788
3 TraesCS6D01G115600 chr1B 194357424 194358160 736 True 697 697 84.106 719 1455 1 chr1B.!!$R1 736
4 TraesCS6D01G115600 chr1D 144677459 144678200 741 True 689 689 83.947 719 1455 1 chr1D.!!$R1 736
5 TraesCS6D01G115600 chr1A 144552438 144553165 727 False 588 588 81.722 719 1455 1 chr1A.!!$F1 736

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
298 299 0.329596 GTGGAGCAAGGGTGAAGGAT 59.670 55.0 0.0 0.0 0.00 3.24 F
477 478 0.441533 GGCTGAATATGAGCGATGCG 59.558 55.0 0.0 0.0 37.32 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1298 1.804326 CCGACCCGTGAACGACATC 60.804 63.158 4.03 0.0 43.02 3.06 R
1572 1646 2.480845 AGAAAGAAGAACGACCGTTGG 58.519 47.619 12.79 0.0 38.60 3.77 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
22 23 2.032681 GGCTTCCTTGCCGACAGT 59.967 61.111 0.00 0.00 43.74 3.55
35 36 1.428620 GACAGTAGGTCGGACGAGC 59.571 63.158 15.28 15.28 42.36 5.03
65 66 2.225066 GGGGATACATCCTCCTAGACGT 60.225 54.545 8.14 0.00 46.35 4.34
78 79 2.159226 CCTAGACGTCCACAACATCCTC 60.159 54.545 13.01 0.00 0.00 3.71
84 85 0.608130 TCCACAACATCCTCTGTCGG 59.392 55.000 0.00 0.00 36.98 4.79
97 98 1.005394 TGTCGGAACTTCCTTCGCC 60.005 57.895 6.25 0.00 33.30 5.54
107 108 4.394712 CCTTCGCCACCGCTTCCT 62.395 66.667 0.00 0.00 0.00 3.36
117 118 4.854784 CGCTTCCTGCTCGCGCTA 62.855 66.667 5.56 0.00 40.42 4.26
125 126 2.950194 GCTCGCGCTACTTCCGTC 60.950 66.667 5.56 0.00 0.00 4.79
128 129 2.503375 CGCGCTACTTCCGTCGTT 60.503 61.111 5.56 0.00 0.00 3.85
137 138 1.878656 CTTCCGTCGTTGCTCCCTCT 61.879 60.000 0.00 0.00 0.00 3.69
138 139 0.609957 TTCCGTCGTTGCTCCCTCTA 60.610 55.000 0.00 0.00 0.00 2.43
142 143 1.390565 GTCGTTGCTCCCTCTAGCTA 58.609 55.000 0.00 0.00 43.19 3.32
252 253 0.815734 CCGACGACAACATCTAGGGT 59.184 55.000 0.00 0.00 0.00 4.34
254 255 1.469251 CGACGACAACATCTAGGGTGG 60.469 57.143 0.00 0.00 0.00 4.61
265 266 2.946988 CTAGGGTGGCGGATGGAGGA 62.947 65.000 0.00 0.00 0.00 3.71
268 269 4.554036 GTGGCGGATGGAGGAGGC 62.554 72.222 0.00 0.00 0.00 4.70
298 299 0.329596 GTGGAGCAAGGGTGAAGGAT 59.670 55.000 0.00 0.00 0.00 3.24
301 302 1.000396 AGCAAGGGTGAAGGATGGC 60.000 57.895 0.00 0.00 0.00 4.40
374 375 7.307131 AGATTTGATGGACTTGGTCAATTTT 57.693 32.000 0.14 0.00 33.68 1.82
375 376 7.738847 AGATTTGATGGACTTGGTCAATTTTT 58.261 30.769 0.14 0.00 33.68 1.94
449 450 1.594310 GCCTCTCCCATATCCGCTC 59.406 63.158 0.00 0.00 0.00 5.03
477 478 0.441533 GGCTGAATATGAGCGATGCG 59.558 55.000 0.00 0.00 37.32 4.73
546 547 2.753446 GGCTTGAGGAGGCTTGCC 60.753 66.667 2.97 2.97 46.86 4.52
798 822 1.732259 AGCCACAAATTCGATCGTCAC 59.268 47.619 15.94 0.00 0.00 3.67
799 823 1.526986 GCCACAAATTCGATCGTCACG 60.527 52.381 15.94 0.00 0.00 4.35
817 841 2.425592 CCGCCACTCCACACTCAA 59.574 61.111 0.00 0.00 0.00 3.02
827 851 1.872952 TCCACACTCAATCGCACAAAG 59.127 47.619 0.00 0.00 0.00 2.77
833 857 4.153986 CACTCAATCGCACAAAGTTGATC 58.846 43.478 0.00 0.00 30.97 2.92
851 887 1.000771 CGTCACCTCCTCCCTCTCA 60.001 63.158 0.00 0.00 0.00 3.27
877 913 4.263506 ACCTATAAATACATGCCCAGGCTC 60.264 45.833 10.58 0.00 42.51 4.70
935 977 3.009033 CACAAACCCATTCAGTCCCTCTA 59.991 47.826 0.00 0.00 0.00 2.43
936 978 3.264450 ACAAACCCATTCAGTCCCTCTAG 59.736 47.826 0.00 0.00 0.00 2.43
937 979 3.491766 AACCCATTCAGTCCCTCTAGA 57.508 47.619 0.00 0.00 0.00 2.43
938 980 3.039252 ACCCATTCAGTCCCTCTAGAG 57.961 52.381 13.18 13.18 0.00 2.43
939 981 2.316372 ACCCATTCAGTCCCTCTAGAGT 59.684 50.000 18.42 0.00 0.00 3.24
940 982 3.246167 ACCCATTCAGTCCCTCTAGAGTT 60.246 47.826 18.42 0.00 0.00 3.01
967 1022 9.781633 AGATATACACTCACGTTAGAGTTAGAT 57.218 33.333 3.23 4.91 46.26 1.98
1243 1298 1.299165 AAGCGTAGGCGTGCTATCG 60.299 57.895 1.05 0.00 46.35 2.92
1254 1312 1.513178 CGTGCTATCGATGTCGTTCAC 59.487 52.381 8.54 5.93 40.80 3.18
1266 1324 2.422591 GTTCACGGGTCGGTTCCA 59.577 61.111 0.00 0.00 0.00 3.53
1291 1349 2.279517 GCGTCGGCCATCACTAGG 60.280 66.667 2.24 0.00 0.00 3.02
1293 1351 1.515954 CGTCGGCCATCACTAGGTT 59.484 57.895 2.24 0.00 0.00 3.50
1349 1407 9.899226 TCTCTACATTTTACACATATCGATCTG 57.101 33.333 0.00 4.98 0.00 2.90
1572 1646 8.766151 GGATAAGTCCGTTTTCTGATTAAGATC 58.234 37.037 0.00 0.00 32.40 2.75
1649 1740 6.601613 TCGACTTACCCAAATAGCAAATTCAT 59.398 34.615 0.00 0.00 0.00 2.57
2000 2094 0.526954 GCTGCCTTGGAATTGCGATG 60.527 55.000 0.00 0.00 0.00 3.84
2019 2113 4.501071 GATGCCTGTTTCATGCATTTCTT 58.499 39.130 12.14 0.00 43.52 2.52
2101 2199 4.753107 TGACGTCTCTTTAACCAACAATCC 59.247 41.667 17.92 0.00 0.00 3.01
2108 2206 7.926018 GTCTCTTTAACCAACAATCCAACAAAT 59.074 33.333 0.00 0.00 0.00 2.32
2141 2239 1.404035 GATTGGTTCGCCGGCTAATTT 59.596 47.619 26.68 6.13 41.18 1.82
2228 2326 5.599999 ATCATCGACTATATAACTGGCCC 57.400 43.478 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.741221 CCTACTGTCGGCAAGGAAGC 60.741 60.000 1.23 0.00 0.00 3.86
22 23 3.807538 GTGCGCTCGTCCGACCTA 61.808 66.667 9.73 0.00 0.00 3.08
29 30 4.803426 CCCTCTGGTGCGCTCGTC 62.803 72.222 9.73 0.00 0.00 4.20
35 36 0.034059 GATGTATCCCCTCTGGTGCG 59.966 60.000 0.00 0.00 34.77 5.34
65 66 0.608130 CCGACAGAGGATGTTGTGGA 59.392 55.000 0.00 0.00 44.17 4.02
78 79 1.014564 GGCGAAGGAAGTTCCGACAG 61.015 60.000 16.31 10.20 42.75 3.51
84 85 2.677979 GCGGTGGCGAAGGAAGTTC 61.678 63.158 0.00 0.00 0.00 3.01
125 126 2.166664 ACTTTAGCTAGAGGGAGCAACG 59.833 50.000 15.21 0.00 45.43 4.10
128 129 3.702045 GAGAACTTTAGCTAGAGGGAGCA 59.298 47.826 15.21 0.00 45.43 4.26
137 138 3.007940 TGCAAGGCAGAGAACTTTAGCTA 59.992 43.478 0.00 0.00 33.32 3.32
138 139 2.224621 TGCAAGGCAGAGAACTTTAGCT 60.225 45.455 0.00 0.00 33.32 3.32
190 191 0.460109 TGGATGATGCCTTCGTGTCG 60.460 55.000 0.00 0.00 0.00 4.35
228 229 2.865343 AGATGTTGTCGTCGGGTATC 57.135 50.000 0.00 0.00 35.01 2.24
238 239 0.462047 CCGCCACCCTAGATGTTGTC 60.462 60.000 0.00 0.00 0.00 3.18
241 242 0.469917 CATCCGCCACCCTAGATGTT 59.530 55.000 0.00 0.00 33.09 2.71
265 266 4.033776 CCACCATCCACACCGCCT 62.034 66.667 0.00 0.00 0.00 5.52
268 269 2.436646 GCTCCACCATCCACACCG 60.437 66.667 0.00 0.00 0.00 4.94
434 435 1.801242 TTTGGAGCGGATATGGGAGA 58.199 50.000 0.00 0.00 0.00 3.71
436 437 2.976185 TGTATTTGGAGCGGATATGGGA 59.024 45.455 0.00 0.00 0.00 4.37
438 439 3.338249 CCTGTATTTGGAGCGGATATGG 58.662 50.000 0.00 0.00 0.00 2.74
446 447 5.065914 TCATATTCAGCCTGTATTTGGAGC 58.934 41.667 2.86 0.00 0.00 4.70
449 450 4.083643 CGCTCATATTCAGCCTGTATTTGG 60.084 45.833 2.86 0.00 32.83 3.28
546 547 2.607635 CCTGTCATAAAATCGTGACCCG 59.392 50.000 3.38 0.00 43.09 5.28
682 704 5.006746 GCATGTGTACTATTTGGAGCACTAC 59.993 44.000 0.00 0.00 0.00 2.73
799 823 3.825160 TTGAGTGTGGAGTGGCGGC 62.825 63.158 0.00 0.00 0.00 6.53
817 841 2.157668 GTGACGATCAACTTTGTGCGAT 59.842 45.455 11.25 0.00 32.98 4.58
827 851 0.175989 GGGAGGAGGTGACGATCAAC 59.824 60.000 0.00 0.00 33.32 3.18
833 857 0.396417 ATGAGAGGGAGGAGGTGACG 60.396 60.000 0.00 0.00 0.00 4.35
851 887 5.807721 GCCTGGGCATGTATTTATAGGTGAT 60.808 44.000 6.75 0.00 41.49 3.06
877 913 1.293924 GCGATGAGGTGAATGTGAGG 58.706 55.000 0.00 0.00 0.00 3.86
967 1022 1.112113 ATCGAGCTAAGCCCGAAGAA 58.888 50.000 0.00 0.00 35.87 2.52
1243 1298 1.804326 CCGACCCGTGAACGACATC 60.804 63.158 4.03 0.00 43.02 3.06
1291 1349 7.582435 TTCACTTGATTAGAAGATCGACAAC 57.418 36.000 0.00 0.00 0.00 3.32
1369 1427 4.640201 GCCATTATGTTGGACGGCATATAT 59.360 41.667 0.00 0.00 39.25 0.86
1370 1428 4.006989 GCCATTATGTTGGACGGCATATA 58.993 43.478 0.00 0.00 39.25 0.86
1412 1476 3.700154 GCTTCAATAGCTAAGCTTTGGC 58.300 45.455 3.20 10.18 46.77 4.52
1572 1646 2.480845 AGAAAGAAGAACGACCGTTGG 58.519 47.619 12.79 0.00 38.60 3.77
1822 1913 5.711698 TCAAGGTACCCTCAAGGAAATTTT 58.288 37.500 8.74 0.00 39.89 1.82
1826 1917 6.457159 TTTATCAAGGTACCCTCAAGGAAA 57.543 37.500 8.74 0.00 39.89 3.13
1827 1918 6.652205 ATTTATCAAGGTACCCTCAAGGAA 57.348 37.500 8.74 0.00 39.89 3.36
1846 1938 6.653320 CAGCTGGTTACCTCACACTTAATTTA 59.347 38.462 5.57 0.00 0.00 1.40
1860 1952 3.010420 GGAATTCAGTCAGCTGGTTACC 58.990 50.000 15.13 0.00 42.78 2.85
2000 2094 4.751098 TCAAAAGAAATGCATGAAACAGGC 59.249 37.500 0.00 1.46 41.79 4.85
2019 2113 4.455190 TCGACATGATCACAGCAAATCAAA 59.545 37.500 0.00 0.00 35.64 2.69
2101 2199 7.439056 ACCAATCTTAGCTTTTGTCATTTGTTG 59.561 33.333 0.00 0.00 0.00 3.33
2108 2206 4.320202 GCGAACCAATCTTAGCTTTTGTCA 60.320 41.667 0.00 0.00 0.00 3.58
2141 2239 7.479980 CGCATACATTCCTTATTTTTCTTCCA 58.520 34.615 0.00 0.00 0.00 3.53
2228 2326 7.822334 TGACACTTTATATTGACTACCACCTTG 59.178 37.037 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.