Multiple sequence alignment - TraesCS1A01G309300

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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 TraesCS1A01G309300 chr1A 100.000 2983 0 0 1 2983 500284594 500287576 0.000000e+00 5509.0
1 TraesCS1A01G309300 chr1D 93.364 2381 94 26 636 2983 404655067 404657416 0.000000e+00 3463.0
2 TraesCS1A01G309300 chr1D 80.217 369 39 10 1 339 404654443 404654807 2.300000e-61 246.0
3 TraesCS1A01G309300 chr1B 91.737 1186 60 19 1819 2983 544492665 544493833 0.000000e+00 1613.0
4 TraesCS1A01G309300 chr1B 94.892 1018 28 6 816 1820 544491576 544492582 0.000000e+00 1570.0
5 TraesCS1A01G309300 chr1B 88.889 423 24 15 374 791 544491174 544491578 1.600000e-137 499.0
6 TraesCS1A01G309300 chr3A 87.313 134 17 0 1284 1417 580608681 580608814 1.430000e-33 154.0
7 TraesCS1A01G309300 chr3B 85.821 134 19 0 1284 1417 577490359 577490492 3.100000e-30 143.0
8 TraesCS1A01G309300 chr5D 100.000 28 0 0 349 376 270070114 270070141 5.000000e-03 52.8


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 TraesCS1A01G309300 chr1A 500284594 500287576 2982 False 5509.000000 5509 100.000000 1 2983 1 chr1A.!!$F1 2982
1 TraesCS1A01G309300 chr1D 404654443 404657416 2973 False 1854.500000 3463 86.790500 1 2983 2 chr1D.!!$F1 2982
2 TraesCS1A01G309300 chr1B 544491174 544493833 2659 False 1227.333333 1613 91.839333 374 2983 3 chr1B.!!$F1 2609

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
344 405 0.036164 ACACACACACACACACACCT 59.964 50.0 0.0 0.0 0.0 4.00 F
1107 1240 0.610232 GGCCAAATCAGCACACTCCT 60.610 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1807 0.596083 CAGATCGATCACCACTCGGC 60.596 60.000 26.47 0.0 36.78 5.54 R
2284 2513 1.964223 AGGGACACGTATGCATCCTAG 59.036 52.381 0.19 0.0 0.00 3.02 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
53 54 3.674997 TGCAACATCCTTAGAGTTGGTC 58.325 45.455 0.00 0.00 42.07 4.02
55 56 3.686726 GCAACATCCTTAGAGTTGGTCTG 59.313 47.826 0.00 0.00 42.07 3.51
56 57 3.618690 ACATCCTTAGAGTTGGTCTGC 57.381 47.619 0.00 0.00 36.64 4.26
64 65 5.335191 CCTTAGAGTTGGTCTGCAATTTGAC 60.335 44.000 0.00 0.00 36.64 3.18
93 101 5.435373 AGCCTTAATTAAACACCTATCCCCT 59.565 40.000 0.00 0.00 0.00 4.79
95 103 6.636336 GCCTTAATTAAACACCTATCCCCTCA 60.636 42.308 0.00 0.00 0.00 3.86
133 141 3.304458 CGCGTATGCTATCAACAGGTCTA 60.304 47.826 5.20 0.00 39.65 2.59
173 200 7.962964 TGTGTATCACAAAAGAAGTAGAAGG 57.037 36.000 0.00 0.00 41.69 3.46
188 215 8.527810 AGAAGTAGAAGGAAACTCATTAGTCAG 58.472 37.037 0.00 0.00 42.68 3.51
227 254 9.865321 CAATGATGAACCATAAATATTCCATCC 57.135 33.333 0.00 0.00 0.00 3.51
231 258 9.696917 GATGAACCATAAATATTCCATCCAAAC 57.303 33.333 0.00 0.00 0.00 2.93
247 274 9.790344 TCCATCCAAACAAAATTAATTTCACAT 57.210 25.926 13.68 0.00 0.00 3.21
261 288 8.846943 TTAATTTCACATCAAGACTAGAAGCA 57.153 30.769 0.00 0.00 0.00 3.91
262 289 7.934855 AATTTCACATCAAGACTAGAAGCAT 57.065 32.000 0.00 0.00 0.00 3.79
288 315 8.751302 AATTATTTTTAAAAACACGCGGATCT 57.249 26.923 15.35 0.00 0.00 2.75
307 342 3.291584 TCTTCTCTCTCACACACACACT 58.708 45.455 0.00 0.00 0.00 3.55
311 346 2.360483 CTCTCTCACACACACACTCACT 59.640 50.000 0.00 0.00 0.00 3.41
314 349 2.695147 TCTCACACACACACTCACTCAT 59.305 45.455 0.00 0.00 0.00 2.90
315 350 3.055591 CTCACACACACACTCACTCATC 58.944 50.000 0.00 0.00 0.00 2.92
317 352 1.070758 ACACACACACTCACTCATCCC 59.929 52.381 0.00 0.00 0.00 3.85
318 353 1.345741 CACACACACTCACTCATCCCT 59.654 52.381 0.00 0.00 0.00 4.20
319 354 2.562738 CACACACACTCACTCATCCCTA 59.437 50.000 0.00 0.00 0.00 3.53
320 355 3.196469 CACACACACTCACTCATCCCTAT 59.804 47.826 0.00 0.00 0.00 2.57
321 356 3.196469 ACACACACTCACTCATCCCTATG 59.804 47.826 0.00 0.00 0.00 2.23
322 357 3.448660 CACACACTCACTCATCCCTATGA 59.551 47.826 0.00 0.00 39.87 2.15
343 404 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
344 405 0.036164 ACACACACACACACACACCT 59.964 50.000 0.00 0.00 0.00 4.00
348 412 1.668751 CACACACACACACACCTTACC 59.331 52.381 0.00 0.00 0.00 2.85
436 560 1.543802 GCGGGTTGATTCCATCACAAA 59.456 47.619 0.00 0.00 39.39 2.83
444 568 7.286316 GGGTTGATTCCATCACAAAGAATCTAT 59.714 37.037 11.87 0.00 44.02 1.98
592 716 8.441312 TTCTTGTAAACTTTGACTTATCGGTT 57.559 30.769 0.00 0.00 0.00 4.44
604 728 6.837992 TGACTTATCGGTTGAAAATAAGCAC 58.162 36.000 0.00 0.00 36.76 4.40
605 729 6.428465 TGACTTATCGGTTGAAAATAAGCACA 59.572 34.615 0.00 0.00 36.76 4.57
610 734 5.277825 TCGGTTGAAAATAAGCACAAACAG 58.722 37.500 0.00 0.00 31.38 3.16
616 740 6.815089 TGAAAATAAGCACAAACAGATTGGT 58.185 32.000 0.00 0.00 43.66 3.67
710 837 3.771216 AGTCAAAGCAAGATGATGGGTT 58.229 40.909 0.00 0.00 0.00 4.11
711 838 4.922206 AGTCAAAGCAAGATGATGGGTTA 58.078 39.130 0.00 0.00 0.00 2.85
712 839 4.702131 AGTCAAAGCAAGATGATGGGTTAC 59.298 41.667 0.00 0.00 0.00 2.50
713 840 4.702131 GTCAAAGCAAGATGATGGGTTACT 59.298 41.667 0.00 0.00 0.00 2.24
714 841 4.943705 TCAAAGCAAGATGATGGGTTACTC 59.056 41.667 0.00 0.00 0.00 2.59
715 842 4.851639 AAGCAAGATGATGGGTTACTCT 57.148 40.909 0.00 0.00 0.00 3.24
716 843 4.851639 AGCAAGATGATGGGTTACTCTT 57.148 40.909 0.00 0.00 0.00 2.85
815 944 1.482182 GCATTTGGGGGTTTCCTGATC 59.518 52.381 0.00 0.00 35.33 2.92
852 982 4.011698 GACGTAACAAATTACACCCCCAT 58.988 43.478 0.00 0.00 40.77 4.00
917 1047 1.284982 CGTCCCTTTCTCACAGCGTG 61.285 60.000 2.79 2.79 34.45 5.34
1039 1172 6.347483 GCTTCTAAAAGTAGAAACCAGAACCG 60.347 42.308 0.00 0.00 44.05 4.44
1107 1240 0.610232 GGCCAAATCAGCACACTCCT 60.610 55.000 0.00 0.00 0.00 3.69
1188 1321 1.315257 CCGCAGCCCATACTTTGCTT 61.315 55.000 0.00 0.00 34.50 3.91
1213 1346 3.963374 TCGATCTTGGTCATGGAGAAGAT 59.037 43.478 11.50 11.50 37.77 2.40
1557 1696 4.619227 ACAACGTCCCGGCCACAG 62.619 66.667 2.24 0.00 0.00 3.66
1634 1773 2.183478 TCGACAACAGGTACTCCGTA 57.817 50.000 0.00 0.00 34.60 4.02
1668 1807 3.047718 TTCCTCTACGGCTCGCACG 62.048 63.158 0.00 0.00 37.36 5.34
1915 2139 0.539986 CCAGCGCTCTACCCCTTTTA 59.460 55.000 7.13 0.00 0.00 1.52
1916 2140 1.065709 CCAGCGCTCTACCCCTTTTAA 60.066 52.381 7.13 0.00 0.00 1.52
1917 2141 2.421529 CCAGCGCTCTACCCCTTTTAAT 60.422 50.000 7.13 0.00 0.00 1.40
1918 2142 3.279434 CAGCGCTCTACCCCTTTTAATT 58.721 45.455 7.13 0.00 0.00 1.40
1919 2143 3.694566 CAGCGCTCTACCCCTTTTAATTT 59.305 43.478 7.13 0.00 0.00 1.82
1923 2147 4.201920 CGCTCTACCCCTTTTAATTTCTGC 60.202 45.833 0.00 0.00 0.00 4.26
1960 2184 0.466372 TGTTGGATTTCGTGGGTGCA 60.466 50.000 0.00 0.00 0.00 4.57
1962 2186 0.958091 TTGGATTTCGTGGGTGCAAG 59.042 50.000 0.00 0.00 0.00 4.01
1984 2208 4.729227 CCCGGTTGGCTGTTAATTAATT 57.271 40.909 5.89 5.89 0.00 1.40
1985 2209 5.838531 CCCGGTTGGCTGTTAATTAATTA 57.161 39.130 0.00 3.71 0.00 1.40
2007 2231 8.827177 ATTAATGATGATTTGCAATGTGGATC 57.173 30.769 0.00 0.00 0.00 3.36
2048 2277 3.283259 ACAAAGGGGATCGGATTCTTC 57.717 47.619 0.00 0.00 0.00 2.87
2050 2279 3.118223 ACAAAGGGGATCGGATTCTTCTC 60.118 47.826 0.00 0.00 0.00 2.87
2107 2336 2.721274 TTTGATTTCATGCACGGTGG 57.279 45.000 10.60 0.00 0.00 4.61
2108 2337 1.902938 TTGATTTCATGCACGGTGGA 58.097 45.000 10.60 7.67 0.00 4.02
2150 2379 2.467880 AGGACCGGCTAGAAAGATTGA 58.532 47.619 0.00 0.00 0.00 2.57
2284 2513 0.676151 CTCTGAGGGGCTTGCAGAAC 60.676 60.000 0.00 0.00 38.12 3.01
2367 2600 2.016318 CCAAGATGCGCATGGTTTAGA 58.984 47.619 30.76 0.00 0.00 2.10
2389 2622 7.206981 AGATTTTGGGATGCTAATAACATCG 57.793 36.000 0.00 0.00 43.98 3.84
2394 2627 3.498397 GGGATGCTAATAACATCGGTGTG 59.502 47.826 0.00 0.00 43.98 3.82
2651 2895 0.036671 GTGGTAAAGAGGACCCACCG 60.037 60.000 0.00 0.00 44.74 4.94
2722 2966 8.311120 GTCTTTTTGTTGTGATGACTTTTAACG 58.689 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.327757 AGACCAACTCTAAGGATGTTGCA 59.672 43.478 0.00 0.00 39.53 4.08
35 36 3.327757 TGCAGACCAACTCTAAGGATGTT 59.672 43.478 0.00 0.00 0.00 2.71
39 40 4.640771 AATTGCAGACCAACTCTAAGGA 57.359 40.909 0.00 0.00 35.99 3.36
53 54 4.460948 AAGGCTAATGGTCAAATTGCAG 57.539 40.909 0.00 0.00 0.00 4.41
55 56 8.940768 TTAATTAAGGCTAATGGTCAAATTGC 57.059 30.769 0.00 0.00 0.00 3.56
64 65 8.793592 GGATAGGTGTTTAATTAAGGCTAATGG 58.206 37.037 0.00 0.00 0.00 3.16
65 66 8.793592 GGGATAGGTGTTTAATTAAGGCTAATG 58.206 37.037 0.00 0.00 0.00 1.90
69 70 5.435373 AGGGGATAGGTGTTTAATTAAGGCT 59.565 40.000 0.00 0.00 0.00 4.58
100 108 0.597637 GCATACGCGCTCAGTACCAT 60.598 55.000 5.73 0.00 0.00 3.55
102 110 0.309922 TAGCATACGCGCTCAGTACC 59.690 55.000 5.73 0.00 42.62 3.34
110 118 0.508641 CCTGTTGATAGCATACGCGC 59.491 55.000 5.73 0.00 45.49 6.86
114 122 8.077836 GTCAATTAGACCTGTTGATAGCATAC 57.922 38.462 0.00 0.00 41.56 2.39
133 141 7.041440 TGTGATACACAAATCTTCGTGTCAATT 60.041 33.333 1.99 0.00 44.93 2.32
200 227 9.362539 GATGGAATATTTATGGTTCATCATTGC 57.637 33.333 0.00 0.00 0.00 3.56
262 289 9.843334 AGATCCGCGTGTTTTTAAAAATAATTA 57.157 25.926 16.02 0.00 0.00 1.40
273 300 2.737252 GAGAGAAGATCCGCGTGTTTTT 59.263 45.455 4.92 0.00 0.00 1.94
282 309 2.489722 TGTGTGTGAGAGAGAAGATCCG 59.510 50.000 0.00 0.00 0.00 4.18
288 315 3.023832 TGAGTGTGTGTGTGAGAGAGAA 58.976 45.455 0.00 0.00 0.00 2.87
307 342 3.837731 TGTGTGTTCATAGGGATGAGTGA 59.162 43.478 0.00 0.00 43.03 3.41
311 346 3.326297 TGTGTGTGTGTTCATAGGGATGA 59.674 43.478 0.00 0.00 40.45 2.92
314 349 2.436173 TGTGTGTGTGTGTTCATAGGGA 59.564 45.455 0.00 0.00 0.00 4.20
315 350 2.548057 GTGTGTGTGTGTGTTCATAGGG 59.452 50.000 0.00 0.00 0.00 3.53
317 352 3.620821 TGTGTGTGTGTGTGTGTTCATAG 59.379 43.478 0.00 0.00 0.00 2.23
318 353 3.372514 GTGTGTGTGTGTGTGTGTTCATA 59.627 43.478 0.00 0.00 0.00 2.15
319 354 2.161410 GTGTGTGTGTGTGTGTGTTCAT 59.839 45.455 0.00 0.00 0.00 2.57
320 355 1.533299 GTGTGTGTGTGTGTGTGTTCA 59.467 47.619 0.00 0.00 0.00 3.18
321 356 1.533299 TGTGTGTGTGTGTGTGTGTTC 59.467 47.619 0.00 0.00 0.00 3.18
322 357 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
343 404 2.693591 TCGAAGGTGCTCATAGGGTAAG 59.306 50.000 0.00 0.00 0.00 2.34
344 405 2.693591 CTCGAAGGTGCTCATAGGGTAA 59.306 50.000 0.00 0.00 0.00 2.85
348 412 2.034053 GTCTCTCGAAGGTGCTCATAGG 59.966 54.545 0.00 0.00 0.00 2.57
467 591 4.023707 GCTTGTCAATTGTGCTTCTAGTGT 60.024 41.667 5.13 0.00 0.00 3.55
592 716 6.700960 CACCAATCTGTTTGTGCTTATTTTCA 59.299 34.615 0.00 0.00 33.15 2.69
600 724 6.403866 TTTTATCACCAATCTGTTTGTGCT 57.596 33.333 0.00 0.00 33.15 4.40
710 837 8.270137 TCTTTAATATGGGGCATACAAGAGTA 57.730 34.615 0.00 0.00 34.10 2.59
711 838 7.149202 TCTTTAATATGGGGCATACAAGAGT 57.851 36.000 0.00 0.00 0.00 3.24
712 839 9.911788 ATATCTTTAATATGGGGCATACAAGAG 57.088 33.333 0.00 0.00 30.63 2.85
763 892 8.418662 TGCCGTTATGTGTCTAAAATATACTCT 58.581 33.333 0.00 0.00 0.00 3.24
805 934 2.547211 CCAGCGATGATGATCAGGAAAC 59.453 50.000 0.06 0.00 0.00 2.78
815 944 0.385751 ACGTCTACCCAGCGATGATG 59.614 55.000 0.06 0.00 0.00 3.07
852 982 3.824133 CCTTGGATAATGCATGGTCAGA 58.176 45.455 0.00 0.00 30.17 3.27
917 1047 2.630580 ACTCAAACTCCTCTCCTCACAC 59.369 50.000 0.00 0.00 0.00 3.82
1107 1240 2.846827 GAGATGAAAGGGAAAGGAGGGA 59.153 50.000 0.00 0.00 0.00 4.20
1188 1321 3.299503 TCTCCATGACCAAGATCGATCA 58.700 45.455 26.47 7.41 0.00 2.92
1213 1346 2.594303 CCTTGGAACCGCACTGCA 60.594 61.111 1.11 0.00 0.00 4.41
1532 1671 2.904866 GGGACGTTGTGGCTGCAA 60.905 61.111 0.50 0.00 0.00 4.08
1580 1719 1.000993 GCTGTCCTCCTCCTCCTCA 59.999 63.158 0.00 0.00 0.00 3.86
1634 1773 4.430765 AACGTCGGCGGCGAGAAT 62.431 61.111 41.39 19.76 43.45 2.40
1668 1807 0.596083 CAGATCGATCACCACTCGGC 60.596 60.000 26.47 0.00 36.78 5.54
1669 1808 0.741326 ACAGATCGATCACCACTCGG 59.259 55.000 26.47 3.42 36.78 4.63
1901 2125 4.201920 CGCAGAAATTAAAAGGGGTAGAGC 60.202 45.833 0.00 0.00 0.00 4.09
1915 2139 4.516698 ACACATTTCTCACTCGCAGAAATT 59.483 37.500 6.30 0.00 44.67 1.82
1916 2140 4.067896 ACACATTTCTCACTCGCAGAAAT 58.932 39.130 3.73 3.73 46.88 2.17
1917 2141 3.466836 ACACATTTCTCACTCGCAGAAA 58.533 40.909 0.00 0.00 42.63 2.52
1918 2142 3.059884 GACACATTTCTCACTCGCAGAA 58.940 45.455 0.00 0.00 34.09 3.02
1919 2143 2.610479 GGACACATTTCTCACTCGCAGA 60.610 50.000 0.00 0.00 0.00 4.26
1923 2147 3.032017 ACAGGACACATTTCTCACTCG 57.968 47.619 0.00 0.00 0.00 4.18
1984 2208 6.324254 TGGATCCACATTGCAAATCATCATTA 59.676 34.615 11.44 0.00 0.00 1.90
1985 2209 5.129650 TGGATCCACATTGCAAATCATCATT 59.870 36.000 11.44 0.00 0.00 2.57
2007 2231 8.430801 TTTGTTTCAAACACTCCATTATTTGG 57.569 30.769 1.28 0.00 43.58 3.28
2018 2247 3.317993 CGATCCCCTTTGTTTCAAACACT 59.682 43.478 1.28 0.00 41.97 3.55
2027 2256 3.267031 AGAAGAATCCGATCCCCTTTGTT 59.733 43.478 0.00 0.00 0.00 2.83
2058 2287 8.664798 CATTAAATCGGTGTTGAAACTGATAGA 58.335 33.333 0.00 0.00 43.83 1.98
2107 2336 2.347697 TGTGTACATGTGTCGCTCTC 57.652 50.000 9.11 0.00 0.00 3.20
2108 2337 2.812358 TTGTGTACATGTGTCGCTCT 57.188 45.000 9.11 0.00 0.00 4.09
2284 2513 1.964223 AGGGACACGTATGCATCCTAG 59.036 52.381 0.19 0.00 0.00 3.02
2367 2600 5.833131 ACCGATGTTATTAGCATCCCAAAAT 59.167 36.000 13.05 0.00 39.48 1.82
2389 2622 8.190784 AGCAAATTATAGCACTAAAATCACACC 58.809 33.333 0.00 0.00 0.00 4.16
2651 2895 4.317530 AGGAAAACCTCCCCACTAATTC 57.682 45.455 0.00 0.00 46.81 2.17
2722 2966 6.902341 TGTACAATGAAAAGAGTGATTCTGC 58.098 36.000 0.00 0.00 35.91 4.26
2839 3114 6.043243 TCTCACTTGTCCTCAAAACCTAGAAT 59.957 38.462 0.00 0.00 32.87 2.40
2929 3204 8.608844 GCTCCAGCTACATAATTAAACAGTAT 57.391 34.615 0.00 0.00 38.21 2.12


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

AutoCloner maintained by Alex Coulton.