Multiple sequence alignment - TraesCS2A01G369500

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 TraesCS2A01G369500 chr2A 100.00 2070 0 0 553 2622 612396902 612398971 0.000000e+00 3823
1 TraesCS2A01G369500 chr2A 100.00 214 0 0 1 214 612396350 612396563 1.890000e-106 396
2 TraesCS2A01G369500 chr7A 97.05 2068 58 3 553 2618 644619692 644617626 0.000000e+00 3478
3 TraesCS2A01G369500 chr7A 97.17 212 6 0 3 214 644619922 644619711 2.480000e-95 359


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 TraesCS2A01G369500 chr2A 612396350 612398971 2621 False 2109.5 3823 100.00 1 2622 2 chr2A.!!$F1 2621
1 TraesCS2A01G369500 chr7A 644617626 644619922 2296 True 1918.5 3478 97.11 3 2618 2 chr7A.!!$R1 2615

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
64 65 1.061131 CATCGTCATCCGTGCAAGAAC 59.939 52.381 0.0 0.0 37.94 3.01 F
1305 1308 0.182775 ATTTCTTATTCGCCCCCGCT 59.817 50.000 0.0 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1576 0.250513 GGACCTTCCAGAACGCATCT 59.749 55.0 0.00 0.00 39.68 2.90 R
2322 2325 0.820871 TGGGAGGTGTTTGTTGCAAC 59.179 50.0 22.83 22.83 0.00 4.17 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
64 65 1.061131 CATCGTCATCCGTGCAAGAAC 59.939 52.381 0.00 0.00 37.94 3.01
68 69 2.535984 CGTCATCCGTGCAAGAACTATC 59.464 50.000 0.00 0.00 0.00 2.08
89 90 1.298339 GGTCAGTGTGCACGCAAAC 60.298 57.895 30.53 24.96 34.50 2.93
119 120 7.722363 TCCTGCTAGATCATACACGATTTTTA 58.278 34.615 0.00 0.00 0.00 1.52
125 126 6.658831 AGATCATACACGATTTTTATTGCGG 58.341 36.000 0.00 0.00 0.00 5.69
182 183 4.202090 GGAATTTCCTGGTTCATGAGATGC 60.202 45.833 8.25 0.00 32.53 3.91
580 581 5.586243 CCCTAATTGATCACGAGTTGATGTT 59.414 40.000 0.00 0.00 45.67 2.71
592 593 5.995282 ACGAGTTGATGTTTGTAATCCTTCA 59.005 36.000 0.00 0.00 0.00 3.02
603 604 9.613428 TGTTTGTAATCCTTCATCGATATTCTT 57.387 29.630 0.00 0.00 0.00 2.52
672 673 2.366916 CACCCTATCGAGCCAGATTTCT 59.633 50.000 0.00 0.00 32.39 2.52
674 675 2.630098 CCCTATCGAGCCAGATTTCTCA 59.370 50.000 0.00 0.00 32.39 3.27
679 680 4.377839 TCGAGCCAGATTTCTCAGTAAG 57.622 45.455 0.00 0.00 0.00 2.34
818 819 2.103263 GGCAGAGTACGATTTCCTCCAT 59.897 50.000 0.00 0.00 0.00 3.41
987 989 1.301423 TTTACACACCTGTTCCACGC 58.699 50.000 0.00 0.00 0.00 5.34
1153 1155 6.951256 TCACTTGTCTGAATGAATTCTACG 57.049 37.500 7.05 0.00 37.67 3.51
1163 1165 1.230324 GAATTCTACGCTGGATGGCC 58.770 55.000 0.00 0.00 0.00 5.36
1207 1209 2.040278 CTCAAGTTCCCTTCCATGACCA 59.960 50.000 0.00 0.00 0.00 4.02
1305 1308 0.182775 ATTTCTTATTCGCCCCCGCT 59.817 50.000 0.00 0.00 0.00 5.52
1320 1323 0.471211 CCGCTCCTCCCATAACCCTA 60.471 60.000 0.00 0.00 0.00 3.53
1332 1335 5.044476 TCCCATAACCCTACAAATGTGATGT 60.044 40.000 0.00 0.00 34.81 3.06
1459 1462 6.764379 TCCCATGTTTCGCACATTATATCTA 58.236 36.000 0.00 0.00 44.40 1.98
1464 1467 7.869016 TGTTTCGCACATTATATCTACTAGC 57.131 36.000 0.00 0.00 0.00 3.42
1569 1572 1.728068 GGAAACTTCTCTTCCCTCGC 58.272 55.000 0.00 0.00 37.03 5.03
1573 1576 0.836400 ACTTCTCTTCCCTCGCCCAA 60.836 55.000 0.00 0.00 0.00 4.12
1608 1611 3.304829 AGGTCCTAGCTCCTTCAGATTC 58.695 50.000 0.00 0.00 0.00 2.52
1617 1620 3.442977 GCTCCTTCAGATTCTGCATTTGT 59.557 43.478 8.89 0.00 0.00 2.83
1634 1637 5.467063 GCATTTGTCTAGTAGGGAGTTATGC 59.533 44.000 0.00 0.00 0.00 3.14
1638 1641 5.133941 TGTCTAGTAGGGAGTTATGCTGAG 58.866 45.833 0.00 0.00 0.00 3.35
1675 1678 6.509418 TTAGTCTTGTTGCATGGTTTATCC 57.491 37.500 0.00 0.00 0.00 2.59
1710 1713 4.189231 AGTTATGTTCGTAGCATGGGTTC 58.811 43.478 0.00 0.00 0.00 3.62
1717 1720 1.867233 CGTAGCATGGGTTCTGTATGC 59.133 52.381 0.00 0.00 45.64 3.14
1743 1746 2.477825 CTGCGAGCATGTATGTAAGCT 58.522 47.619 0.00 0.00 40.60 3.74
1783 1786 8.814553 CCCAGCATTTGGCACCTATCATATATC 61.815 44.444 0.00 0.00 46.32 1.63
1786 1789 8.915057 GCATTTGGCACCTATCATATATCTAT 57.085 34.615 0.00 0.00 43.97 1.98
1866 1869 6.407299 CCAACTATCATTATTTGGCCTTGCTT 60.407 38.462 3.32 0.00 33.09 3.91
1871 1874 4.282957 TCATTATTTGGCCTTGCTTGTTCA 59.717 37.500 3.32 0.00 0.00 3.18
1880 1883 3.303526 GCCTTGCTTGTTCATTTGCAAAG 60.304 43.478 18.19 9.78 43.45 2.77
1905 1908 2.659428 ACTTCCATTTATCTGCCCTGC 58.341 47.619 0.00 0.00 0.00 4.85
1940 1943 4.383661 GGTTTGTTTCCAAGGGTCAACAAT 60.384 41.667 12.83 0.00 37.07 2.71
1943 1946 4.222336 TGTTTCCAAGGGTCAACAATGAT 58.778 39.130 0.00 0.00 38.01 2.45
1972 1975 2.596346 TGGGCATTGTGTTCATTCAGT 58.404 42.857 0.00 0.00 0.00 3.41
2075 2078 4.096833 TCTCATGTTGTGGCAATGAATAGC 59.903 41.667 1.64 0.00 0.00 2.97
2078 2081 3.156293 TGTTGTGGCAATGAATAGCTGT 58.844 40.909 0.00 0.00 0.00 4.40
2080 2083 2.009051 TGTGGCAATGAATAGCTGTCG 58.991 47.619 0.00 0.00 0.00 4.35
2129 2132 2.482721 GTGTACCTTGGAACCATGTTCG 59.517 50.000 0.00 0.00 0.00 3.95
2147 2150 8.453320 CCATGTTCGCACACATATATCAATATT 58.547 33.333 0.00 0.00 35.51 1.28
2187 2190 0.251341 AGCCGAATGAGCCTGGTTTT 60.251 50.000 0.00 0.00 0.00 2.43
2191 2194 2.817258 CCGAATGAGCCTGGTTTTGTAA 59.183 45.455 0.00 0.00 0.00 2.41
2236 2239 1.228124 CAAGCCTTGTTCCCGTCCA 60.228 57.895 0.00 0.00 0.00 4.02
2251 2254 1.032014 GTCCAAAGCTTTCAGGCACA 58.968 50.000 9.23 0.00 34.17 4.57
2288 2291 8.206189 ACATTAATTCATCCCCAAATCAACATC 58.794 33.333 0.00 0.00 0.00 3.06
2322 2325 6.348786 CCTTCCAAATATTCAGTGATATGCCG 60.349 42.308 0.00 0.00 0.00 5.69
2348 2351 1.339929 ACAAACACCTCCCAAATTCGC 59.660 47.619 0.00 0.00 0.00 4.70
2374 2377 3.328637 ACATGCAGGCAGTATATCATCCA 59.671 43.478 0.00 0.00 0.00 3.41
2381 2384 4.469227 AGGCAGTATATCATCCATGGTCTC 59.531 45.833 12.58 0.00 0.00 3.36
2473 2476 5.700373 TCTTTGCATACCAAATTTTTCAGGC 59.300 36.000 0.00 0.00 42.22 4.85
2586 2589 1.068333 CCGAACAAACATTGCTCCCAG 60.068 52.381 0.00 0.00 0.00 4.45
2587 2590 1.608590 CGAACAAACATTGCTCCCAGT 59.391 47.619 0.00 0.00 0.00 4.00
2592 2595 3.957497 ACAAACATTGCTCCCAGTAAACA 59.043 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.795525 CGTGCACACTGACCTCGATAG 60.796 57.143 18.64 0.00 0.00 2.08
68 69 3.406361 GCGTGCACACTGACCTCG 61.406 66.667 18.64 0.00 0.00 4.63
89 90 4.155099 CGTGTATGATCTAGCAGGAGGTAG 59.845 50.000 0.00 0.00 45.09 3.18
119 120 0.525761 GTACATGGTGTTGCCGCAAT 59.474 50.000 9.46 0.00 41.21 3.56
125 126 7.969387 CAACATAATTAGTACATGGTGTTGC 57.031 36.000 9.95 0.00 38.82 4.17
182 183 4.072088 GACGCGTGCAAACCTCGG 62.072 66.667 20.70 0.00 0.00 4.63
603 604 4.772100 TGGATCATATTGCTGGTCGATCTA 59.228 41.667 0.00 0.00 31.92 1.98
672 673 5.480422 TGTCTTAGACTTGCATCCTTACTGA 59.520 40.000 13.86 0.00 33.15 3.41
674 675 6.552445 ATGTCTTAGACTTGCATCCTTACT 57.448 37.500 13.86 0.00 33.15 2.24
679 680 7.615403 TGGATATATGTCTTAGACTTGCATCC 58.385 38.462 22.06 22.06 35.07 3.51
719 720 4.142227 GGTCTCACGACATACCATTGTAGT 60.142 45.833 0.00 0.00 42.05 2.73
818 819 0.813184 GGTTCTGGATCGACACGGTA 59.187 55.000 0.00 0.00 0.00 4.02
1095 1097 3.370366 GCAGCTTCCATGCTATAATCTCG 59.630 47.826 0.00 0.00 41.98 4.04
1153 1155 0.680921 TTGCTAGTTGGCCATCCAGC 60.681 55.000 22.76 22.76 44.53 4.85
1163 1165 6.352516 AGAGTCCAATTATCCTTGCTAGTTG 58.647 40.000 0.00 0.00 0.00 3.16
1207 1209 2.871096 TACCGGGAGAAAATGCAGTT 57.129 45.000 6.32 0.00 0.00 3.16
1247 1249 7.720074 TGGACCGTAAAAATATTGCATGGTATA 59.280 33.333 7.66 0.00 0.00 1.47
1305 1308 4.080015 CACATTTGTAGGGTTATGGGAGGA 60.080 45.833 0.00 0.00 0.00 3.71
1320 1323 2.742053 GTCGGCACTACATCACATTTGT 59.258 45.455 0.00 0.00 0.00 2.83
1464 1467 3.181510 GGCGAATGGTTTGCACTAGTAAG 60.182 47.826 0.00 0.00 42.00 2.34
1537 1540 1.734655 AGTTTCCCTGGAGCTTGAGA 58.265 50.000 0.00 0.00 0.00 3.27
1568 1571 0.960364 TTCCAGAACGCATCTTGGGC 60.960 55.000 0.00 0.00 35.73 5.36
1569 1572 1.089920 CTTCCAGAACGCATCTTGGG 58.910 55.000 0.00 0.00 35.73 4.12
1573 1576 0.250513 GGACCTTCCAGAACGCATCT 59.749 55.000 0.00 0.00 39.68 2.90
1579 1582 1.483004 GGAGCTAGGACCTTCCAGAAC 59.517 57.143 0.00 0.00 39.61 3.01
1608 1611 4.744795 ACTCCCTACTAGACAAATGCAG 57.255 45.455 0.00 0.00 0.00 4.41
1617 1620 5.133941 CACTCAGCATAACTCCCTACTAGA 58.866 45.833 0.00 0.00 0.00 2.43
1710 1713 2.586079 CGCAGGTCCGGCATACAG 60.586 66.667 14.68 0.00 0.00 2.74
1717 1720 2.369257 ATACATGCTCGCAGGTCCGG 62.369 60.000 12.75 0.00 40.28 5.14
1743 1746 2.899975 TGCTGGGGGATTTGAATTGAA 58.100 42.857 0.00 0.00 0.00 2.69
1783 1786 5.069648 AGGGTACACACATCTGACATGATAG 59.930 44.000 0.00 0.00 0.00 2.08
1786 1789 3.055891 CAGGGTACACACATCTGACATGA 60.056 47.826 0.00 0.00 32.49 3.07
1866 1869 5.580297 GGAAGTTGAACTTTGCAAATGAACA 59.420 36.000 13.23 8.16 38.80 3.18
1871 1874 8.907222 ATAAATGGAAGTTGAACTTTGCAAAT 57.093 26.923 13.23 0.00 38.80 2.32
1880 1883 4.706962 AGGGCAGATAAATGGAAGTTGAAC 59.293 41.667 0.00 0.00 0.00 3.18
1905 1908 3.726517 CAAACCAGGCTCGCACGG 61.727 66.667 0.00 0.00 0.00 4.94
1940 1943 2.898612 ACAATGCCCATGTTCACAATCA 59.101 40.909 0.00 0.00 0.00 2.57
1943 1946 2.037901 ACACAATGCCCATGTTCACAA 58.962 42.857 0.00 0.00 0.00 3.33
2075 2078 0.174845 TAGGGCCACGAATTCGACAG 59.825 55.000 33.05 20.45 43.02 3.51
2078 2081 1.143183 GCTAGGGCCACGAATTCGA 59.857 57.895 33.05 8.85 43.02 3.71
2080 2083 0.107654 ACAGCTAGGGCCACGAATTC 60.108 55.000 6.18 0.00 39.73 2.17
2129 2132 9.964303 TTGGTTCAAATATTGATATATGTGTGC 57.036 29.630 0.00 0.00 39.84 4.57
2147 2150 6.349777 CGGCTAGAAATGGTAAATTGGTTCAA 60.350 38.462 0.00 0.00 0.00 2.69
2236 2239 4.342092 ACTTTGTATGTGCCTGAAAGCTTT 59.658 37.500 12.53 12.53 0.00 3.51
2251 2254 8.695456 GGGGATGAATTAATGTTCACTTTGTAT 58.305 33.333 0.00 0.00 40.60 2.29
2288 2291 4.887071 TGAATATTTGGAAGGGTTCATCCG 59.113 41.667 0.00 0.00 38.63 4.18
2322 2325 0.820871 TGGGAGGTGTTTGTTGCAAC 59.179 50.000 22.83 22.83 0.00 4.17
2348 2351 4.747810 TGATATACTGCCTGCATGTATCG 58.252 43.478 13.66 0.00 0.00 2.92
2374 2377 7.370905 TCACAGAATGATAGATTGAGACCAT 57.629 36.000 0.00 0.00 39.69 3.55
2381 2384 7.905265 ACCTATCCTCACAGAATGATAGATTG 58.095 38.462 6.89 0.00 39.21 2.67


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

AutoCloner maintained by Alex Coulton.