Multiple sequence alignment - TraesCS6D01G150400

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 TraesCS6D01G150400 chr6D 100.000 2579 0 0 1 2579 124141941 124144519 0 4763
1 TraesCS6D01G150400 chr6B 93.916 2597 122 20 1 2579 219213615 219216193 0 3888
2 TraesCS6D01G150400 chr6A 89.769 1906 106 36 4 1895 157029469 157027639 0 2357
3 TraesCS6D01G150400 chr6A 93.621 580 31 6 2004 2579 157027645 157027068 0 861


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 TraesCS6D01G150400 chr6D 124141941 124144519 2578 False 4763 4763 100.000 1 2579 1 chr6D.!!$F1 2578
1 TraesCS6D01G150400 chr6B 219213615 219216193 2578 False 3888 3888 93.916 1 2579 1 chr6B.!!$F1 2578
2 TraesCS6D01G150400 chr6A 157027068 157029469 2401 True 1609 2357 91.695 4 2579 2 chr6A.!!$R1 2575

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
581 591 0.099436 CTTATGTTGCTCGCCCTTGC 59.901 55.000 0.00 0.00 0.00 4.01 F
837 856 1.136419 CGACGCATATGCTTCTCATGC 60.136 52.381 26.07 5.63 41.29 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1461 1.507140 TCAGCCCCAGATCGGTAAAT 58.493 50.000 3.47 0.0 0.00 1.40 R
1916 1945 1.741394 GCCATGCTCAAAAATCTGGCC 60.741 52.381 0.00 0.0 42.59 5.36 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
103 104 2.542411 GCATCAATCCATTCGGCTTGTC 60.542 50.000 0.00 0.00 39.11 3.18
126 127 1.009449 GTTTGTTTGCTGCGCGGTA 60.009 52.632 19.23 11.31 0.00 4.02
133 134 1.592400 TTGCTGCGCGGTAGAGTAGT 61.592 55.000 19.23 0.00 32.98 2.73
134 135 1.139095 GCTGCGCGGTAGAGTAGTT 59.861 57.895 19.23 0.00 32.98 2.24
163 165 3.506067 ACAAGAGCAGTTTATTTTCCGGG 59.494 43.478 0.00 0.00 0.00 5.73
245 247 2.097142 GCTGATTGACACCTGATGAAGC 59.903 50.000 0.00 0.00 0.00 3.86
247 249 3.340928 TGATTGACACCTGATGAAGCTG 58.659 45.455 0.00 0.00 0.00 4.24
248 250 2.936919 TTGACACCTGATGAAGCTGT 57.063 45.000 0.00 0.00 0.00 4.40
249 251 4.020307 TGATTGACACCTGATGAAGCTGTA 60.020 41.667 0.00 0.00 0.00 2.74
250 252 3.599730 TGACACCTGATGAAGCTGTAG 57.400 47.619 0.00 0.00 0.00 2.74
251 253 3.165071 TGACACCTGATGAAGCTGTAGA 58.835 45.455 0.00 0.00 0.00 2.59
252 254 3.056536 TGACACCTGATGAAGCTGTAGAC 60.057 47.826 0.00 0.00 0.00 2.59
253 255 3.169099 ACACCTGATGAAGCTGTAGACT 58.831 45.455 0.00 0.00 0.00 3.24
254 256 3.580458 ACACCTGATGAAGCTGTAGACTT 59.420 43.478 0.00 0.00 0.00 3.01
255 257 3.931468 CACCTGATGAAGCTGTAGACTTG 59.069 47.826 0.00 0.00 0.00 3.16
266 268 4.218852 AGCTGTAGACTTGTAGTTGAGGTC 59.781 45.833 0.00 0.00 0.00 3.85
272 274 5.068636 AGACTTGTAGTTGAGGTCGTCTAA 58.931 41.667 0.00 0.00 32.86 2.10
312 321 1.686115 CCATGGCTGAGGGTTTTAGGG 60.686 57.143 0.00 0.00 0.00 3.53
389 398 6.380846 TGCTTTATCAGATAAATTGGCCTGTT 59.619 34.615 14.78 0.00 34.50 3.16
403 412 2.359900 GCCTGTTGGTCTGGTTCATAG 58.640 52.381 0.00 0.00 37.45 2.23
412 422 2.237392 GTCTGGTTCATAGTCTTGGCCT 59.763 50.000 3.32 0.00 0.00 5.19
452 462 3.788227 TTCACTGGGTGAGCTGTAATT 57.212 42.857 0.00 0.00 43.69 1.40
465 475 3.763897 AGCTGTAATTTTCCGGCTCATTT 59.236 39.130 0.00 0.00 38.99 2.32
581 591 0.099436 CTTATGTTGCTCGCCCTTGC 59.901 55.000 0.00 0.00 0.00 4.01
670 682 4.226168 TGTGAAAGGGTTTGGTGGAAAATT 59.774 37.500 0.00 0.00 0.00 1.82
719 731 2.483877 CTGCGCATTTAGTTCCAAGTCA 59.516 45.455 12.24 0.00 0.00 3.41
724 743 5.511729 GCGCATTTAGTTCCAAGTCAAATAC 59.488 40.000 0.30 0.00 0.00 1.89
725 744 6.622896 GCGCATTTAGTTCCAAGTCAAATACT 60.623 38.462 0.30 0.00 41.49 2.12
726 745 6.961554 CGCATTTAGTTCCAAGTCAAATACTC 59.038 38.462 0.00 0.00 37.50 2.59
727 746 7.251281 GCATTTAGTTCCAAGTCAAATACTCC 58.749 38.462 0.00 0.00 37.50 3.85
728 747 7.094377 GCATTTAGTTCCAAGTCAAATACTCCA 60.094 37.037 0.00 0.00 37.50 3.86
729 748 8.960591 CATTTAGTTCCAAGTCAAATACTCCAT 58.039 33.333 0.00 0.00 37.50 3.41
767 786 2.758009 ACGTTGCCGTCTAAGCTTAAA 58.242 42.857 7.74 0.00 46.28 1.52
833 852 4.444388 TGAAATACGACGCATATGCTTCTC 59.556 41.667 26.07 18.37 37.20 2.87
834 853 3.643159 ATACGACGCATATGCTTCTCA 57.357 42.857 26.07 16.43 37.20 3.27
836 855 2.130395 ACGACGCATATGCTTCTCATG 58.870 47.619 26.07 15.80 37.20 3.07
837 856 1.136419 CGACGCATATGCTTCTCATGC 60.136 52.381 26.07 5.63 41.29 4.06
850 874 5.819379 TGCTTCTCATGCTAGAGGTTATTTG 59.181 40.000 0.00 0.00 36.30 2.32
961 985 7.171653 CCAATCTTTAGTTTCTTCTCCTTCCT 58.828 38.462 0.00 0.00 0.00 3.36
994 1018 2.967362 TGTGCCAATACCTAGTTGACG 58.033 47.619 0.00 0.00 0.00 4.35
1128 1152 3.389983 ACACTGGTGCTAAGAGGTACAAA 59.610 43.478 0.17 0.00 0.00 2.83
1257 1281 1.959508 GCTCCAGCTCTCCTTCTCAGA 60.960 57.143 0.00 0.00 38.21 3.27
1366 1390 3.817647 TGAAGAGAAAAAGGCTGAGAAGC 59.182 43.478 0.00 0.00 0.00 3.86
1413 1437 1.171308 TTGAGGCTGCTGCAAAGATC 58.829 50.000 17.89 7.34 41.91 2.75
1437 1461 8.082672 TCAAGATTATCAAGGAGATCAGAACA 57.917 34.615 0.00 0.00 38.19 3.18
1447 1471 5.848406 AGGAGATCAGAACATTTACCGATC 58.152 41.667 0.00 0.00 0.00 3.69
1464 1488 2.335092 ATCTGGGGCTGAAGGATGCG 62.335 60.000 0.00 0.00 0.00 4.73
1471 1495 0.107945 GCTGAAGGATGCGAAGGAGT 60.108 55.000 0.00 0.00 0.00 3.85
1491 1515 2.539081 GGTGGAGAAGGCCCCTGTT 61.539 63.158 0.00 0.00 0.00 3.16
1593 1617 5.503634 TGGAGTGAAGGATCAAATTCTGA 57.496 39.130 0.00 0.00 37.30 3.27
1597 1621 6.348868 GGAGTGAAGGATCAAATTCTGAACAC 60.349 42.308 0.00 0.00 37.67 3.32
1647 1671 3.216800 TGTTAGCATGATGGAGCATTCC 58.783 45.455 0.00 0.00 44.31 3.01
1787 1813 6.596309 TCAGTATCGCATATCTTTCCTGAT 57.404 37.500 0.00 0.00 0.00 2.90
1826 1854 3.117701 TGGAACTGGGTGAAGAAATGTCA 60.118 43.478 0.00 0.00 0.00 3.58
1830 1858 2.738846 CTGGGTGAAGAAATGTCAGACG 59.261 50.000 0.00 0.00 0.00 4.18
1833 1861 1.126846 GTGAAGAAATGTCAGACGCCG 59.873 52.381 0.00 0.00 0.00 6.46
1869 1898 2.429971 TGCTGATGCCTTTTGTTTGTCA 59.570 40.909 0.00 0.00 38.71 3.58
1921 1950 4.386867 TTTACTACAGATCGAAGGCCAG 57.613 45.455 5.01 0.00 0.00 4.85
1928 1957 3.441572 ACAGATCGAAGGCCAGATTTTTG 59.558 43.478 5.01 9.33 0.00 2.44
1941 1970 4.331717 CCAGATTTTTGAGCATGGCAAATC 59.668 41.667 0.00 0.00 35.41 2.17
1945 1974 2.634982 TTGAGCATGGCAAATCGAAC 57.365 45.000 0.00 0.00 0.00 3.95
1946 1975 1.532523 TGAGCATGGCAAATCGAACA 58.467 45.000 0.00 0.00 0.00 3.18
1947 1976 1.885233 TGAGCATGGCAAATCGAACAA 59.115 42.857 0.00 0.00 0.00 2.83
1989 2021 5.336690 GCTGTGAGGATGCCAATTTTCTTTA 60.337 40.000 0.00 0.00 0.00 1.85
2001 2033 6.710295 GCCAATTTTCTTTACCAAACATTCCT 59.290 34.615 0.00 0.00 0.00 3.36
2009 2041 8.055279 TCTTTACCAAACATTCCTGATCATTC 57.945 34.615 0.00 0.00 0.00 2.67
2042 2074 6.257630 CGTCCTTTTGGTGTTTGATTTGAAAT 59.742 34.615 0.00 0.00 41.38 2.17
2182 2215 5.707764 AGCCTAGTGATTTGAAGTTCCTTTC 59.292 40.000 0.00 0.00 0.00 2.62
2299 2333 5.449725 GCATGAAGAAAGAAGCTGTAATCCC 60.450 44.000 0.00 0.00 0.00 3.85
2493 2527 2.351276 CCCCGGAACTTCCACTGG 59.649 66.667 0.73 5.08 35.91 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 3.029735 GCAGCAAACAAACCCGCG 61.030 61.111 0.00 0.00 0.00 6.46
163 165 1.012086 GGGCGGACCTAACGAAATTC 58.988 55.000 0.00 0.00 35.85 2.17
245 247 4.215827 ACGACCTCAACTACAAGTCTACAG 59.784 45.833 0.00 0.00 0.00 2.74
247 249 4.455190 AGACGACCTCAACTACAAGTCTAC 59.545 45.833 0.00 0.00 36.15 2.59
248 250 4.649692 AGACGACCTCAACTACAAGTCTA 58.350 43.478 0.00 0.00 36.15 2.59
249 251 3.488363 AGACGACCTCAACTACAAGTCT 58.512 45.455 0.00 0.00 33.47 3.24
250 252 3.919223 AGACGACCTCAACTACAAGTC 57.081 47.619 0.00 0.00 0.00 3.01
251 253 5.068636 TCTTAGACGACCTCAACTACAAGT 58.931 41.667 0.00 0.00 0.00 3.16
252 254 5.392165 CCTCTTAGACGACCTCAACTACAAG 60.392 48.000 0.00 0.00 0.00 3.16
253 255 4.458295 CCTCTTAGACGACCTCAACTACAA 59.542 45.833 0.00 0.00 0.00 2.41
254 256 4.008330 CCTCTTAGACGACCTCAACTACA 58.992 47.826 0.00 0.00 0.00 2.74
255 257 3.377798 CCCTCTTAGACGACCTCAACTAC 59.622 52.174 0.00 0.00 0.00 2.73
266 268 2.544685 CACATGAAGCCCTCTTAGACG 58.455 52.381 0.00 0.00 31.48 4.18
298 300 3.332783 ACCCTAAACCCTAAAACCCTCAG 59.667 47.826 0.00 0.00 0.00 3.35
312 321 0.034089 AGCAGATGCCCACCCTAAAC 60.034 55.000 0.14 0.00 43.38 2.01
337 346 0.888736 TGAAATGACAGCGGGGTGTG 60.889 55.000 8.41 0.00 0.00 3.82
338 347 0.179004 TTGAAATGACAGCGGGGTGT 60.179 50.000 2.75 2.75 0.00 4.16
371 380 4.016444 GACCAACAGGCCAATTTATCTGA 58.984 43.478 5.01 0.00 0.00 3.27
383 392 2.290323 ACTATGAACCAGACCAACAGGC 60.290 50.000 0.00 0.00 0.00 4.85
389 398 2.027192 GCCAAGACTATGAACCAGACCA 60.027 50.000 0.00 0.00 0.00 4.02
403 412 2.479566 TCAATCTCACAGGCCAAGAC 57.520 50.000 5.01 0.00 0.00 3.01
412 422 0.322366 TGGCCGCAATCAATCTCACA 60.322 50.000 0.00 0.00 0.00 3.58
452 462 1.243902 GTCACCAAATGAGCCGGAAA 58.756 50.000 5.05 0.00 38.28 3.13
465 475 1.431633 TCTCTGGTTAGGAGGTCACCA 59.568 52.381 0.00 0.00 38.30 4.17
581 591 2.539547 CGAAATTCCGCACAGCAATAGG 60.540 50.000 0.00 0.00 0.00 2.57
719 731 8.478877 ACTGACGATTTAGAGAATGGAGTATTT 58.521 33.333 0.00 0.00 0.00 1.40
724 743 7.687005 GTAACTGACGATTTAGAGAATGGAG 57.313 40.000 0.00 0.00 0.00 3.86
754 773 8.753175 GTCATGGTAACTATTTAAGCTTAGACG 58.247 37.037 6.24 0.44 37.61 4.18
755 774 9.819267 AGTCATGGTAACTATTTAAGCTTAGAC 57.181 33.333 6.24 6.00 37.61 2.59
767 786 6.213600 AGAAGTGGACAAGTCATGGTAACTAT 59.786 38.462 2.29 0.00 37.61 2.12
994 1018 4.553330 TGGAAGACAAACTCATCCTACC 57.447 45.455 0.00 0.00 0.00 3.18
1098 1122 2.340210 TAGCACCAGTGTCTTTTGCA 57.660 45.000 0.00 0.00 35.57 4.08
1128 1152 7.346698 CCATATGGGTCATAGACTTCAGGATAT 59.653 40.741 14.52 0.00 32.47 1.63
1257 1281 2.113986 GGTGCTGGCTGGTTCAGT 59.886 61.111 0.00 0.00 34.89 3.41
1366 1390 6.796426 TCTCCAACTTGACATCGAATACTAG 58.204 40.000 0.00 0.00 0.00 2.57
1413 1437 8.905660 ATGTTCTGATCTCCTTGATAATCTTG 57.094 34.615 0.00 0.00 35.14 3.02
1437 1461 1.507140 TCAGCCCCAGATCGGTAAAT 58.493 50.000 3.47 0.00 0.00 1.40
1447 1471 2.515523 CGCATCCTTCAGCCCCAG 60.516 66.667 0.00 0.00 0.00 4.45
1464 1488 1.611936 GCCTTCTCCACCAACTCCTTC 60.612 57.143 0.00 0.00 0.00 3.46
1471 1495 2.121506 AGGGGCCTTCTCCACCAA 60.122 61.111 0.84 0.00 0.00 3.67
1491 1515 3.506067 TCGTGAGTGACTGCTTCAGAATA 59.494 43.478 0.00 0.00 33.71 1.75
1593 1617 7.530426 AGAAAGAAATAAGGATTGCAGTGTT 57.470 32.000 0.00 0.00 0.00 3.32
1597 1621 8.048534 TCAGAAGAAAGAAATAAGGATTGCAG 57.951 34.615 0.00 0.00 0.00 4.41
1647 1671 7.432869 CAAAAGTATAGAGATCCTCAGACCTG 58.567 42.308 0.00 0.00 32.06 4.00
1787 1813 4.102524 AGTTCCAGTATCAACAGTGTTCCA 59.897 41.667 5.27 0.00 0.00 3.53
1826 1854 3.331150 TCACATTCATAAAACGGCGTCT 58.669 40.909 15.17 6.39 0.00 4.18
1830 1858 3.792956 CAGCATCACATTCATAAAACGGC 59.207 43.478 0.00 0.00 0.00 5.68
1833 1861 5.461078 GGCATCAGCATCACATTCATAAAAC 59.539 40.000 0.00 0.00 44.61 2.43
1895 1924 5.453480 GGCCTTCGATCTGTAGTAAAATCCT 60.453 44.000 0.00 0.00 0.00 3.24
1903 1932 2.145397 TCTGGCCTTCGATCTGTAGT 57.855 50.000 3.32 0.00 0.00 2.73
1913 1942 3.518590 CATGCTCAAAAATCTGGCCTTC 58.481 45.455 3.32 0.00 0.00 3.46
1916 1945 1.741394 GCCATGCTCAAAAATCTGGCC 60.741 52.381 0.00 0.00 42.59 5.36
1921 1950 4.175516 TCGATTTGCCATGCTCAAAAATC 58.824 39.130 13.06 9.60 37.04 2.17
1928 1957 2.253603 GTTGTTCGATTTGCCATGCTC 58.746 47.619 0.00 0.00 0.00 4.26
1941 1970 2.791383 TTTGCCATCTTGGTTGTTCG 57.209 45.000 0.00 0.00 40.46 3.95
1966 1995 4.796038 AAGAAAATTGGCATCCTCACAG 57.204 40.909 0.00 0.00 0.00 3.66
1977 2009 7.930865 TCAGGAATGTTTGGTAAAGAAAATTGG 59.069 33.333 0.00 0.00 0.00 3.16
1989 2021 8.599624 ATTTAGAATGATCAGGAATGTTTGGT 57.400 30.769 0.09 0.00 0.00 3.67
2001 2033 7.148255 CCAAAAGGACGTGATTTAGAATGATCA 60.148 37.037 0.00 0.00 0.00 2.92
2009 2041 5.432885 AACACCAAAAGGACGTGATTTAG 57.567 39.130 0.00 0.00 0.00 1.85
2042 2074 4.710423 TCGCTATAAAAATTGCAAGGCA 57.290 36.364 4.94 0.00 36.47 4.75


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

AutoCloner maintained by Alex Coulton.