Multiple sequence alignment - TraesCS6D01G150500

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 TraesCS6D01G150500 chr6D 100.000 2942 0 0 1 2942 124146141 124143200 0 5433
1 TraesCS6D01G150500 chr6B 94.377 2792 115 27 162 2940 219217633 219214871 0 4248
2 TraesCS6D01G150500 chr6A 94.642 2221 86 19 1 2198 157025435 157027645 0 3411
3 TraesCS6D01G150500 chr6A 88.768 641 45 10 2307 2942 157027639 157028257 0 760


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 TraesCS6D01G150500 chr6D 124143200 124146141 2941 True 5433.0 5433 100.000 1 2942 1 chr6D.!!$R1 2941
1 TraesCS6D01G150500 chr6B 219214871 219217633 2762 True 4248.0 4248 94.377 162 2940 1 chr6B.!!$R1 2778
2 TraesCS6D01G150500 chr6A 157025435 157028257 2822 False 2085.5 3411 91.705 1 2942 2 chr6A.!!$F1 2941

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
936 956 0.385473 GTTCCACGCCGATGTGTTTG 60.385 55.0 0.0 0.0 38.2 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2729 2760 0.107945 GCTGAAGGATGCGAAGGAGT 60.108 55.0 0.0 0.0 0.0 3.85 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
32 33 2.124151 GGGCCGGCATCACATCTT 60.124 61.111 30.85 0.00 0.00 2.40
33 34 1.148273 GGGCCGGCATCACATCTTA 59.852 57.895 30.85 0.00 0.00 2.10
35 36 1.388547 GGCCGGCATCACATCTTAAA 58.611 50.000 30.85 0.00 0.00 1.52
40 41 4.362279 CCGGCATCACATCTTAAAATTGG 58.638 43.478 0.00 0.00 0.00 3.16
51 54 6.014327 ACATCTTAAAATTGGCAAGTCACCAT 60.014 34.615 5.96 0.00 36.96 3.55
61 64 1.478510 CAAGTCACCATAGGCGACTCT 59.521 52.381 0.00 0.00 43.30 3.24
68 71 4.519350 TCACCATAGGCGACTCTATAGTTG 59.481 45.833 0.00 0.00 43.67 3.16
70 73 4.519730 ACCATAGGCGACTCTATAGTTGAC 59.480 45.833 0.00 0.00 44.70 3.18
73 76 1.001597 GGCGACTCTATAGTTGACGGG 60.002 57.143 16.06 0.00 39.21 5.28
136 139 0.831288 CCAATGCAAACCCTGGTGGA 60.831 55.000 0.00 0.00 38.00 4.02
148 151 1.961180 CTGGTGGAGGGCTAGTTCCG 61.961 65.000 0.00 0.00 36.22 4.30
183 186 7.798071 ACCTAACCCATGAAGATACGATTTTA 58.202 34.615 0.00 0.00 0.00 1.52
191 194 8.509690 CCATGAAGATACGATTTTAGCATGATT 58.490 33.333 0.00 0.00 34.18 2.57
270 280 3.701241 ACACTATGTTTTGTTGTTGGCG 58.299 40.909 0.00 0.00 0.00 5.69
616 634 2.710096 TCCATTTTCCTCCCACGATC 57.290 50.000 0.00 0.00 0.00 3.69
623 641 1.480789 TCCTCCCACGATCGATCAAA 58.519 50.000 24.34 2.00 0.00 2.69
652 670 1.007964 CGAGACCAGATAGGCGCAG 60.008 63.158 10.83 0.00 43.14 5.18
798 818 4.006989 TCGTTGTCCCCTTGATTGTTATG 58.993 43.478 0.00 0.00 0.00 1.90
936 956 0.385473 GTTCCACGCCGATGTGTTTG 60.385 55.000 0.00 0.00 38.20 2.93
941 961 1.291877 ACGCCGATGTGTTTGCTCTC 61.292 55.000 0.00 0.00 0.00 3.20
944 964 1.148310 CCGATGTGTTTGCTCTCGTT 58.852 50.000 0.00 0.00 0.00 3.85
945 965 1.136252 CCGATGTGTTTGCTCTCGTTG 60.136 52.381 0.00 0.00 0.00 4.10
957 977 3.243101 TGCTCTCGTTGTAGCTAGCATAC 60.243 47.826 18.83 15.83 39.53 2.39
958 978 3.243101 GCTCTCGTTGTAGCTAGCATACA 60.243 47.826 18.83 18.08 35.80 2.29
959 979 4.557695 GCTCTCGTTGTAGCTAGCATACAT 60.558 45.833 18.83 0.00 35.80 2.29
960 980 5.334957 GCTCTCGTTGTAGCTAGCATACATA 60.335 44.000 18.83 10.12 35.80 2.29
2158 2181 4.710423 TCGCTATAAAAATTGCAAGGCA 57.290 36.364 4.94 0.00 36.47 4.75
2191 2214 5.432885 AACACCAAAAGGACGTGATTTAG 57.567 39.130 0.00 0.00 0.00 1.85
2199 2222 7.148255 CCAAAAGGACGTGATTTAGAATGATCA 60.148 37.037 0.00 0.00 0.00 2.92
2211 2234 8.599624 ATTTAGAATGATCAGGAATGTTTGGT 57.400 30.769 0.09 0.00 0.00 3.67
2223 2246 7.930865 TCAGGAATGTTTGGTAAAGAAAATTGG 59.069 33.333 0.00 0.00 0.00 3.16
2234 2260 4.796038 AAGAAAATTGGCATCCTCACAG 57.204 40.909 0.00 0.00 0.00 3.66
2259 2285 2.791383 TTTGCCATCTTGGTTGTTCG 57.209 45.000 0.00 0.00 40.46 3.95
2272 2298 2.253603 GTTGTTCGATTTGCCATGCTC 58.746 47.619 0.00 0.00 0.00 4.26
2279 2305 4.175516 TCGATTTGCCATGCTCAAAAATC 58.824 39.130 13.06 9.60 37.04 2.17
2284 2310 1.741394 GCCATGCTCAAAAATCTGGCC 60.741 52.381 0.00 0.00 42.59 5.36
2287 2313 3.518590 CATGCTCAAAAATCTGGCCTTC 58.481 45.455 3.32 0.00 0.00 3.46
2297 2323 2.145397 TCTGGCCTTCGATCTGTAGT 57.855 50.000 3.32 0.00 0.00 2.73
2305 2331 5.453480 GGCCTTCGATCTGTAGTAAAATCCT 60.453 44.000 0.00 0.00 0.00 3.24
2367 2393 5.461078 GGCATCAGCATCACATTCATAAAAC 59.539 40.000 0.00 0.00 44.61 2.43
2370 2397 3.792956 CAGCATCACATTCATAAAACGGC 59.207 43.478 0.00 0.00 0.00 5.68
2374 2401 3.331150 TCACATTCATAAAACGGCGTCT 58.669 40.909 15.17 6.39 0.00 4.18
2413 2442 4.102524 AGTTCCAGTATCAACAGTGTTCCA 59.897 41.667 5.27 0.00 0.00 3.53
2553 2584 7.432869 CAAAAGTATAGAGATCCTCAGACCTG 58.567 42.308 0.00 0.00 32.06 4.00
2603 2634 8.048534 TCAGAAGAAAGAAATAAGGATTGCAG 57.951 34.615 0.00 0.00 0.00 4.41
2607 2638 7.530426 AGAAAGAAATAAGGATTGCAGTGTT 57.470 32.000 0.00 0.00 0.00 3.32
2709 2740 3.506067 TCGTGAGTGACTGCTTCAGAATA 59.494 43.478 0.00 0.00 33.71 1.75
2729 2760 2.121506 AGGGGCCTTCTCCACCAA 60.122 61.111 0.84 0.00 0.00 3.67
2736 2767 1.611936 GCCTTCTCCACCAACTCCTTC 60.612 57.143 0.00 0.00 0.00 3.46
2753 2784 2.515523 CGCATCCTTCAGCCCCAG 60.516 66.667 0.00 0.00 0.00 4.45
2763 2794 1.507140 TCAGCCCCAGATCGGTAAAT 58.493 50.000 3.47 0.00 0.00 1.40
2787 2818 8.905660 ATGTTCTGATCTCCTTGATAATCTTG 57.094 34.615 0.00 0.00 35.14 3.02
2834 2865 6.796426 TCTCCAACTTGACATCGAATACTAG 58.204 40.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.179018 GCCGGCCCAGTATCTTGAAT 60.179 55.000 18.11 0.00 0.00 2.57
9 10 1.598130 GTGATGCCGGCCCAGTATC 60.598 63.158 26.77 19.90 0.00 2.24
11 12 2.324014 GATGTGATGCCGGCCCAGTA 62.324 60.000 26.77 13.76 0.00 2.74
32 33 4.159506 GCCTATGGTGACTTGCCAATTTTA 59.840 41.667 0.00 0.00 39.72 1.52
33 34 3.055891 GCCTATGGTGACTTGCCAATTTT 60.056 43.478 0.00 0.00 39.72 1.82
35 36 2.102578 GCCTATGGTGACTTGCCAATT 58.897 47.619 0.00 0.00 39.72 2.32
40 41 4.932789 TCGCCTATGGTGACTTGC 57.067 55.556 0.00 0.00 37.29 4.01
51 54 3.136763 CCGTCAACTATAGAGTCGCCTA 58.863 50.000 6.78 0.00 33.58 3.93
70 73 1.860676 TGTGAAAGAAGACGTTCCCG 58.139 50.000 0.00 0.00 40.83 5.14
73 76 5.817616 TCGTTATGTGAAAGAAGACGTTC 57.182 39.130 0.00 0.00 35.64 3.95
130 133 1.987855 CGGAACTAGCCCTCCACCA 60.988 63.158 6.86 0.00 0.00 4.17
131 134 1.957765 GACGGAACTAGCCCTCCACC 61.958 65.000 6.86 0.00 0.00 4.61
132 135 1.255667 TGACGGAACTAGCCCTCCAC 61.256 60.000 6.86 1.94 0.00 4.02
136 139 1.002087 CTTTGTGACGGAACTAGCCCT 59.998 52.381 0.00 0.00 0.00 5.19
142 145 4.124970 GTTAGGTTCTTTGTGACGGAACT 58.875 43.478 12.76 5.27 39.20 3.01
148 151 4.394729 TCATGGGTTAGGTTCTTTGTGAC 58.605 43.478 0.00 0.00 0.00 3.67
183 186 3.479489 TGGCATCGTGATAAATCATGCT 58.521 40.909 13.73 1.06 42.21 3.79
191 194 4.457257 TGTGATTGTTTGGCATCGTGATAA 59.543 37.500 0.00 0.00 0.00 1.75
270 280 3.755378 ACAATCTTCTTCTGCACCATGAC 59.245 43.478 0.00 0.00 0.00 3.06
327 337 4.042809 AGTGTCATTTGGGAAGTGGTATGA 59.957 41.667 0.00 0.00 0.00 2.15
623 641 2.160205 TCTGGTCTCGAGAACACGAAT 58.840 47.619 28.98 0.00 41.67 3.34
916 936 1.512156 AAACACATCGGCGTGGAACC 61.512 55.000 6.85 0.00 41.38 3.62
936 956 2.500509 ATGCTAGCTACAACGAGAGC 57.499 50.000 17.23 0.00 39.08 4.09
941 961 4.217767 TCCCTATGTATGCTAGCTACAACG 59.782 45.833 22.38 17.35 33.12 4.10
944 964 5.256806 TCTCCCTATGTATGCTAGCTACA 57.743 43.478 21.42 21.42 33.86 2.74
945 965 4.642885 CCTCTCCCTATGTATGCTAGCTAC 59.357 50.000 17.23 15.25 0.00 3.58
957 977 2.755439 ATCGGCCCCCTCTCCCTATG 62.755 65.000 0.00 0.00 0.00 2.23
958 978 2.463497 GATCGGCCCCCTCTCCCTAT 62.463 65.000 0.00 0.00 0.00 2.57
959 979 3.117648 ATCGGCCCCCTCTCCCTA 61.118 66.667 0.00 0.00 0.00 3.53
960 980 4.565850 GATCGGCCCCCTCTCCCT 62.566 72.222 0.00 0.00 0.00 4.20
1083 1104 3.443045 GCCACCTTGCCCGTGATG 61.443 66.667 0.00 0.00 32.77 3.07
1276 1297 3.123620 CACCTTGAGGCTGAGCGC 61.124 66.667 0.00 0.00 39.32 5.92
1707 1728 2.351276 CCCCGGAACTTCCACTGG 59.649 66.667 0.73 5.08 35.91 4.00
1901 1922 5.449725 GCATGAAGAAAGAAGCTGTAATCCC 60.450 44.000 0.00 0.00 0.00 3.85
2018 2040 5.707764 AGCCTAGTGATTTGAAGTTCCTTTC 59.292 40.000 0.00 0.00 0.00 2.62
2158 2181 6.257630 CGTCCTTTTGGTGTTTGATTTGAAAT 59.742 34.615 0.00 0.00 41.38 2.17
2191 2214 8.055279 TCTTTACCAAACATTCCTGATCATTC 57.945 34.615 0.00 0.00 0.00 2.67
2199 2222 6.710295 GCCAATTTTCTTTACCAAACATTCCT 59.290 34.615 0.00 0.00 0.00 3.36
2211 2234 5.336690 GCTGTGAGGATGCCAATTTTCTTTA 60.337 40.000 0.00 0.00 0.00 1.85
2253 2279 1.885233 TGAGCATGGCAAATCGAACAA 59.115 42.857 0.00 0.00 0.00 2.83
2254 2280 1.532523 TGAGCATGGCAAATCGAACA 58.467 45.000 0.00 0.00 0.00 3.18
2255 2281 2.634982 TTGAGCATGGCAAATCGAAC 57.365 45.000 0.00 0.00 0.00 3.95
2259 2285 4.331717 CCAGATTTTTGAGCATGGCAAATC 59.668 41.667 0.00 0.00 35.41 2.17
2272 2298 3.441572 ACAGATCGAAGGCCAGATTTTTG 59.558 43.478 5.01 9.33 0.00 2.44
2279 2305 4.386867 TTTACTACAGATCGAAGGCCAG 57.613 45.455 5.01 0.00 0.00 4.85
2331 2357 2.429971 TGCTGATGCCTTTTGTTTGTCA 59.570 40.909 0.00 0.00 38.71 3.58
2367 2393 1.126846 GTGAAGAAATGTCAGACGCCG 59.873 52.381 0.00 0.00 0.00 6.46
2370 2397 2.738846 CTGGGTGAAGAAATGTCAGACG 59.261 50.000 0.00 0.00 0.00 4.18
2374 2401 3.117701 TGGAACTGGGTGAAGAAATGTCA 60.118 43.478 0.00 0.00 0.00 3.58
2413 2442 6.596309 TCAGTATCGCATATCTTTCCTGAT 57.404 37.500 0.00 0.00 0.00 2.90
2553 2584 3.216800 TGTTAGCATGATGGAGCATTCC 58.783 45.455 0.00 0.00 44.31 3.01
2603 2634 6.348868 GGAGTGAAGGATCAAATTCTGAACAC 60.349 42.308 0.00 0.00 37.67 3.32
2607 2638 5.503634 TGGAGTGAAGGATCAAATTCTGA 57.496 39.130 0.00 0.00 37.30 3.27
2709 2740 2.539081 GGTGGAGAAGGCCCCTGTT 61.539 63.158 0.00 0.00 0.00 3.16
2729 2760 0.107945 GCTGAAGGATGCGAAGGAGT 60.108 55.000 0.00 0.00 0.00 3.85
2736 2767 2.335092 ATCTGGGGCTGAAGGATGCG 62.335 60.000 0.00 0.00 0.00 4.73
2753 2784 5.848406 AGGAGATCAGAACATTTACCGATC 58.152 41.667 0.00 0.00 0.00 3.69
2763 2794 8.082672 TCAAGATTATCAAGGAGATCAGAACA 57.917 34.615 0.00 0.00 38.19 3.18
2787 2818 1.171308 TTGAGGCTGCTGCAAAGATC 58.829 50.000 17.89 7.34 41.91 2.75
2834 2865 3.817647 TGAAGAGAAAAAGGCTGAGAAGC 59.182 43.478 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.