Multiple sequence alignment - TraesCS6D01G230800

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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 TraesCS6D01G230800 chr6D 100.000 2451 0 0 498 2948 324247954 324250404 0.000000e+00 4527
1 TraesCS6D01G230800 chr6D 100.000 176 0 0 1 176 324247457 324247632 2.830000e-85 326
2 TraesCS6D01G230800 chr6B 94.075 2481 76 23 498 2948 499579136 499576697 0.000000e+00 3701
3 TraesCS6D01G230800 chr6B 94.253 174 10 0 1 174 499579364 499579191 1.740000e-67 267
4 TraesCS6D01G230800 chr6A 93.479 2515 81 27 498 2948 461644443 461646938 0.000000e+00 3659
5 TraesCS6D01G230800 chr6A 94.318 176 10 0 1 176 461644227 461644402 1.350000e-68 270
6 TraesCS6D01G230800 chr2D 76.176 957 148 57 993 1921 524932529 524931625 5.840000e-117 431
7 TraesCS6D01G230800 chr2B 75.707 955 162 47 993 1921 620861719 620860809 5.880000e-112 414
8 TraesCS6D01G230800 chr2A 76.165 944 132 62 993 1921 670315092 670314227 7.600000e-111 411


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 TraesCS6D01G230800 chr6D 324247457 324250404 2947 False 2426.5 4527 100.0000 1 2948 2 chr6D.!!$F1 2947
1 TraesCS6D01G230800 chr6B 499576697 499579364 2667 True 1984.0 3701 94.1640 1 2948 2 chr6B.!!$R1 2947
2 TraesCS6D01G230800 chr6A 461644227 461646938 2711 False 1964.5 3659 93.8985 1 2948 2 chr6A.!!$F1 2947
3 TraesCS6D01G230800 chr2D 524931625 524932529 904 True 431.0 431 76.1760 993 1921 1 chr2D.!!$R1 928
4 TraesCS6D01G230800 chr2B 620860809 620861719 910 True 414.0 414 75.7070 993 1921 1 chr2B.!!$R1 928
5 TraesCS6D01G230800 chr2A 670314227 670315092 865 True 411.0 411 76.1650 993 1921 1 chr2A.!!$R1 928

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
55 56 0.460987 GCACCCATGAAGTCGAGGAG 60.461 60.000 0.00 0.00 0.00 3.69 F
116 117 1.075601 TGAGGAAAGGGGTCATGCTT 58.924 50.000 0.00 0.00 0.00 3.91 F
761 767 2.015587 TGTGATTTGATATGCTGCGCA 58.984 42.857 10.98 10.98 44.86 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1725 0.744414 CCCTCGCGTTCCATCAATGT 60.744 55.000 5.77 0.00 0.00 2.71 R
1893 1967 2.283532 ACGGCAGAGAGCTCCACT 60.284 61.111 10.93 7.69 44.79 4.00 R
2551 2646 0.179029 AAACAGGAACACAGGGGACG 60.179 55.000 0.00 0.00 0.00 4.79 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
55 56 0.460987 GCACCCATGAAGTCGAGGAG 60.461 60.000 0.00 0.00 0.00 3.69
116 117 1.075601 TGAGGAAAGGGGTCATGCTT 58.924 50.000 0.00 0.00 0.00 3.91
145 146 5.031578 GTGGCACGCAAATCGAATAATTTA 58.968 37.500 0.00 0.00 41.67 1.40
167 168 3.302555 TGTAACAAGTTACGCTCACTCG 58.697 45.455 15.88 0.00 46.19 4.18
526 527 4.090498 GGTAGTAATCGTCGTTTGTGGTTC 59.910 45.833 0.00 0.00 0.00 3.62
612 613 4.746115 TGCTCGTTACATCGTGTTAACTTT 59.254 37.500 7.22 0.00 0.00 2.66
761 767 2.015587 TGTGATTTGATATGCTGCGCA 58.984 42.857 10.98 10.98 44.86 6.09
1566 1625 4.753662 TACCAGGCTCTCGGCGGT 62.754 66.667 7.21 0.00 42.15 5.68
1642 1704 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1782 1844 2.034221 GGGCACAAGAGGTCCCAC 59.966 66.667 0.00 0.00 37.03 4.61
2029 2116 4.294347 TCCATCCAAGAAACCAAAAGGTT 58.706 39.130 0.00 0.00 0.00 3.50
2030 2117 4.100808 TCCATCCAAGAAACCAAAAGGTTG 59.899 41.667 0.00 0.00 31.96 3.77
2150 2240 9.372369 TGTTTTTACAGGATTTTAAACTGTTGG 57.628 29.630 13.32 0.00 42.38 3.77
2164 2254 5.373981 AACTGTTGGTGTTCGTTTTGTTA 57.626 34.783 0.00 0.00 0.00 2.41
2167 2257 5.642919 ACTGTTGGTGTTCGTTTTGTTACTA 59.357 36.000 0.00 0.00 0.00 1.82
2298 2388 2.444706 TGAGCCATCTCCTCCCCG 60.445 66.667 0.00 0.00 38.58 5.73
2548 2643 2.510238 GCAGCTGCTCGTACCCTG 60.510 66.667 31.33 0.00 38.21 4.45
2549 2644 2.510238 CAGCTGCTCGTACCCTGC 60.510 66.667 0.00 0.00 0.00 4.85
2550 2645 4.135153 AGCTGCTCGTACCCTGCG 62.135 66.667 0.00 0.00 0.00 5.18
2555 2650 4.849329 CTCGTACCCTGCGCGTCC 62.849 72.222 8.43 0.00 0.00 4.79
2590 2685 3.713826 TGTTCCCCACCACTATTTCTC 57.286 47.619 0.00 0.00 0.00 2.87
2721 2831 1.825622 GATAACAGCCAGCCAGCCC 60.826 63.158 0.00 0.00 0.00 5.19
2749 2869 3.071479 GTTTATGGAGAAACGGCAGTCA 58.929 45.455 0.00 0.00 30.14 3.41
2861 2999 0.823356 AGTTGGTGGTGCTGCGAATT 60.823 50.000 0.00 0.00 0.00 2.17
2939 3077 2.174592 CGCGGTTTAATGTGCGCA 59.825 55.556 5.66 5.66 44.30 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.611714 ATGGGGTGAACGTGACCTAC 59.388 55.000 14.88 9.89 33.58 3.18
116 117 0.878416 GATTTGCGTGCCACAAGGTA 59.122 50.000 0.00 0.00 37.19 3.08
145 146 3.918591 CGAGTGAGCGTAACTTGTTACAT 59.081 43.478 19.52 10.09 0.00 2.29
156 157 1.986698 GCCTTTTACGAGTGAGCGTA 58.013 50.000 0.00 0.00 43.61 4.42
502 503 2.595536 CCACAAACGACGATTACTACCG 59.404 50.000 0.00 0.00 0.00 4.02
504 505 4.090498 GGAACCACAAACGACGATTACTAC 59.910 45.833 0.00 0.00 0.00 2.73
526 527 3.426159 GCAAGTATCAACCATTCACACGG 60.426 47.826 0.00 0.00 0.00 4.94
792 798 1.619654 TGACACTTTCCATTGCTGGG 58.380 50.000 0.00 0.00 43.34 4.45
1407 1439 3.845259 TAGCCGTGCCCCATCGAC 61.845 66.667 0.00 0.00 0.00 4.20
1626 1685 3.036959 GGGGGAGGAGGAGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
1663 1725 0.744414 CCCTCGCGTTCCATCAATGT 60.744 55.000 5.77 0.00 0.00 2.71
1893 1967 2.283532 ACGGCAGAGAGCTCCACT 60.284 61.111 10.93 7.69 44.79 4.00
2150 2240 7.881516 AAACGAATAGTAACAAAACGAACAC 57.118 32.000 0.00 0.00 0.00 3.32
2167 2257 7.759433 CACCAATTCCATAGCTTTTAAACGAAT 59.241 33.333 0.00 0.00 0.00 3.34
2284 2374 2.198304 AAACACGGGGAGGAGATGGC 62.198 60.000 0.00 0.00 0.00 4.40
2298 2388 0.453390 GCTCTGGGCTATGCAAACAC 59.547 55.000 0.00 0.00 38.06 3.32
2418 2510 2.808543 GTGACTTTGGACACTAGGCAAG 59.191 50.000 0.00 0.00 35.78 4.01
2549 2644 4.003788 AGGAACACAGGGGACGCG 62.004 66.667 3.53 3.53 0.00 6.01
2550 2645 2.358737 CAGGAACACAGGGGACGC 60.359 66.667 0.00 0.00 0.00 5.19
2551 2646 0.179029 AAACAGGAACACAGGGGACG 60.179 55.000 0.00 0.00 0.00 4.79
2552 2647 1.318576 CAAACAGGAACACAGGGGAC 58.681 55.000 0.00 0.00 0.00 4.46
2553 2648 0.923358 ACAAACAGGAACACAGGGGA 59.077 50.000 0.00 0.00 0.00 4.81
2554 2649 1.681264 GAACAAACAGGAACACAGGGG 59.319 52.381 0.00 0.00 0.00 4.79
2555 2650 1.681264 GGAACAAACAGGAACACAGGG 59.319 52.381 0.00 0.00 0.00 4.45
2556 2651 1.681264 GGGAACAAACAGGAACACAGG 59.319 52.381 0.00 0.00 0.00 4.00
2557 2652 1.681264 GGGGAACAAACAGGAACACAG 59.319 52.381 0.00 0.00 0.00 3.66
2590 2685 2.092212 AGAGGCATGGGTGGTTAATGAG 60.092 50.000 0.00 0.00 0.00 2.90
2637 2732 2.032178 GCAACCTAGTACCGTACGTAGG 59.968 54.545 21.71 21.71 36.49 3.18
2721 2831 5.154222 GCCGTTTCTCCATAAACAAAGAAG 58.846 41.667 0.00 0.00 38.93 2.85
2749 2869 0.331616 AGCCCGAGCCCTACAAAAAT 59.668 50.000 0.00 0.00 41.25 1.82
2839 2959 2.908073 CGCAGCACCACCAACTTCC 61.908 63.158 0.00 0.00 0.00 3.46
2840 2960 1.444119 TTCGCAGCACCACCAACTTC 61.444 55.000 0.00 0.00 0.00 3.01
2841 2961 0.823356 ATTCGCAGCACCACCAACTT 60.823 50.000 0.00 0.00 0.00 2.66
2842 2962 0.823356 AATTCGCAGCACCACCAACT 60.823 50.000 0.00 0.00 0.00 3.16
2843 2963 0.387239 GAATTCGCAGCACCACCAAC 60.387 55.000 0.00 0.00 0.00 3.77
2844 2964 1.851021 CGAATTCGCAGCACCACCAA 61.851 55.000 15.93 0.00 0.00 3.67
2861 2999 4.467084 GCCTGAATGACCGGCCGA 62.467 66.667 30.73 7.23 41.93 5.54
2881 3019 4.789173 TCCCCCGGAATCAGCGGA 62.789 66.667 0.73 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.