Multiple sequence alignment - TraesCS3B01G084800

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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 TraesCS3B01G084800 chr3B 100.000 2853 0 0 1 2853 53472532 53469680 0.000000e+00 5269
1 TraesCS3B01G084800 chr3D 97.684 2720 48 10 1 2717 30928932 30926225 0.000000e+00 4660
2 TraesCS3B01G084800 chr3D 97.059 102 3 0 2752 2853 30926227 30926126 3.780000e-39 172


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 TraesCS3B01G084800 chr3B 53469680 53472532 2852 True 5269 5269 100.0000 1 2853 1 chr3B.!!$R1 2852
1 TraesCS3B01G084800 chr3D 30926126 30928932 2806 True 2416 4660 97.3715 1 2853 2 chr3D.!!$R1 2852

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
368 369 0.776451 CGTGTACGCCTAATCGATGC 59.224 55.0 0.0 0.00 0.00 3.91 F
1088 1089 0.167470 CGTCTGCATTCTGTTGCTGG 59.833 55.0 0.0 3.92 43.18 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1638 1.404391 ACCGGAACAGCGTATACAGAG 59.596 52.381 9.46 0.00 0.0 3.35 R
2605 2609 1.003223 GACCAAAAGCAAACTACGCGT 60.003 47.619 19.17 19.17 0.0 6.01 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
235 236 4.803098 TCCTCTGTTTTAGGTAGTGCTC 57.197 45.455 0.00 0.00 35.48 4.26
243 244 1.384989 TAGGTAGTGCTCAGCTCCGC 61.385 60.000 0.00 0.00 0.00 5.54
261 262 4.227134 CCGCCCCACATCTCTCCG 62.227 72.222 0.00 0.00 0.00 4.63
270 271 2.060383 CATCTCTCCGGTCCAGCCA 61.060 63.158 0.00 0.00 36.97 4.75
328 329 1.874019 CGTGAGCCTCCGACGATTG 60.874 63.158 0.00 0.00 35.05 2.67
332 333 1.078759 GAGCCTCCGACGATTGTGTG 61.079 60.000 0.00 0.00 0.00 3.82
368 369 0.776451 CGTGTACGCCTAATCGATGC 59.224 55.000 0.00 0.00 0.00 3.91
700 701 1.665735 CGTTGTAGTGCAAACCATGGC 60.666 52.381 13.04 0.00 39.03 4.40
746 747 1.517361 CTAGCTCCACACGCATGGA 59.483 57.895 7.92 7.92 46.92 3.41
752 753 1.078214 CCACACGCATGGATCCAGT 60.078 57.895 21.33 10.03 43.02 4.00
795 796 3.423154 CGGTCTTGCCAAGTCGCC 61.423 66.667 4.04 5.08 36.97 5.54
889 890 1.479709 AGGTAGCTGGAGTAGTGCAG 58.520 55.000 14.35 14.35 44.77 4.41
1088 1089 0.167470 CGTCTGCATTCTGTTGCTGG 59.833 55.000 0.00 3.92 43.18 4.85
1099 1100 6.619874 GCATTCTGTTGCTGGAAATGATTTTG 60.620 38.462 0.00 0.00 39.57 2.44
1103 1104 3.681593 TGCTGGAAATGATTTTGGTGG 57.318 42.857 0.00 0.00 0.00 4.61
1333 1334 4.039973 TGAGGTTCTTTGACTCACCGTATT 59.960 41.667 0.00 0.00 36.41 1.89
1359 1360 1.812571 GGATGGAATGTTGTCGCACTT 59.187 47.619 0.00 0.00 0.00 3.16
1484 1485 6.827586 TTTGTCCCTATTTTATCAGCGTTT 57.172 33.333 0.00 0.00 0.00 3.60
1566 1567 4.537135 AGTTGTTCATCTAAGGAAGCGA 57.463 40.909 0.00 0.00 0.00 4.93
1903 1906 7.759886 GGTAAATTTAGTGCCCTTTCTGAAATC 59.240 37.037 2.88 0.00 0.00 2.17
2031 2034 6.013206 AGTTTACCCCATGACACATGTAGTAA 60.013 38.462 0.00 12.51 0.00 2.24
2118 2121 1.539827 ACAATTACTTTGGACAGGCGC 59.460 47.619 0.00 0.00 39.80 6.53
2291 2294 7.660208 TGAGAAGTTGTAGGAAATGGTCTTAAC 59.340 37.037 0.00 0.00 0.00 2.01
2336 2339 7.310734 GGCATAGTCCTAGGCTTCATAATTAGT 60.311 40.741 2.96 0.00 41.96 2.24
2605 2609 5.107182 CGGCATAATTTGTTTCATTGTTGCA 60.107 36.000 0.00 0.00 31.01 4.08
2635 2639 5.534654 AGTTTGCTTTTGGTCATAGTTGCTA 59.465 36.000 0.00 0.00 0.00 3.49
2683 2687 3.543641 GGCACCTATACGCCCCGT 61.544 66.667 0.00 0.00 42.82 5.28
2686 2690 2.042639 ACCTATACGCCCCGTGGT 60.043 61.111 0.00 0.00 41.39 4.16
2707 2711 2.358247 GTCCAACCGCGTCCACAT 60.358 61.111 4.92 0.00 0.00 3.21
2714 2718 2.738139 CGCGTCCACATGCACTGA 60.738 61.111 0.00 0.00 33.65 3.41
2715 2719 2.863153 GCGTCCACATGCACTGAC 59.137 61.111 0.00 0.00 34.29 3.51
2716 2720 2.680913 GCGTCCACATGCACTGACC 61.681 63.158 0.00 0.00 34.29 4.02
2717 2721 2.382746 CGTCCACATGCACTGACCG 61.383 63.158 0.00 0.00 0.00 4.79
2718 2722 2.034879 GTCCACATGCACTGACCGG 61.035 63.158 0.00 0.00 0.00 5.28
2719 2723 2.032528 CCACATGCACTGACCGGT 59.967 61.111 6.92 6.92 0.00 5.28
2720 2724 2.034879 CCACATGCACTGACCGGTC 61.035 63.158 28.17 28.17 0.00 4.79
2721 2725 1.301637 CACATGCACTGACCGGTCA 60.302 57.895 34.13 34.13 38.06 4.02
2722 2726 1.301716 ACATGCACTGACCGGTCAC 60.302 57.895 33.23 23.26 35.46 3.67
2723 2727 1.301637 CATGCACTGACCGGTCACA 60.302 57.895 33.23 27.91 35.46 3.58
2724 2728 1.301716 ATGCACTGACCGGTCACAC 60.302 57.895 33.23 23.46 35.46 3.82
2725 2729 2.038814 ATGCACTGACCGGTCACACA 62.039 55.000 33.23 27.81 35.46 3.72
2726 2730 1.522806 GCACTGACCGGTCACACAA 60.523 57.895 33.23 12.45 35.46 3.33
2727 2731 0.884704 GCACTGACCGGTCACACAAT 60.885 55.000 33.23 13.32 35.46 2.71
2728 2732 1.606994 GCACTGACCGGTCACACAATA 60.607 52.381 33.23 10.87 35.46 1.90
2729 2733 2.761559 CACTGACCGGTCACACAATAA 58.238 47.619 33.23 10.07 35.46 1.40
2730 2734 3.135225 CACTGACCGGTCACACAATAAA 58.865 45.455 33.23 9.29 35.46 1.40
2731 2735 3.562141 CACTGACCGGTCACACAATAAAA 59.438 43.478 33.23 8.50 35.46 1.52
2732 2736 4.035792 CACTGACCGGTCACACAATAAAAA 59.964 41.667 33.23 7.94 35.46 1.94
2766 2770 6.772716 ACATTCATGTACCTCAAATCCATACC 59.227 38.462 0.00 0.00 39.68 2.73
2806 2810 7.884816 AAACATATGTACTGCATACGTATCC 57.115 36.000 9.21 0.00 41.98 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.463833 GTTATGACAAGAGGCCCCCG 60.464 60.000 0.00 0.00 0.00 5.73
97 98 4.613929 CAGGTGGAGAGAAGCTGC 57.386 61.111 0.00 0.00 36.46 5.25
145 146 4.537433 GCCGGCCAGATTCGCTCT 62.537 66.667 18.11 0.00 33.14 4.09
243 244 3.866582 GGAGAGATGTGGGGCGGG 61.867 72.222 0.00 0.00 0.00 6.13
246 247 3.083997 ACCGGAGAGATGTGGGGC 61.084 66.667 9.46 0.00 0.00 5.80
314 315 1.079819 CACACAATCGTCGGAGGCT 60.080 57.895 0.00 0.00 0.00 4.58
328 329 0.321653 CCAGGGACTTACCAGCACAC 60.322 60.000 0.00 0.00 41.20 3.82
332 333 2.272471 GGCCAGGGACTTACCAGC 59.728 66.667 0.00 0.00 41.20 4.85
368 369 2.747989 TCCTGACTACTGACTAAGCACG 59.252 50.000 0.00 0.00 0.00 5.34
476 477 2.628657 GGGCGTTCTCTATCAGTGGTAT 59.371 50.000 0.00 0.00 0.00 2.73
477 478 2.029623 GGGCGTTCTCTATCAGTGGTA 58.970 52.381 0.00 0.00 0.00 3.25
486 487 2.707849 GCTCACCGGGCGTTCTCTA 61.708 63.158 6.32 0.00 0.00 2.43
700 701 1.819632 GGAGCGGTGCCATGGTAAG 60.820 63.158 14.67 7.89 0.00 2.34
746 747 3.211865 CTGCTGTGCATATTGACTGGAT 58.788 45.455 0.00 0.00 38.13 3.41
795 796 4.233408 GCAAGAGCACAAAAGCCG 57.767 55.556 0.00 0.00 41.58 5.52
1088 1089 3.127376 GCCATTGCCACCAAAATCATTTC 59.873 43.478 0.00 0.00 34.05 2.17
1099 1100 2.497273 AGACAATAAAGCCATTGCCACC 59.503 45.455 3.82 0.00 39.13 4.61
1103 1104 6.135290 TGTGATAGACAATAAAGCCATTGC 57.865 37.500 3.82 0.00 39.13 3.56
1195 1196 5.633830 ACACTGTTGGAGAAATAAGCATG 57.366 39.130 0.00 0.00 0.00 4.06
1333 1334 3.599343 CGACAACATTCCATCCAGAAGA 58.401 45.455 0.00 0.00 0.00 2.87
1359 1360 6.009589 TGAAGCACCCAATGAGATAAAAGAA 58.990 36.000 0.00 0.00 0.00 2.52
1637 1638 1.404391 ACCGGAACAGCGTATACAGAG 59.596 52.381 9.46 0.00 0.00 3.35
1683 1684 2.435059 GACTCCACCAAGGCGCTC 60.435 66.667 7.64 0.00 37.29 5.03
1747 1748 1.946768 CTCAGTCAAACCAAAAGGCGA 59.053 47.619 0.00 0.00 0.00 5.54
1903 1906 7.661127 ATCAATTGACACATGATGGTTTTTG 57.339 32.000 11.07 1.52 32.77 2.44
2031 2034 4.377431 CGCGTTTTCAGTTTTGAGATAGCT 60.377 41.667 0.00 0.00 34.15 3.32
2118 2121 1.540707 TGTACATGCACATGCTGTTGG 59.459 47.619 10.50 0.00 42.39 3.77
2188 2191 9.261035 GAATATATTAGATGTGAAGGAGAGGGA 57.739 37.037 0.00 0.00 0.00 4.20
2201 2204 7.884877 TCCTGCCACCAAAGAATATATTAGATG 59.115 37.037 0.00 0.00 0.00 2.90
2291 2294 2.194733 GTGCGCACGACAACTTTTG 58.805 52.632 26.77 0.00 0.00 2.44
2311 2314 7.616313 ACTAATTATGAAGCCTAGGACTATGC 58.384 38.462 14.75 0.00 0.00 3.14
2605 2609 1.003223 GACCAAAAGCAAACTACGCGT 60.003 47.619 19.17 19.17 0.00 6.01
2635 2639 2.245028 TGACCAGGGCTGTAGATACTCT 59.755 50.000 0.00 0.00 0.00 3.24
2647 2651 2.310538 CCCAAATTAGATGACCAGGGC 58.689 52.381 0.00 0.00 0.00 5.19
2695 2699 4.314440 AGTGCATGTGGACGCGGT 62.314 61.111 12.47 0.00 41.53 5.68
2707 2711 2.108157 GTGTGACCGGTCAGTGCA 59.892 61.111 37.04 27.37 40.75 4.57
2729 2733 6.713450 AGGTACATGAATGTAGGAACGTTTTT 59.287 34.615 0.46 0.00 43.32 1.94
2730 2734 6.235664 AGGTACATGAATGTAGGAACGTTTT 58.764 36.000 0.46 0.00 43.32 2.43
2731 2735 5.801380 AGGTACATGAATGTAGGAACGTTT 58.199 37.500 0.46 0.00 43.32 3.60
2732 2736 5.046878 TGAGGTACATGAATGTAGGAACGTT 60.047 40.000 0.00 0.00 43.32 3.99
2733 2737 4.464951 TGAGGTACATGAATGTAGGAACGT 59.535 41.667 0.00 0.00 43.32 3.99
2734 2738 5.006153 TGAGGTACATGAATGTAGGAACG 57.994 43.478 0.00 0.00 43.32 3.95
2735 2739 7.012421 GGATTTGAGGTACATGAATGTAGGAAC 59.988 40.741 0.00 0.00 43.32 3.62
2736 2740 7.054124 GGATTTGAGGTACATGAATGTAGGAA 58.946 38.462 0.00 0.00 43.32 3.36
2737 2741 6.157820 TGGATTTGAGGTACATGAATGTAGGA 59.842 38.462 0.00 0.00 43.32 2.94
2738 2742 6.356556 TGGATTTGAGGTACATGAATGTAGG 58.643 40.000 0.00 0.00 43.32 3.18
2739 2743 8.993121 GTATGGATTTGAGGTACATGAATGTAG 58.007 37.037 0.00 0.00 43.32 2.74
2740 2744 7.936847 GGTATGGATTTGAGGTACATGAATGTA 59.063 37.037 0.00 0.00 41.97 2.29
2741 2745 6.772716 GGTATGGATTTGAGGTACATGAATGT 59.227 38.462 0.00 0.95 44.48 2.71
2742 2746 6.073058 CGGTATGGATTTGAGGTACATGAATG 60.073 42.308 0.00 0.00 0.00 2.67
2743 2747 5.997746 CGGTATGGATTTGAGGTACATGAAT 59.002 40.000 0.00 0.00 0.00 2.57
2744 2748 5.104693 ACGGTATGGATTTGAGGTACATGAA 60.105 40.000 0.00 0.00 0.00 2.57
2745 2749 4.407621 ACGGTATGGATTTGAGGTACATGA 59.592 41.667 0.00 0.00 0.00 3.07
2746 2750 4.703897 ACGGTATGGATTTGAGGTACATG 58.296 43.478 0.00 0.00 0.00 3.21
2747 2751 4.407621 TGACGGTATGGATTTGAGGTACAT 59.592 41.667 0.00 0.00 0.00 2.29
2748 2752 3.770388 TGACGGTATGGATTTGAGGTACA 59.230 43.478 0.00 0.00 0.00 2.90
2749 2753 4.395959 TGACGGTATGGATTTGAGGTAC 57.604 45.455 0.00 0.00 0.00 3.34
2750 2754 4.742440 GCATGACGGTATGGATTTGAGGTA 60.742 45.833 0.00 0.00 0.00 3.08
2797 2801 7.554211 TGACGATGAGTAGATAGGATACGTAT 58.446 38.462 8.05 8.05 46.39 3.06
2806 2810 6.254804 CGATACCTCTGACGATGAGTAGATAG 59.745 46.154 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.