Multiple sequence alignment - TraesCS3B01G380300

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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 TraesCS3B01G380300 chr3B 100.000 2624 0 0 1 2624 597815162 597817785 0.000000e+00 4846
1 TraesCS3B01G380300 chr3D 94.655 1983 65 12 657 2624 454903654 454905610 0.000000e+00 3037
2 TraesCS3B01G380300 chr3D 91.887 604 29 7 1 586 454902341 454902942 0.000000e+00 826
3 TraesCS3B01G380300 chr3A 93.264 1915 69 18 725 2621 597183966 597185838 0.000000e+00 2767
4 TraesCS3B01G380300 chr3A 90.469 640 50 10 1 637 597181836 597182467 0.000000e+00 833
5 TraesCS3B01G380300 chr1D 85.243 515 55 9 1085 1599 392697009 392697502 6.480000e-141 510
6 TraesCS3B01G380300 chr1A 85.135 518 56 11 1088 1605 492652781 492652285 6.480000e-141 510
7 TraesCS3B01G380300 chr1A 85.833 120 17 0 1480 1599 492654809 492654690 7.620000e-26 128
8 TraesCS3B01G380300 chr1B 84.961 512 56 11 1088 1599 529998580 529998090 1.400000e-137 499


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 TraesCS3B01G380300 chr3B 597815162 597817785 2623 False 4846.0 4846 100.0000 1 2624 1 chr3B.!!$F1 2623
1 TraesCS3B01G380300 chr3D 454902341 454905610 3269 False 1931.5 3037 93.2710 1 2624 2 chr3D.!!$F1 2623
2 TraesCS3B01G380300 chr3A 597181836 597185838 4002 False 1800.0 2767 91.8665 1 2621 2 chr3A.!!$F1 2620
3 TraesCS3B01G380300 chr1A 492652285 492654809 2524 True 319.0 510 85.4840 1088 1605 2 chr1A.!!$R1 517

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
984 2459 0.179161 AACTCAGAATCTCGACCGCG 60.179 55.0 0.0 0.0 39.35 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 3580 0.538057 TCGTGGTACAGTTCGTCCCT 60.538 55.0 0.0 0.0 41.8 4.2 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
238 241 5.336372 GCATAGAGCAGTAATCTCTAGGTGG 60.336 48.000 11.61 2.04 43.83 4.61
615 634 9.480053 CAAAATTAAGCTCAAAATTCAAGAGGA 57.520 29.630 0.00 0.00 0.00 3.71
617 636 6.824305 TTAAGCTCAAAATTCAAGAGGAGG 57.176 37.500 0.00 0.00 0.00 4.30
641 660 2.577449 GGGGGTCATTTTACATTGCG 57.423 50.000 0.00 0.00 0.00 4.85
642 661 1.136110 GGGGGTCATTTTACATTGCGG 59.864 52.381 0.00 0.00 0.00 5.69
643 662 1.136110 GGGGTCATTTTACATTGCGGG 59.864 52.381 0.00 0.00 0.00 6.13
644 663 1.136110 GGGTCATTTTACATTGCGGGG 59.864 52.381 0.00 0.00 0.00 5.73
654 673 2.760477 TTGCGGGGCAATGGTAGT 59.240 55.556 0.00 0.00 43.99 2.73
655 674 1.377987 TTGCGGGGCAATGGTAGTC 60.378 57.895 0.00 0.00 43.99 2.59
677 2148 5.932883 GTCTTTACCACCCTTCTAGAGTTTG 59.067 44.000 0.00 0.00 0.00 2.93
722 2193 3.617263 CGTTTAGGCTTCACTGTCCATAC 59.383 47.826 0.00 0.00 0.00 2.39
949 2423 4.401925 CCACCCACTCTTCTGAAATTTCT 58.598 43.478 18.64 0.00 0.00 2.52
984 2459 0.179161 AACTCAGAATCTCGACCGCG 60.179 55.000 0.00 0.00 39.35 6.46
987 2462 3.812019 AGAATCTCGACCGCGCGT 61.812 61.111 29.95 17.00 37.46 6.01
998 2473 2.885644 CGCGCGTGGCTTGTCTAT 60.886 61.111 24.19 0.00 40.44 1.98
1008 2483 4.315803 GTGGCTTGTCTATAATGCCGTAT 58.684 43.478 0.00 0.00 45.90 3.06
1113 2588 2.584608 GAGGTGGCGCTGTACCAT 59.415 61.111 23.75 13.11 39.95 3.55
1383 2858 1.880340 GCTCAGCTTCCGGATCGTG 60.880 63.158 4.15 2.68 0.00 4.35
1620 3095 4.666532 GCTGTGCCGCACGTCAAC 62.667 66.667 18.41 2.54 37.14 3.18
1712 3187 0.106967 GGGGTTCTGGAATCTGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
1879 3358 9.541143 TTACTCGAACTTTGCATATGATATCAA 57.459 29.630 9.99 0.00 0.00 2.57
1932 3416 9.817365 CTAACTGACAAACTAAATGATGAAGTG 57.183 33.333 0.00 0.00 0.00 3.16
1980 3464 8.213518 TCTCATGTGCTTAATCCTAATCAAAC 57.786 34.615 0.00 0.00 0.00 2.93
1997 3481 3.943034 CGAACCGCGTGCACCAAA 61.943 61.111 12.15 0.00 34.64 3.28
1998 3482 2.642700 GAACCGCGTGCACCAAAT 59.357 55.556 12.15 0.00 0.00 2.32
1999 3483 1.007849 GAACCGCGTGCACCAAATT 60.008 52.632 12.15 0.65 0.00 1.82
2000 3484 0.238817 GAACCGCGTGCACCAAATTA 59.761 50.000 12.15 0.00 0.00 1.40
2001 3485 0.669077 AACCGCGTGCACCAAATTAA 59.331 45.000 12.15 0.00 0.00 1.40
2002 3486 0.885196 ACCGCGTGCACCAAATTAAT 59.115 45.000 12.15 0.00 0.00 1.40
2003 3487 1.135517 ACCGCGTGCACCAAATTAATC 60.136 47.619 12.15 0.00 0.00 1.75
2004 3488 1.544686 CGCGTGCACCAAATTAATCC 58.455 50.000 12.15 0.00 0.00 3.01
2005 3489 1.544686 GCGTGCACCAAATTAATCCG 58.455 50.000 12.15 0.00 0.00 4.18
2006 3490 1.544686 CGTGCACCAAATTAATCCGC 58.455 50.000 12.15 0.00 0.00 5.54
2007 3491 1.135546 CGTGCACCAAATTAATCCGCA 60.136 47.619 12.15 0.00 0.00 5.69
2008 3492 2.258755 GTGCACCAAATTAATCCGCAC 58.741 47.619 5.22 10.10 41.12 5.34
2009 3493 1.203523 TGCACCAAATTAATCCGCACC 59.796 47.619 0.00 0.00 0.00 5.01
2040 3524 2.148916 TCCGTGTTGCTGTCTAAGTG 57.851 50.000 0.00 0.00 0.00 3.16
2202 3692 0.179018 ACACTGCACCTTCCAAGTCC 60.179 55.000 0.00 0.00 0.00 3.85
2250 3740 4.603535 AGCCCACACCCACTTGCC 62.604 66.667 0.00 0.00 0.00 4.52
2363 3853 4.102681 CCTTGTACGGGGAATATCTTTCCT 59.897 45.833 4.51 0.00 38.61 3.36
2490 3980 4.120792 TGTGCAAGTTGCTCATTTTTCA 57.879 36.364 27.17 11.03 45.31 2.69
2527 4017 1.268589 CGTGCGTAGAATCTGGTCGAT 60.269 52.381 0.00 0.00 0.00 3.59
2600 4092 5.940470 CAGTTTCTCTGGTTGGTAGCTAATT 59.060 40.000 0.00 0.00 40.23 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 3.248024 ACTGGTGTTGGTGATCTCCTAA 58.752 45.455 14.65 5.24 0.00 2.69
127 130 3.972403 ACAAAGGCATTAACCGTTTGAC 58.028 40.909 20.72 1.42 34.57 3.18
238 241 9.871238 TGTAAGGTTGTCTTCTCTTAATGATAC 57.129 33.333 0.00 0.00 36.93 2.24
532 551 7.288810 ACCATTGCAAATCTCTTTCAGTTAA 57.711 32.000 1.71 0.00 0.00 2.01
549 568 8.676454 TGTCGTAAAAATGTTAATACCATTGC 57.324 30.769 0.00 0.00 33.01 3.56
597 616 3.563043 CCCCTCCTCTTGAATTTTGAGCT 60.563 47.826 0.00 0.00 0.00 4.09
598 617 2.757314 CCCCTCCTCTTGAATTTTGAGC 59.243 50.000 0.00 0.00 0.00 4.26
625 644 1.470805 GCCCCGCAATGTAAAATGACC 60.471 52.381 0.00 0.00 0.00 4.02
628 647 2.376808 TTGCCCCGCAATGTAAAATG 57.623 45.000 0.00 0.00 43.99 2.32
638 657 1.847798 AAGACTACCATTGCCCCGCA 61.848 55.000 0.00 0.00 36.47 5.69
639 658 0.679960 AAAGACTACCATTGCCCCGC 60.680 55.000 0.00 0.00 0.00 6.13
640 659 2.285977 GTAAAGACTACCATTGCCCCG 58.714 52.381 0.00 0.00 0.00 5.73
641 660 2.025699 TGGTAAAGACTACCATTGCCCC 60.026 50.000 0.00 0.00 42.21 5.80
642 661 3.359695 TGGTAAAGACTACCATTGCCC 57.640 47.619 0.00 0.00 42.21 5.36
652 671 5.013258 ACTCTAGAAGGGTGGTAAAGACT 57.987 43.478 0.00 0.00 0.00 3.24
653 672 5.741962 AACTCTAGAAGGGTGGTAAAGAC 57.258 43.478 0.00 0.00 0.00 3.01
654 673 5.605488 ACAAACTCTAGAAGGGTGGTAAAGA 59.395 40.000 0.00 0.00 0.00 2.52
655 674 5.866207 ACAAACTCTAGAAGGGTGGTAAAG 58.134 41.667 0.00 0.00 0.00 1.85
677 2148 5.565242 CGGGGGTGGTTAATTTTAGTTTGAC 60.565 44.000 0.00 0.00 0.00 3.18
684 2155 5.015515 CCTAAACGGGGGTGGTTAATTTTA 58.984 41.667 0.00 0.00 0.00 1.52
685 2156 3.833650 CCTAAACGGGGGTGGTTAATTTT 59.166 43.478 0.00 0.00 0.00 1.82
686 2157 3.433343 CCTAAACGGGGGTGGTTAATTT 58.567 45.455 0.00 0.00 0.00 1.82
687 2158 2.885137 GCCTAAACGGGGGTGGTTAATT 60.885 50.000 0.00 0.00 0.00 1.40
688 2159 1.341285 GCCTAAACGGGGGTGGTTAAT 60.341 52.381 0.00 0.00 0.00 1.40
689 2160 0.038021 GCCTAAACGGGGGTGGTTAA 59.962 55.000 0.00 0.00 0.00 2.01
722 2193 6.155049 AGGAATTGTTTCTAATGAATGGGTGG 59.845 38.462 0.00 0.00 32.16 4.61
949 2423 5.538118 TCTGAGTTTTATCGCTGTGAAGAA 58.462 37.500 0.00 0.00 0.00 2.52
984 2459 1.264288 GGCATTATAGACAAGCCACGC 59.736 52.381 0.00 0.00 44.59 5.34
987 2462 4.314961 CATACGGCATTATAGACAAGCCA 58.685 43.478 0.00 0.00 45.47 4.75
1028 2503 3.258228 ATCCGGCTGTGCTGCTGAA 62.258 57.895 10.77 0.00 41.56 3.02
1362 2837 1.522580 GATCCGGAAGCTGAGCACC 60.523 63.158 9.01 8.95 0.00 5.01
1473 2948 1.293963 CGTACGACTCGACCACCAGA 61.294 60.000 10.44 0.00 0.00 3.86
1509 2984 3.220999 CTCGTCGCTGGTGTTCCCA 62.221 63.158 0.00 0.00 42.51 4.37
1620 3095 1.434622 GAGTGCATGACGGGCATCAG 61.435 60.000 0.00 0.00 44.11 2.90
1668 3143 3.254654 CGCGCATGGTACGGTCTG 61.255 66.667 8.75 0.00 0.00 3.51
1712 3187 3.440173 AGTTTAGGGTGCAAATCATGTCG 59.560 43.478 0.00 0.00 0.00 4.35
1879 3358 8.432110 TTTACACGCATATGTACAAGATTCAT 57.568 30.769 0.00 0.00 34.79 2.57
1932 3416 2.125673 ACACGGCCACATAGACGC 60.126 61.111 2.24 0.00 0.00 5.19
1980 3464 2.725275 AATTTGGTGCACGCGGTTCG 62.725 55.000 12.47 0.00 45.38 3.95
1995 3479 4.850680 TGTTAGGAGGTGCGGATTAATTT 58.149 39.130 0.00 0.00 0.00 1.82
1996 3480 4.497291 TGTTAGGAGGTGCGGATTAATT 57.503 40.909 0.00 0.00 0.00 1.40
1997 3481 4.706842 ATGTTAGGAGGTGCGGATTAAT 57.293 40.909 0.00 0.00 0.00 1.40
1998 3482 4.497291 AATGTTAGGAGGTGCGGATTAA 57.503 40.909 0.00 0.00 0.00 1.40
1999 3483 5.279809 GGATAATGTTAGGAGGTGCGGATTA 60.280 44.000 0.00 0.00 0.00 1.75
2000 3484 4.505039 GGATAATGTTAGGAGGTGCGGATT 60.505 45.833 0.00 0.00 0.00 3.01
2001 3485 3.008049 GGATAATGTTAGGAGGTGCGGAT 59.992 47.826 0.00 0.00 0.00 4.18
2002 3486 2.367567 GGATAATGTTAGGAGGTGCGGA 59.632 50.000 0.00 0.00 0.00 5.54
2003 3487 2.767505 GGATAATGTTAGGAGGTGCGG 58.232 52.381 0.00 0.00 0.00 5.69
2004 3488 2.223971 ACGGATAATGTTAGGAGGTGCG 60.224 50.000 0.00 0.00 0.00 5.34
2005 3489 3.131396 CACGGATAATGTTAGGAGGTGC 58.869 50.000 0.00 0.00 0.00 5.01
2006 3490 4.402056 ACACGGATAATGTTAGGAGGTG 57.598 45.455 0.00 0.00 0.00 4.00
2007 3491 4.766375 CAACACGGATAATGTTAGGAGGT 58.234 43.478 0.00 0.00 38.22 3.85
2008 3492 3.560068 GCAACACGGATAATGTTAGGAGG 59.440 47.826 0.00 0.00 38.22 4.30
2009 3493 4.271049 CAGCAACACGGATAATGTTAGGAG 59.729 45.833 0.00 0.00 38.22 3.69
2096 3580 0.538057 TCGTGGTACAGTTCGTCCCT 60.538 55.000 0.00 0.00 41.80 4.20
2222 3712 1.447838 TGTGGGCTCGCGAGATTTC 60.448 57.895 38.74 23.57 40.84 2.17
2225 3715 4.148825 GGTGTGGGCTCGCGAGAT 62.149 66.667 38.74 0.00 40.84 2.75
2250 3740 2.052237 GAAATGTATGCGCGCGGG 60.052 61.111 33.06 20.05 0.00 6.13
2289 3779 5.192327 ACTTTGTTGAATTGAGCTTGGAG 57.808 39.130 0.00 0.00 0.00 3.86
2363 3853 2.418368 ATTACTCGATTGCAGGCCAA 57.582 45.000 5.01 0.00 37.94 4.52
2490 3980 3.692576 GCACGTACATCGACTTGTAGAT 58.307 45.455 0.00 0.00 42.86 1.98
2600 4092 0.811219 GCTCATGCATGACGCCACTA 60.811 55.000 25.42 2.70 41.33 2.74


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

AutoCloner maintained by Alex Coulton.