Multiple sequence alignment - TraesCS1D01G202200

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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 TraesCS1D01G202200 chr1D 100.000 3433 0 0 1 3433 285058201 285054769 0.000000e+00 6340.0
1 TraesCS1D01G202200 chr1B 93.592 2840 117 28 1 2795 387309081 387306262 0.000000e+00 4176.0
2 TraesCS1D01G202200 chr1B 96.000 625 22 2 2811 3433 387306198 387305575 0.000000e+00 1013.0
3 TraesCS1D01G202200 chr1B 83.333 114 15 3 2624 2736 387306237 387306127 6.060000e-18 102.0
4 TraesCS1D01G202200 chr1A 92.767 2848 131 33 1 2817 356476947 356474144 0.000000e+00 4048.0
5 TraesCS1D01G202200 chr1A 98.758 483 5 1 2952 3433 356474004 356473522 0.000000e+00 857.0
6 TraesCS1D01G202200 chr1A 92.593 108 6 1 2811 2916 356474110 356474003 1.650000e-33 154.0
7 TraesCS1D01G202200 chr1A 85.965 114 13 2 2624 2736 356474149 356474038 6.020000e-23 119.0
8 TraesCS1D01G202200 chr4A 86.792 53 5 2 1074 1125 705180324 705180273 1.330000e-04 58.4


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 TraesCS1D01G202200 chr1D 285054769 285058201 3432 True 6340.000000 6340 100.00000 1 3433 1 chr1D.!!$R1 3432
1 TraesCS1D01G202200 chr1B 387305575 387309081 3506 True 1763.666667 4176 90.97500 1 3433 3 chr1B.!!$R1 3432
2 TraesCS1D01G202200 chr1A 356473522 356476947 3425 True 1294.500000 4048 92.52075 1 3433 4 chr1A.!!$R1 3432

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
677 703 1.150536 TTGGTTGGTGGGTCTCTGC 59.849 57.895 0.0 0.0 0.00 4.26 F
1113 1140 1.135083 AGGAACATCAACGAGCCTACG 60.135 52.381 0.0 0.0 39.31 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2372 0.401738 TGAGCTCCCAGTTTTCAGGG 59.598 55.0 12.15 0.0 46.51 4.45 R
2759 2816 0.236711 CGACTGCTGGAGCTTTTGTG 59.763 55.0 0.00 0.0 42.66 3.33 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
17 18 2.862436 TGCAATTCGCTGTCGCTG 59.138 55.556 0.00 0.0 43.06 5.18
95 96 1.679977 ATGTGCTGATGGGTGTGCC 60.680 57.895 0.00 0.0 0.00 5.01
342 358 2.800629 GCCGAATTCGATTTAGGACGGA 60.801 50.000 28.76 0.0 43.02 4.69
375 391 3.191371 GGTTGATTGGTTACTCTGCAAGG 59.809 47.826 0.00 0.0 0.00 3.61
392 408 1.153429 GGTTAGCATCGCCCTCGTT 60.153 57.895 0.00 0.0 36.96 3.85
408 424 4.873827 CCCTCGTTGAATTCGATTTAGGAA 59.126 41.667 16.82 0.0 36.73 3.36
420 436 1.681229 TTTAGGAAGGATGGGTGGCT 58.319 50.000 0.00 0.0 0.00 4.75
465 484 2.222886 CCTGCGAAGATTGAACATCACG 60.223 50.000 0.00 0.0 0.00 4.35
466 485 2.667969 CTGCGAAGATTGAACATCACGA 59.332 45.455 0.00 0.0 0.00 4.35
500 520 1.368641 TGCGATTCCGACCAAATCTG 58.631 50.000 0.00 0.0 38.22 2.90
501 521 1.338674 TGCGATTCCGACCAAATCTGT 60.339 47.619 0.00 0.0 38.22 3.41
502 522 1.737793 GCGATTCCGACCAAATCTGTT 59.262 47.619 0.00 0.0 38.22 3.16
534 554 3.438520 GCCCCTATCATTTCCCCTGATTT 60.439 47.826 0.00 0.0 35.12 2.17
618 644 5.477984 TCATTCCAACCAAGAAGATGAAAGG 59.522 40.000 0.00 0.0 0.00 3.11
622 648 3.795688 ACCAAGAAGATGAAAGGAGCA 57.204 42.857 0.00 0.0 0.00 4.26
632 658 8.713036 AGAAGATGAAAGGAGCAGATACTAATT 58.287 33.333 0.00 0.0 0.00 1.40
633 659 9.988815 GAAGATGAAAGGAGCAGATACTAATTA 57.011 33.333 0.00 0.0 0.00 1.40
634 660 9.771534 AAGATGAAAGGAGCAGATACTAATTAC 57.228 33.333 0.00 0.0 0.00 1.89
635 661 8.085296 AGATGAAAGGAGCAGATACTAATTACG 58.915 37.037 0.00 0.0 0.00 3.18
677 703 1.150536 TTGGTTGGTGGGTCTCTGC 59.849 57.895 0.00 0.0 0.00 4.26
685 711 1.606601 TGGGTCTCTGCGTAGTGCT 60.607 57.895 0.00 0.0 46.63 4.40
750 776 7.540400 TGGATTAACAAATTGTTTATGACTGCG 59.460 33.333 16.99 0.0 41.45 5.18
821 847 9.388346 GACTGTATTGAGTTAATCTGTCTATCG 57.612 37.037 0.00 0.0 30.94 2.92
837 863 4.745620 GTCTATCGACAGCCTACAAATTCC 59.254 45.833 0.00 0.0 39.98 3.01
868 894 8.737648 GTGCTAAAGAAGATTGAATTTTATCGC 58.262 33.333 0.00 0.0 0.00 4.58
904 931 3.249189 TGGACCTCCACCACAGGC 61.249 66.667 0.00 0.0 42.01 4.85
1113 1140 1.135083 AGGAACATCAACGAGCCTACG 60.135 52.381 0.00 0.0 39.31 3.51
1132 1159 2.806244 ACGAGTTTTTCCTTGACATCCG 59.194 45.455 0.00 0.0 0.00 4.18
1140 1167 8.201464 AGTTTTTCCTTGACATCCGTTAATTTT 58.799 29.630 0.00 0.0 0.00 1.82
1193 1224 9.670442 ACCCCTCTTTATCTGAATAAGTGTATA 57.330 33.333 3.17 0.0 0.00 1.47
1221 1252 8.238481 TGTTATTTATTTGCTTGCTAAACTGC 57.762 30.769 0.00 0.0 0.00 4.40
1542 1582 4.636206 AGGTAATTCTTTTCCTCGTGCATC 59.364 41.667 0.00 0.0 26.95 3.91
1591 1639 8.664798 TCCTTGTGTTAGAATGTTTCATTATCG 58.335 33.333 0.00 0.0 0.00 2.92
1624 1672 6.521151 AGCCTTTAGATGAGACCAATTTTG 57.479 37.500 0.00 0.0 0.00 2.44
1722 1771 9.890085 CAAATATTGAAACAAGCAACGAATATG 57.110 29.630 0.00 0.0 0.00 1.78
1880 1929 7.307870 CCTCTTGCAAAGTCATATAGAGCAATC 60.308 40.741 0.00 0.0 46.34 2.67
2210 2259 1.428869 CCCTTACCATAGCTGCCTCT 58.571 55.000 0.00 0.0 0.00 3.69
2323 2372 2.768834 GGATTGAAGCTCCGGTGAC 58.231 57.895 7.92 0.0 0.00 3.67
2429 2478 0.796312 CGACTGTTGGTGCCATGTAC 59.204 55.000 0.00 0.0 0.00 2.90
2551 2600 7.072454 AGGATTACTGGCTACATTGGATTCTTA 59.928 37.037 0.00 0.0 0.00 2.10
2650 2702 9.265901 CTGGTTAGACTATTTCTATGTTCCATG 57.734 37.037 0.00 0.0 36.65 3.66
2698 2755 2.158623 AGAACACAACAGCTCCCAATCA 60.159 45.455 0.00 0.0 0.00 2.57
2699 2756 2.592102 ACACAACAGCTCCCAATCAT 57.408 45.000 0.00 0.0 0.00 2.45
2715 2772 4.681025 CCAATCATATACCAAATGCAACGC 59.319 41.667 0.00 0.0 0.00 4.84
2738 2795 5.221165 GCCCAACAAAGTCTACTGCTAAAAA 60.221 40.000 0.00 0.0 0.00 1.94
2759 2816 6.864560 AAAAAGTGTTACGTCTTTGCTTTC 57.135 33.333 0.00 0.0 34.67 2.62
2777 2834 1.597742 TCACAAAAGCTCCAGCAGTC 58.402 50.000 0.48 0.0 45.16 3.51
2800 2866 0.602562 TGCTGTGCAAAATACAGGCC 59.397 50.000 0.00 0.0 44.36 5.19
2802 2868 1.205417 GCTGTGCAAAATACAGGCCAT 59.795 47.619 5.01 0.0 44.36 4.40
2826 2931 1.133790 GCTAGCTTGGTCAAATGCCAG 59.866 52.381 7.70 0.0 37.31 4.85
2831 2936 2.224018 GCTTGGTCAAATGCCAGAACAA 60.224 45.455 0.00 0.0 39.00 2.83
2900 3007 7.989826 ACTGCTAAGGATTACATCATTTGTTC 58.010 34.615 0.00 0.0 39.87 3.18
2903 3010 7.498900 TGCTAAGGATTACATCATTTGTTCGAT 59.501 33.333 0.00 0.0 39.87 3.59
2930 3037 2.358003 AGCGACTGCCTGCTGTTC 60.358 61.111 3.12 0.0 44.31 3.18
2947 3054 4.436050 GCTGTTCGAAATACATGTGACTGG 60.436 45.833 9.11 0.0 0.00 4.00
3317 3424 2.601067 CTGGTGTTGGGCATGGCA 60.601 61.111 22.06 4.4 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.515521 CGGAAGGTTTGACCCTGTGC 61.516 60.000 0.00 0.00 39.75 4.57
342 358 1.448985 CAATCAACCAATCCGTCCGT 58.551 50.000 0.00 0.00 0.00 4.69
375 391 0.459585 TCAACGAGGGCGATGCTAAC 60.460 55.000 0.00 0.00 39.75 2.34
392 408 5.104109 ACCCATCCTTCCTAAATCGAATTCA 60.104 40.000 6.22 0.00 0.00 2.57
451 467 3.245797 CACTCGTCGTGATGTTCAATCT 58.754 45.455 0.56 0.00 46.81 2.40
452 468 2.345641 CCACTCGTCGTGATGTTCAATC 59.654 50.000 0.56 0.00 46.81 2.67
453 469 2.029380 TCCACTCGTCGTGATGTTCAAT 60.029 45.455 0.56 0.00 46.81 2.57
454 470 1.338655 TCCACTCGTCGTGATGTTCAA 59.661 47.619 0.56 0.00 46.81 2.69
492 512 3.367703 GGCAAGGATCACAACAGATTTGG 60.368 47.826 0.00 0.00 0.00 3.28
500 520 2.092429 TGATAGGGGCAAGGATCACAAC 60.092 50.000 0.00 0.00 0.00 3.32
501 521 2.204463 TGATAGGGGCAAGGATCACAA 58.796 47.619 0.00 0.00 0.00 3.33
502 522 1.891933 TGATAGGGGCAAGGATCACA 58.108 50.000 0.00 0.00 0.00 3.58
618 644 9.596677 CTGTTACTACGTAATTAGTATCTGCTC 57.403 37.037 0.00 0.00 35.06 4.26
622 648 8.001292 ACCCCTGTTACTACGTAATTAGTATCT 58.999 37.037 0.00 0.00 35.06 1.98
632 658 2.562298 CAACCACCCCTGTTACTACGTA 59.438 50.000 0.00 0.00 0.00 3.57
633 659 1.345415 CAACCACCCCTGTTACTACGT 59.655 52.381 0.00 0.00 0.00 3.57
634 660 1.942586 GCAACCACCCCTGTTACTACG 60.943 57.143 0.00 0.00 0.00 3.51
635 661 1.350019 AGCAACCACCCCTGTTACTAC 59.650 52.381 0.00 0.00 0.00 2.73
677 703 6.367969 ACTCACCTATAAAAACAAGCACTACG 59.632 38.462 0.00 0.00 0.00 3.51
685 711 9.146984 CATCGAACTACTCACCTATAAAAACAA 57.853 33.333 0.00 0.00 0.00 2.83
748 774 2.396157 GGTCGGATTGGTTGACCGC 61.396 63.158 0.00 0.00 45.25 5.68
821 847 1.659098 CGACGGAATTTGTAGGCTGTC 59.341 52.381 0.00 0.00 34.21 3.51
830 856 2.739913 TCTTTAGCACCGACGGAATTTG 59.260 45.455 23.38 9.56 0.00 2.32
831 857 3.048337 TCTTTAGCACCGACGGAATTT 57.952 42.857 23.38 5.56 0.00 1.82
837 863 3.250744 TCAATCTTCTTTAGCACCGACG 58.749 45.455 0.00 0.00 0.00 5.12
868 894 7.052873 AGGTCCATGATCAGAACTTATGAAAG 58.947 38.462 0.09 0.00 38.77 2.62
904 931 1.783031 GAGATGCAGCTGCCAATCGG 61.783 60.000 34.64 0.00 41.18 4.18
1077 1104 2.428530 GTTCCTCAGGAATGGGCATTTC 59.571 50.000 10.09 0.00 44.04 2.17
1113 1140 4.830826 AACGGATGTCAAGGAAAAACTC 57.169 40.909 0.00 0.00 0.00 3.01
1221 1252 3.730061 GCCTTCACGAGCAGAAAATGATG 60.730 47.826 0.00 0.00 0.00 3.07
1542 1582 7.995488 AGGATGGTAATTTGAAGGATAGAACAG 59.005 37.037 0.00 0.00 0.00 3.16
1591 1639 2.342910 TCTAAAGGCTCGTTCGACAC 57.657 50.000 0.00 0.00 0.00 3.67
1624 1672 9.384764 AGATAGATTTGCTTTCTTTGGTACTAC 57.615 33.333 0.00 0.00 31.86 2.73
1704 1753 5.296813 ACCTCATATTCGTTGCTTGTTTC 57.703 39.130 0.00 0.00 0.00 2.78
1880 1929 2.932234 AAGAGGCACGACTCCACCG 61.932 63.158 0.00 0.00 38.26 4.94
2210 2259 6.726379 TGAACCAATTGTCTGACCCAATATA 58.274 36.000 5.17 0.00 32.40 0.86
2323 2372 0.401738 TGAGCTCCCAGTTTTCAGGG 59.598 55.000 12.15 0.00 46.51 4.45
2363 2412 2.604686 ACTCTGAGGCCAAGCGGA 60.605 61.111 5.01 3.35 0.00 5.54
2429 2478 5.178438 CAGTGAAGCATGATCATCTCATCAG 59.822 44.000 4.86 0.00 42.91 2.90
2463 2512 6.333416 TCTGGAACTCTTGATACAATTCTCG 58.667 40.000 0.00 0.00 0.00 4.04
2650 2702 3.096489 TGACCAAGCAAATGAAAGCAC 57.904 42.857 0.00 0.00 0.00 4.40
2698 2755 2.660572 TGGGCGTTGCATTTGGTATAT 58.339 42.857 0.00 0.00 0.00 0.86
2699 2756 2.130272 TGGGCGTTGCATTTGGTATA 57.870 45.000 0.00 0.00 0.00 1.47
2715 2772 6.385649 TTTTTAGCAGTAGACTTTGTTGGG 57.614 37.500 0.00 0.00 0.00 4.12
2738 2795 5.106475 TGTGAAAGCAAAGACGTAACACTTT 60.106 36.000 0.00 0.00 36.89 2.66
2755 2812 2.360165 ACTGCTGGAGCTTTTGTGAAAG 59.640 45.455 0.00 0.00 44.10 2.62
2759 2816 0.236711 CGACTGCTGGAGCTTTTGTG 59.763 55.000 0.00 0.00 42.66 3.33
2800 2866 2.408271 TTGACCAAGCTAGCCTCATG 57.592 50.000 12.13 5.79 0.00 3.07
2802 2868 2.715046 CATTTGACCAAGCTAGCCTCA 58.285 47.619 12.13 4.51 0.00 3.86
2900 3007 0.459237 AGTCGCTGGAGCTTTCATCG 60.459 55.000 7.60 7.60 39.32 3.84
2903 3010 1.669115 GCAGTCGCTGGAGCTTTCA 60.669 57.895 8.57 0.00 39.32 2.69
2930 3037 2.352651 CCTGCCAGTCACATGTATTTCG 59.647 50.000 0.00 0.00 0.00 3.46
2947 3054 5.906113 TGAGATATACTAAGCTAGCCTGC 57.094 43.478 12.13 0.00 0.00 4.85
3116 3223 1.225704 CATGGGTCCTCTTGAGGCC 59.774 63.158 11.61 14.52 0.00 5.19
3317 3424 0.943835 GCGCAAAGGGCAAACGATTT 60.944 50.000 0.30 0.00 45.17 2.17


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

AutoCloner maintained by Alex Coulton.