Multiple sequence alignment - TraesCS1A01G144600

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 TraesCS1A01G144600 chr1A 100.000 3662 0 0 1 3662 250529063 250525402 0.000000e+00 6763.0
1 TraesCS1A01G144600 chr1D 92.994 3711 174 36 3 3660 199336999 199333322 0.000000e+00 5334.0
2 TraesCS1A01G144600 chr1B 92.817 2492 102 14 472 2947 279574031 279571601 0.000000e+00 3539.0
3 TraesCS1A01G144600 chr1B 83.691 466 35 17 3 441 279574484 279574033 5.700000e-108 401.0
4 TraesCS1A01G144600 chr5D 79.545 264 38 13 3355 3609 232249564 232249820 1.350000e-39 174.0
5 TraesCS1A01G144600 chr3B 100.000 28 0 0 3101 3128 173246153 173246180 7.000000e-03 52.8


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 TraesCS1A01G144600 chr1A 250525402 250529063 3661 True 6763 6763 100.000 1 3662 1 chr1A.!!$R1 3661
1 TraesCS1A01G144600 chr1D 199333322 199336999 3677 True 5334 5334 92.994 3 3660 1 chr1D.!!$R1 3657
2 TraesCS1A01G144600 chr1B 279571601 279574484 2883 True 1970 3539 88.254 3 2947 2 chr1B.!!$R1 2944

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
788 829 0.954452 CGTTCCTTGCTTCTTGGCTT 59.046 50.0 0.0 0.0 0.00 4.35 F
2059 2103 0.674895 GTCCATCGCAAGCAACCTCT 60.675 55.0 0.0 0.0 37.18 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2445 2489 0.111704 CAAGCTTCGTTGACGTGTCG 60.112 55.0 0.0 0.0 40.80 4.35 R
2924 2969 0.179034 GCCTTGATCCTCGCCTCAAT 60.179 55.0 0.0 0.0 31.39 2.57 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
28 29 3.287867 TCATTGGCAGAAGGAGGAATC 57.712 47.619 0.00 0.00 0.00 2.52
109 110 3.511934 GTCTGACTGACTTGTCCCAGTAT 59.488 47.826 0.00 0.00 43.02 2.12
189 193 6.322712 AGTTTGGCTAGATCCAGTAGTTCTAG 59.677 42.308 0.00 0.00 43.51 2.43
242 248 3.729862 GTCCAAGAGTAATAGGGACGG 57.270 52.381 0.00 0.00 38.71 4.79
357 385 1.408266 GGGCAATACGGGTCACTCAAT 60.408 52.381 0.00 0.00 0.00 2.57
368 396 4.254492 GGGTCACTCAATTCAGGTAAGTC 58.746 47.826 0.00 0.00 0.00 3.01
448 476 4.405680 AGACGTGGATGGTTGATCTGATTA 59.594 41.667 0.00 0.00 0.00 1.75
516 544 1.550976 GACGGGGACAGAAGACTGAAT 59.449 52.381 0.00 0.00 46.03 2.57
520 548 3.447586 CGGGGACAGAAGACTGAATAGAA 59.552 47.826 0.00 0.00 46.03 2.10
555 585 5.835113 AATCCAAAGATAACCACGAATGG 57.165 39.130 0.00 0.00 41.36 3.16
651 681 3.146066 TGTGCCACTTGGACTTGTAATC 58.854 45.455 0.00 0.00 37.39 1.75
788 829 0.954452 CGTTCCTTGCTTCTTGGCTT 59.046 50.000 0.00 0.00 0.00 4.35
789 830 2.151202 CGTTCCTTGCTTCTTGGCTTA 58.849 47.619 0.00 0.00 0.00 3.09
873 917 6.840780 AAAATTGACTTAAGATCCCCACTG 57.159 37.500 10.09 0.00 0.00 3.66
925 969 1.475034 GGAGTGAACACCAAGACTGCA 60.475 52.381 1.11 0.00 0.00 4.41
930 974 2.038952 TGAACACCAAGACTGCAGCTAT 59.961 45.455 15.27 0.00 0.00 2.97
1138 1182 1.134401 GTTCCTTCCTCATCATCGCCA 60.134 52.381 0.00 0.00 0.00 5.69
1833 1877 1.079127 CGACGCTGAGTGGGGAAAT 60.079 57.895 0.00 0.00 0.00 2.17
1870 1914 2.978824 CCGTCCGGAACATGACCT 59.021 61.111 5.23 0.00 37.50 3.85
1872 1916 1.153628 CGTCCGGAACATGACCTCC 60.154 63.158 5.23 1.23 0.00 4.30
1929 1973 2.995547 GCCATTCCGTACCCCACT 59.004 61.111 0.00 0.00 0.00 4.00
2059 2103 0.674895 GTCCATCGCAAGCAACCTCT 60.675 55.000 0.00 0.00 37.18 3.69
2124 2168 3.860930 GAAGGGGCCGAGCAACCAA 62.861 63.158 0.00 0.00 31.16 3.67
2391 2435 4.201679 CAGATACCGCCGGACGCA 62.202 66.667 11.71 0.00 41.76 5.24
2413 2457 4.841617 AGAGGATGAGGGGCGCGA 62.842 66.667 12.10 0.00 0.00 5.87
2491 2535 1.414897 GTGAATGACGCGTTCGACC 59.585 57.895 15.53 0.00 39.41 4.79
2531 2575 0.391130 CGGAAGGTGGCGAAGATGAA 60.391 55.000 0.00 0.00 0.00 2.57
2544 2588 1.009829 AGATGAAGAAACGCATCGCC 58.990 50.000 0.00 0.00 44.23 5.54
2656 2700 1.186200 GGATCCCTTGTTTGCCTTCC 58.814 55.000 0.00 0.00 0.00 3.46
2658 2702 1.546029 GATCCCTTGTTTGCCTTCCAC 59.454 52.381 0.00 0.00 0.00 4.02
2666 2710 4.301072 TGTTTGCCTTCCACTAGCTTAT 57.699 40.909 0.00 0.00 0.00 1.73
2688 2732 5.925506 TCTCCTCGTTGTTGGATTATGTA 57.074 39.130 0.00 0.00 0.00 2.29
2689 2733 5.657474 TCTCCTCGTTGTTGGATTATGTAC 58.343 41.667 0.00 0.00 0.00 2.90
2691 2735 6.604396 TCTCCTCGTTGTTGGATTATGTACTA 59.396 38.462 0.00 0.00 0.00 1.82
2704 2748 9.601810 TGGATTATGTACTATTGATGTACTCCT 57.398 33.333 0.00 0.00 40.44 3.69
2817 2862 5.745227 ACTTAGGTCAGGTGGTAATCATTG 58.255 41.667 0.00 0.00 0.00 2.82
2862 2907 3.602062 GCACATGTACCATTTCGTTTTCG 59.398 43.478 0.00 0.00 45.64 3.46
2866 2911 2.475864 TGTACCATTTCGTTTTCGGACG 59.524 45.455 0.00 1.38 44.25 4.79
2912 2957 0.596577 CCAGGCTATGCATGCATCAC 59.403 55.000 35.35 26.41 39.11 3.06
2943 2988 0.179034 ATTGAGGCGAGGATCAAGGC 60.179 55.000 0.00 0.00 38.72 4.35
2967 3013 4.720046 TCAATGCCAAATATAACGGCCTA 58.280 39.130 0.00 0.00 45.63 3.93
2976 3022 7.094118 GCCAAATATAACGGCCTATAAAATGGA 60.094 37.037 16.91 0.00 40.07 3.41
2983 3029 5.948842 ACGGCCTATAAAATGGATTAAGGT 58.051 37.500 0.00 0.00 0.00 3.50
2986 3032 7.827729 ACGGCCTATAAAATGGATTAAGGTATC 59.172 37.037 0.00 0.00 0.00 2.24
3017 3072 9.985730 TTTAGAAATCATGAACATTTTCAAGCT 57.014 25.926 17.49 4.21 45.01 3.74
3018 3073 7.884816 AGAAATCATGAACATTTTCAAGCTG 57.115 32.000 17.49 0.00 45.01 4.24
3019 3074 7.663827 AGAAATCATGAACATTTTCAAGCTGA 58.336 30.769 17.49 0.00 45.01 4.26
3020 3075 7.813148 AGAAATCATGAACATTTTCAAGCTGAG 59.187 33.333 17.49 0.00 45.01 3.35
3021 3076 5.381174 TCATGAACATTTTCAAGCTGAGG 57.619 39.130 0.00 0.00 45.01 3.86
3022 3077 5.072055 TCATGAACATTTTCAAGCTGAGGA 58.928 37.500 0.00 0.00 45.01 3.71
3023 3078 5.535783 TCATGAACATTTTCAAGCTGAGGAA 59.464 36.000 0.00 0.00 45.01 3.36
3024 3079 5.186996 TGAACATTTTCAAGCTGAGGAAC 57.813 39.130 0.00 0.00 38.87 3.62
3025 3080 4.644234 TGAACATTTTCAAGCTGAGGAACA 59.356 37.500 0.00 0.00 38.87 3.18
3026 3081 5.302568 TGAACATTTTCAAGCTGAGGAACAT 59.697 36.000 0.00 0.00 38.87 2.71
3027 3082 5.796424 ACATTTTCAAGCTGAGGAACATT 57.204 34.783 0.00 0.00 0.00 2.71
3028 3083 6.165700 ACATTTTCAAGCTGAGGAACATTT 57.834 33.333 0.00 0.00 0.00 2.32
3029 3084 6.585416 ACATTTTCAAGCTGAGGAACATTTT 58.415 32.000 0.00 0.00 0.00 1.82
3030 3085 7.725251 ACATTTTCAAGCTGAGGAACATTTTA 58.275 30.769 0.00 0.00 0.00 1.52
3031 3086 8.370182 ACATTTTCAAGCTGAGGAACATTTTAT 58.630 29.630 0.00 0.00 0.00 1.40
3032 3087 9.859427 CATTTTCAAGCTGAGGAACATTTTATA 57.141 29.630 0.00 0.00 0.00 0.98
3129 3201 6.595772 TTTCAAATTGTGAACATTTTCGGG 57.404 33.333 0.00 0.00 46.09 5.14
3235 3307 9.766277 TTGACAAACAATTTTTCTAAAATGCAC 57.234 25.926 0.00 0.00 33.18 4.57
3239 3311 9.649024 CAAACAATTTTTCTAAAATGCACGAAT 57.351 25.926 0.00 0.00 29.06 3.34
3258 3330 7.277539 GCACGAATTTTTCCCAATTCATGAATA 59.722 33.333 21.00 2.90 38.18 1.75
3331 3403 9.936759 AATTTGGGAACATTTTTATAACATCGT 57.063 25.926 0.00 0.00 42.32 3.73
3425 3516 6.980593 TGATCGAACAGTTTTCCAAAATCAT 58.019 32.000 0.00 0.00 0.00 2.45
3426 3517 7.432869 TGATCGAACAGTTTTCCAAAATCATT 58.567 30.769 0.00 0.00 0.00 2.57
3577 3675 7.712205 AGAAATTTGGACTTTTGTGAAATCCTG 59.288 33.333 0.00 0.00 0.00 3.86
3581 3679 7.831691 TTGGACTTTTGTGAAATCCTGAATA 57.168 32.000 0.00 0.00 0.00 1.75
3617 3723 5.372547 AAGAAAAATAAGAAGGTGCCGTC 57.627 39.130 0.00 0.00 0.00 4.79
3660 3766 0.040204 AGATGGGCACTTTTGGGGAG 59.960 55.000 0.00 0.00 0.00 4.30
3661 3767 0.251787 GATGGGCACTTTTGGGGAGT 60.252 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.607771 CCTTCTGCCAATGAAACCAACG 60.608 50.000 0.00 0.00 0.00 4.10
1 2 2.627699 TCCTTCTGCCAATGAAACCAAC 59.372 45.455 0.00 0.00 0.00 3.77
28 29 2.098117 GCCAATGAAACCGAGATCAAGG 59.902 50.000 5.09 5.09 0.00 3.61
37 38 0.667184 GCACTTGGCCAATGAAACCG 60.667 55.000 20.85 7.94 36.11 4.44
109 110 7.187824 AGTCAGCCATCTTTGAGAAATACTA 57.812 36.000 0.00 0.00 0.00 1.82
189 193 3.209429 CGTGATTCGCTTGCATGTC 57.791 52.632 1.14 0.00 0.00 3.06
242 248 2.878520 GACTCTCGCGCTGCTGAC 60.879 66.667 5.56 0.00 0.00 3.51
516 544 3.054728 TGGATTTGAATGGCGAGGTTCTA 60.055 43.478 0.00 0.00 0.00 2.10
520 548 2.214376 TTGGATTTGAATGGCGAGGT 57.786 45.000 0.00 0.00 0.00 3.85
555 585 3.152341 ACTGGCTTGAATATGGCATAGC 58.848 45.455 13.39 11.62 36.24 2.97
651 681 9.809096 TGCTTCTTACTTCTAATTATGACAGAG 57.191 33.333 0.00 0.00 0.00 3.35
1056 1100 4.680237 TTGCCCGTGGTCTGCTCG 62.680 66.667 0.00 0.00 0.00 5.03
1119 1163 1.134401 GTGGCGATGATGAGGAAGGAA 60.134 52.381 0.00 0.00 0.00 3.36
1138 1182 2.185350 CAGCATCGAGAAGGCGGT 59.815 61.111 0.00 0.00 0.00 5.68
1500 1544 4.329545 TTCTGGAGCACGCCACCC 62.330 66.667 0.00 0.00 33.52 4.61
1503 1547 2.343758 GTCTTCTGGAGCACGCCA 59.656 61.111 0.00 0.00 36.30 5.69
1516 1560 1.228675 AGTCGTACCACCCGGTCTT 60.229 57.895 0.00 0.00 44.71 3.01
1587 1631 0.608640 AGGAGTCGTTGGTAAGGCAG 59.391 55.000 0.00 0.00 0.00 4.85
1593 1637 0.679002 CGAGGGAGGAGTCGTTGGTA 60.679 60.000 0.00 0.00 0.00 3.25
1833 1877 0.960364 CTGGCAGGCGGAAAAGCTTA 60.960 55.000 6.61 0.00 37.29 3.09
1870 1914 3.458163 GGCCTCCACGACGATGGA 61.458 66.667 15.32 15.32 46.92 3.41
1872 1916 2.202797 CTGGCCTCCACGACGATG 60.203 66.667 3.32 0.00 0.00 3.84
1917 1961 1.600107 GAATGCAGTGGGGTACGGA 59.400 57.895 0.00 0.00 0.00 4.69
2391 2435 1.456705 GCCCCTCATCCTCTCGACT 60.457 63.158 0.00 0.00 0.00 4.18
2445 2489 0.111704 CAAGCTTCGTTGACGTGTCG 60.112 55.000 0.00 0.00 40.80 4.35
2531 2575 2.509336 CCTCGGCGATGCGTTTCT 60.509 61.111 11.27 0.00 0.00 2.52
2554 2598 0.324738 TCTGGCTTCTCATCCTCCGT 60.325 55.000 0.00 0.00 0.00 4.69
2656 2700 4.640789 ACAACGAGGAGATAAGCTAGTG 57.359 45.455 0.00 0.00 0.00 2.74
2658 2702 4.098044 TCCAACAACGAGGAGATAAGCTAG 59.902 45.833 0.00 0.00 0.00 3.42
2666 2710 4.819105 ACATAATCCAACAACGAGGAGA 57.181 40.909 0.00 0.00 37.34 3.71
2688 2732 5.163437 GGAACGGAAGGAGTACATCAATAGT 60.163 44.000 0.00 0.00 0.00 2.12
2689 2733 5.163447 TGGAACGGAAGGAGTACATCAATAG 60.163 44.000 0.00 0.00 0.00 1.73
2691 2735 3.517901 TGGAACGGAAGGAGTACATCAAT 59.482 43.478 0.00 0.00 0.00 2.57
2704 2748 5.756347 CCACGAGAAATATTATGGAACGGAA 59.244 40.000 0.00 0.00 0.00 4.30
2796 2841 6.575244 ATCAATGATTACCACCTGACCTAA 57.425 37.500 0.00 0.00 0.00 2.69
2800 2845 7.156876 TGAAAATCAATGATTACCACCTGAC 57.843 36.000 9.09 0.00 31.46 3.51
2862 2907 1.021968 ACTTGAAACTTGCACCGTCC 58.978 50.000 0.00 0.00 0.00 4.79
2866 2911 5.108517 TGAATCAAACTTGAAACTTGCACC 58.891 37.500 0.00 0.00 41.13 5.01
2924 2969 0.179034 GCCTTGATCCTCGCCTCAAT 60.179 55.000 0.00 0.00 31.39 2.57
2994 3049 7.663827 TCAGCTTGAAAATGTTCATGATTTCT 58.336 30.769 14.20 0.93 43.29 2.52
2998 3053 5.713389 TCCTCAGCTTGAAAATGTTCATGAT 59.287 36.000 14.20 6.12 43.29 2.45
3001 3056 5.302568 TGTTCCTCAGCTTGAAAATGTTCAT 59.697 36.000 0.00 0.00 43.29 2.57
3003 3058 5.186996 TGTTCCTCAGCTTGAAAATGTTC 57.813 39.130 0.00 0.00 0.00 3.18
3006 3061 8.767478 ATAAAATGTTCCTCAGCTTGAAAATG 57.233 30.769 0.00 0.00 0.00 2.32
3109 3181 5.752955 AGTTCCCGAAAATGTTCACAATTTG 59.247 36.000 0.00 0.00 29.87 2.32
3209 3281 9.766277 GTGCATTTTAGAAAAATTGTTTGTCAA 57.234 25.926 0.00 0.00 40.53 3.18
3211 3283 8.324567 TCGTGCATTTTAGAAAAATTGTTTGTC 58.675 29.630 0.00 0.00 31.55 3.18
3212 3284 8.190888 TCGTGCATTTTAGAAAAATTGTTTGT 57.809 26.923 0.00 0.00 31.55 2.83
3213 3285 9.649024 ATTCGTGCATTTTAGAAAAATTGTTTG 57.351 25.926 0.00 0.00 31.55 2.93
3220 3292 8.338986 GGGAAAAATTCGTGCATTTTAGAAAAA 58.661 29.630 0.00 0.00 35.67 1.94
3221 3293 7.495934 TGGGAAAAATTCGTGCATTTTAGAAAA 59.504 29.630 0.00 0.00 35.67 2.29
3222 3294 6.986817 TGGGAAAAATTCGTGCATTTTAGAAA 59.013 30.769 0.00 0.00 35.67 2.52
3223 3295 6.516718 TGGGAAAAATTCGTGCATTTTAGAA 58.483 32.000 0.00 0.00 35.67 2.10
3224 3296 6.090483 TGGGAAAAATTCGTGCATTTTAGA 57.910 33.333 0.00 0.00 35.67 2.10
3225 3297 6.777526 TTGGGAAAAATTCGTGCATTTTAG 57.222 33.333 0.00 0.00 35.67 1.85
3383 3455 7.200778 TCGATCATTCAAAACAGTTCATGAA 57.799 32.000 3.38 3.38 36.35 2.57
3644 3750 3.352512 ACTCCCCAAAAGTGCCCA 58.647 55.556 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.