Multiple sequence alignment - TraesCS2D01G210500

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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 TraesCS2D01G210500 chr2D 100.000 3875 0 0 1 3875 166866663 166862789 0.000000e+00 7156
1 TraesCS2D01G210500 chr2A 92.661 3488 183 38 1 3459 183513096 183516539 0.000000e+00 4955
2 TraesCS2D01G210500 chr2A 93.452 168 6 2 3712 3875 183516849 183517015 1.080000e-60 244
3 TraesCS2D01G210500 chr2B 94.970 3141 103 17 1 3129 230968080 230971177 0.000000e+00 4874
4 TraesCS2D01G210500 chr2B 92.222 720 27 15 3164 3872 230971176 230971877 0.000000e+00 992
5 TraesCS2D01G210500 chr5D 81.205 415 73 3 1 414 565330025 565329615 2.890000e-86 329
6 TraesCS2D01G210500 chr4A 79.952 414 79 2 1 414 562294841 562295250 6.290000e-78 302


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 TraesCS2D01G210500 chr2D 166862789 166866663 3874 True 7156.0 7156 100.0000 1 3875 1 chr2D.!!$R1 3874
1 TraesCS2D01G210500 chr2A 183513096 183517015 3919 False 2599.5 4955 93.0565 1 3875 2 chr2A.!!$F1 3874
2 TraesCS2D01G210500 chr2B 230968080 230971877 3797 False 2933.0 4874 93.5960 1 3872 2 chr2B.!!$F1 3871


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
175 176 0.738975 TTCTCGCTACACTGATCGGG 59.261 55.0 6.47 0.0 0.00 5.14 F
1906 1935 0.668535 CATCTGCTCCGATCACCGTA 59.331 55.0 0.00 0.0 36.31 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2126 0.468214 CGACCTCCCTGGATGAGCTA 60.468 60.0 0.0 0.0 39.71 3.32 R
3708 3862 0.455410 GAACAACACAGCAGCAACCA 59.545 50.0 0.0 0.0 0.00 3.67 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
172 173 4.046938 TGGAATTCTCGCTACACTGATC 57.953 45.455 5.23 0.00 0.00 2.92
173 174 3.046390 GGAATTCTCGCTACACTGATCG 58.954 50.000 5.23 0.00 0.00 3.69
174 175 2.783828 ATTCTCGCTACACTGATCGG 57.216 50.000 0.00 0.00 0.00 4.18
175 176 0.738975 TTCTCGCTACACTGATCGGG 59.261 55.000 6.47 0.00 0.00 5.14
273 275 5.845103 TGTACTAAGATCAACAAACGGTCA 58.155 37.500 0.00 0.00 0.00 4.02
293 295 6.051717 GGTCATGCACATCTCTGTACTAATT 58.948 40.000 0.00 0.00 33.14 1.40
319 321 3.300852 TGTACGCTTAATGTGACCGAA 57.699 42.857 0.00 0.00 0.00 4.30
321 323 4.056740 TGTACGCTTAATGTGACCGAAAA 58.943 39.130 0.00 0.00 0.00 2.29
367 369 1.761784 CTGATCAGTAGCTTCCTGGCT 59.238 52.381 14.95 0.00 45.29 4.75
368 370 1.483827 TGATCAGTAGCTTCCTGGCTG 59.516 52.381 11.80 3.46 43.01 4.85
369 371 0.835941 ATCAGTAGCTTCCTGGCTGG 59.164 55.000 3.65 3.65 43.01 4.85
370 372 1.451028 CAGTAGCTTCCTGGCTGGC 60.451 63.158 5.39 0.00 43.01 4.85
371 373 1.614824 AGTAGCTTCCTGGCTGGCT 60.615 57.895 5.39 11.29 43.01 4.75
418 428 3.399440 AGCTCTGTGAAGTTCCTTGAG 57.601 47.619 0.00 6.15 0.00 3.02
498 510 3.353557 ACAGTAGCATCTCCGTGAGTTA 58.646 45.455 0.00 0.00 0.00 2.24
556 571 1.096967 TAGCATTGCTGGGCATGTCG 61.097 55.000 21.31 0.00 40.10 4.35
715 741 3.190849 CATCCACAGTCCGCGCTG 61.191 66.667 5.56 11.54 41.92 5.18
1107 1136 4.202243 GCCATAAACTCTCTCATCTCTGCT 60.202 45.833 0.00 0.00 0.00 4.24
1119 1148 1.518133 CTCTGCTTCCTTCTCCGCG 60.518 63.158 0.00 0.00 0.00 6.46
1157 1186 1.300963 GGCAGCTCATCAGGGACAA 59.699 57.895 0.00 0.00 0.00 3.18
1510 1539 2.604686 ACCTCTTCGCCAGGCTCA 60.605 61.111 10.54 0.00 33.84 4.26
1899 1928 3.548745 TTGATCAACATCTGCTCCGAT 57.451 42.857 3.38 0.00 0.00 4.18
1906 1935 0.668535 CATCTGCTCCGATCACCGTA 59.331 55.000 0.00 0.00 36.31 4.02
2097 2126 3.675563 GCGATCGCCTCCGGAGAT 61.676 66.667 33.39 18.66 44.53 2.75
2115 2144 1.899142 GATAGCTCATCCAGGGAGGTC 59.101 57.143 0.00 0.00 41.78 3.85
2231 2260 2.807045 CGCGCTCTGCTTCTCGTT 60.807 61.111 5.56 0.00 43.27 3.85
2235 2264 1.669115 GCTCTGCTTCTCGTTGCCA 60.669 57.895 0.00 0.00 0.00 4.92
2277 2306 2.434359 GCCGTCTTCCTCAACCGG 60.434 66.667 0.00 0.00 41.50 5.28
2320 2349 4.854924 ACACCACGCTGCAGCACA 62.855 61.111 36.03 0.00 42.21 4.57
2434 2463 3.656280 TCCAGGCGGCCAAATCCA 61.656 61.111 23.09 0.00 0.00 3.41
2436 2465 2.492773 CCAGGCGGCCAAATCCATC 61.493 63.158 23.09 0.00 0.00 3.51
2440 2469 2.546494 GCGGCCAAATCCATCGAGG 61.546 63.158 2.24 0.00 39.47 4.63
2565 2594 2.503846 TAGGCCCCGACGAGGAGAAA 62.504 60.000 0.00 0.00 45.00 2.52
2684 2713 7.758495 AGGTAATCACAACATTAAAACGATCC 58.242 34.615 0.00 0.00 0.00 3.36
2688 2717 8.687824 AATCACAACATTAAAACGATCCAATC 57.312 30.769 0.00 0.00 0.00 2.67
2691 2720 7.807433 TCACAACATTAAAACGATCCAATCTTG 59.193 33.333 0.00 0.00 0.00 3.02
2692 2721 7.807433 CACAACATTAAAACGATCCAATCTTGA 59.193 33.333 0.00 0.00 0.00 3.02
2693 2722 8.522830 ACAACATTAAAACGATCCAATCTTGAT 58.477 29.630 0.00 0.00 0.00 2.57
2694 2723 8.800972 CAACATTAAAACGATCCAATCTTGATG 58.199 33.333 0.00 0.00 0.00 3.07
2695 2724 6.974622 ACATTAAAACGATCCAATCTTGATGC 59.025 34.615 0.00 0.00 0.00 3.91
2696 2725 6.757897 TTAAAACGATCCAATCTTGATGCT 57.242 33.333 0.00 0.00 0.00 3.79
2698 2727 6.757897 AAAACGATCCAATCTTGATGCTAA 57.242 33.333 0.00 0.00 0.00 3.09
2699 2728 5.741388 AACGATCCAATCTTGATGCTAAC 57.259 39.130 0.00 0.00 0.00 2.34
2700 2729 4.769688 ACGATCCAATCTTGATGCTAACA 58.230 39.130 0.00 0.00 0.00 2.41
2701 2730 5.185454 ACGATCCAATCTTGATGCTAACAA 58.815 37.500 0.00 0.00 0.00 2.83
2702 2731 5.065218 ACGATCCAATCTTGATGCTAACAAC 59.935 40.000 0.00 0.00 0.00 3.32
2705 2734 6.647334 TCCAATCTTGATGCTAACAACAAA 57.353 33.333 0.00 0.00 38.01 2.83
2723 2752 6.089551 ACAACAAATCTCGACTTCTGAATACG 59.910 38.462 9.09 9.09 0.00 3.06
2727 2756 4.092771 TCTCGACTTCTGAATACGTTGG 57.907 45.455 0.00 7.65 0.00 3.77
2732 2761 4.491676 GACTTCTGAATACGTTGGTGCTA 58.508 43.478 0.00 0.00 0.00 3.49
2799 2828 0.176910 TTGCAGAGACCAACGTGACA 59.823 50.000 0.00 0.00 0.00 3.58
2915 2946 3.567164 CCAGTTCTTGATTGTGCTGTCTT 59.433 43.478 0.00 0.00 0.00 3.01
2969 3000 7.484641 CCATATTTTGTTACAGTGAATGAACGG 59.515 37.037 0.00 0.00 0.00 4.44
2979 3010 4.272018 CAGTGAATGAACGGATGAATCTCC 59.728 45.833 0.00 0.00 0.00 3.71
2995 3027 3.657398 TCTCCCCAGTGTATTCGAGTA 57.343 47.619 0.00 0.00 0.00 2.59
3019 3051 0.950555 GCGATGTGTTGCTCCTGACA 60.951 55.000 0.00 0.00 0.00 3.58
3028 3060 2.047844 CTCCTGACACAGCCCACG 60.048 66.667 0.00 0.00 0.00 4.94
3036 3068 2.687200 ACAGCCCACGCCCTGATA 60.687 61.111 0.00 0.00 34.57 2.15
3041 3073 2.452064 CCCACGCCCTGATACCCAT 61.452 63.158 0.00 0.00 0.00 4.00
3060 3092 1.877576 TACGCACTGGCACTCTCCTG 61.878 60.000 0.00 0.00 41.24 3.86
3126 3158 1.338674 CCGTTCCACAATGCAGGAGTA 60.339 52.381 0.00 0.00 34.91 2.59
3129 3161 2.042686 TCCACAATGCAGGAGTATGC 57.957 50.000 0.00 0.00 46.68 3.14
3171 3203 1.409064 TCAGCGGGTCACTGTATCATC 59.591 52.381 0.00 0.00 36.50 2.92
3337 3369 2.093310 CGCCGATGAGTTATGATGATGC 59.907 50.000 0.00 0.00 0.00 3.91
3558 3634 1.995484 CGATGTAGATTATGCGCCTGG 59.005 52.381 4.18 0.00 0.00 4.45
3583 3659 3.146066 TGCAAGGACATTCTGTGGTAAC 58.854 45.455 0.00 0.00 0.00 2.50
3610 3689 6.662755 TGATGGATGTTTAGTGCTCCTTTAT 58.337 36.000 0.00 0.00 0.00 1.40
3630 3784 1.073284 TGCTGTAGGTTGGTTCCCTTC 59.927 52.381 0.00 0.00 33.35 3.46
3661 3815 2.436292 CTGCTGGTCAGGCTCTGC 60.436 66.667 0.00 0.00 39.15 4.26
3662 3816 2.926779 TGCTGGTCAGGCTCTGCT 60.927 61.111 0.00 0.00 0.00 4.24
3663 3817 2.436292 GCTGGTCAGGCTCTGCTG 60.436 66.667 0.00 0.00 0.00 4.41
3664 3818 2.436292 CTGGTCAGGCTCTGCTGC 60.436 66.667 0.00 0.00 0.00 5.25
3665 3819 3.243816 TGGTCAGGCTCTGCTGCA 61.244 61.111 0.88 0.88 34.04 4.41
3666 3820 2.436292 GGTCAGGCTCTGCTGCAG 60.436 66.667 23.31 23.31 34.04 4.41
3667 3821 2.346739 GTCAGGCTCTGCTGCAGT 59.653 61.111 27.24 7.11 32.61 4.40
3668 3822 2.033755 GTCAGGCTCTGCTGCAGTG 61.034 63.158 27.24 25.20 32.61 3.66
3669 3823 3.432588 CAGGCTCTGCTGCAGTGC 61.433 66.667 35.79 35.79 46.23 4.40
3670 3824 3.638316 AGGCTCTGCTGCAGTGCT 61.638 61.111 38.89 27.88 46.20 4.40
3671 3825 3.432588 GGCTCTGCTGCAGTGCTG 61.433 66.667 38.89 24.30 46.20 4.41
3672 3826 2.668889 GCTCTGCTGCAGTGCTGT 60.669 61.111 35.99 0.00 44.40 4.40
3684 3838 4.141287 TGCAGTGCTGTTGTACCTTAATT 58.859 39.130 17.60 0.00 0.00 1.40
3708 3862 6.735678 TGTTATTACTGATGCATTTGTCGT 57.264 33.333 0.00 0.00 0.00 4.34
3717 3871 1.277495 GCATTTGTCGTGGTTGCTGC 61.277 55.000 0.00 0.00 0.00 5.25
3731 3885 3.057315 GGTTGCTGCTGTGTTGTTCATAT 60.057 43.478 0.00 0.00 0.00 1.78
3751 3905 2.099143 TCGCTCTCGAGGCTAACTG 58.901 57.895 13.56 2.44 40.21 3.16
3808 3966 2.877097 TGGCTGCATTTCTTGGTCTA 57.123 45.000 0.50 0.00 0.00 2.59
3851 4009 1.607251 GCCAACTACACGGCTGTTACT 60.607 52.381 0.00 0.00 45.29 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 269 2.159184 AGTACAGAGATGTGCATGACCG 60.159 50.000 0.00 0.00 0.00 4.79
273 275 7.739825 ACCATAATTAGTACAGAGATGTGCAT 58.260 34.615 0.00 0.00 0.00 3.96
293 295 4.871557 GGTCACATTAAGCGTACAACCATA 59.128 41.667 0.00 0.00 0.00 2.74
319 321 7.133483 AGATAGGGATAGTGTCTAACCAGTTT 58.867 38.462 5.67 0.00 0.00 2.66
321 323 6.282568 AGATAGGGATAGTGTCTAACCAGT 57.717 41.667 5.67 0.00 0.00 4.00
367 369 0.534877 ATGCATTCGCCGAATAGCCA 60.535 50.000 22.29 16.03 37.32 4.75
368 370 0.593128 AATGCATTCGCCGAATAGCC 59.407 50.000 22.29 12.12 37.32 3.93
369 371 1.955762 GAATGCATTCGCCGAATAGC 58.044 50.000 22.90 17.30 37.32 2.97
507 519 5.585047 ACGAAAAATGTTAGGAGATGCTACC 59.415 40.000 0.00 0.00 0.00 3.18
519 534 6.709145 ATGCTACACGTACGAAAAATGTTA 57.291 33.333 24.41 6.07 0.00 2.41
556 571 0.585357 TCTACGAACTAGGATCGCGC 59.415 55.000 17.05 0.00 43.88 6.86
863 889 6.964807 TTACTAGTTATGGTATGCGGAGAA 57.035 37.500 0.00 0.00 0.00 2.87
1107 1136 2.283676 AGGGACGCGGAGAAGGAA 60.284 61.111 12.47 0.00 0.00 3.36
1119 1148 1.219393 CTTGAGCGGGAAGAGGGAC 59.781 63.158 0.00 0.00 0.00 4.46
1157 1186 2.030562 CGTGGAGCCGGTTGAACT 59.969 61.111 1.90 0.00 0.00 3.01
1657 1686 2.815647 GGCCTCTTCTTGGACGCG 60.816 66.667 3.53 3.53 0.00 6.01
1882 1911 2.484417 GGTGATCGGAGCAGATGTTGAT 60.484 50.000 0.00 0.00 0.00 2.57
2097 2126 0.468214 CGACCTCCCTGGATGAGCTA 60.468 60.000 0.00 0.00 39.71 3.32
2115 2144 3.257933 GTGCCTTCTTGGAGCACG 58.742 61.111 0.00 0.00 46.43 5.34
2178 2207 1.228124 CACCTCCCGTGCCTTTGAA 60.228 57.895 0.00 0.00 35.18 2.69
2231 2260 2.761195 CGGTCGATCGAGTCTGGCA 61.761 63.158 20.09 0.00 0.00 4.92
2235 2264 2.124653 AGCCGGTCGATCGAGTCT 60.125 61.111 21.90 10.56 0.00 3.24
2277 2306 1.448717 GCGGAGGAAGAAGAGCACC 60.449 63.158 0.00 0.00 0.00 5.01
2320 2349 2.870372 CGCTGCTTTTAAGGCGCT 59.130 55.556 7.64 0.00 41.08 5.92
2434 2463 2.427245 CCAACTCCCTCGCCTCGAT 61.427 63.158 0.00 0.00 34.61 3.59
2436 2465 4.821589 GCCAACTCCCTCGCCTCG 62.822 72.222 0.00 0.00 0.00 4.63
2684 2713 7.217636 CGAGATTTGTTGTTAGCATCAAGATTG 59.782 37.037 3.71 0.00 36.18 2.67
2688 2717 6.017933 GTCGAGATTTGTTGTTAGCATCAAG 58.982 40.000 3.71 0.00 36.18 3.02
2691 2720 5.786401 AGTCGAGATTTGTTGTTAGCATC 57.214 39.130 0.00 0.00 0.00 3.91
2692 2721 5.934625 AGAAGTCGAGATTTGTTGTTAGCAT 59.065 36.000 0.00 0.00 0.00 3.79
2693 2722 5.177511 CAGAAGTCGAGATTTGTTGTTAGCA 59.822 40.000 0.00 0.00 0.00 3.49
2694 2723 5.405571 TCAGAAGTCGAGATTTGTTGTTAGC 59.594 40.000 0.00 0.00 0.00 3.09
2695 2724 7.408132 TTCAGAAGTCGAGATTTGTTGTTAG 57.592 36.000 0.00 0.00 0.00 2.34
2696 2725 7.962964 ATTCAGAAGTCGAGATTTGTTGTTA 57.037 32.000 0.00 0.00 0.00 2.41
2698 2727 6.089551 CGTATTCAGAAGTCGAGATTTGTTGT 59.910 38.462 4.38 0.00 0.00 3.32
2699 2728 6.089551 ACGTATTCAGAAGTCGAGATTTGTTG 59.910 38.462 14.13 0.00 0.00 3.33
2700 2729 6.157211 ACGTATTCAGAAGTCGAGATTTGTT 58.843 36.000 14.13 0.00 0.00 2.83
2701 2730 5.710984 ACGTATTCAGAAGTCGAGATTTGT 58.289 37.500 14.13 0.00 0.00 2.83
2702 2731 6.454318 CCAACGTATTCAGAAGTCGAGATTTG 60.454 42.308 14.13 9.03 0.00 2.32
2705 2734 4.158025 ACCAACGTATTCAGAAGTCGAGAT 59.842 41.667 14.13 1.40 0.00 2.75
2799 2828 3.690139 TCTTCACGATCTTCTTAGCGTCT 59.310 43.478 0.00 0.00 34.37 4.18
2915 2946 5.887214 ACATATGTGTTAGCTACCCATGA 57.113 39.130 7.78 0.00 34.01 3.07
2969 3000 4.039245 TCGAATACACTGGGGAGATTCATC 59.961 45.833 0.00 0.00 0.00 2.92
2995 3027 1.738099 GAGCAACACATCGCCGAGT 60.738 57.895 0.00 0.00 0.00 4.18
3019 3051 2.687200 TATCAGGGCGTGGGCTGT 60.687 61.111 7.42 0.00 39.81 4.40
3028 3060 0.602905 GTGCGTATGGGTATCAGGGC 60.603 60.000 0.00 0.00 0.00 5.19
3036 3068 2.046314 GTGCCAGTGCGTATGGGT 60.046 61.111 4.08 0.00 41.78 4.51
3041 3073 1.606601 AGGAGAGTGCCAGTGCGTA 60.607 57.895 0.00 0.00 41.78 4.42
3060 3092 1.337823 ACAGAGACGGGCAATGTACAC 60.338 52.381 0.00 0.00 0.00 2.90
3126 3158 1.145598 CTCATCGCTGAGTGGGCAT 59.854 57.895 8.12 0.00 43.35 4.40
3171 3203 3.950087 TCGATCGATTTTGCCATTCTG 57.050 42.857 15.15 0.00 0.00 3.02
3293 3325 2.117156 TAGAGTACGTCGGCCAGGC 61.117 63.158 1.26 1.26 0.00 4.85
3583 3659 2.283298 AGCACTAAACATCCATCAGCG 58.717 47.619 0.00 0.00 0.00 5.18
3653 3807 3.638316 AGCACTGCAGCAGAGCCT 61.638 61.111 33.35 21.17 46.32 4.58
3661 3815 1.597742 AAGGTACAACAGCACTGCAG 58.402 50.000 13.48 13.48 0.00 4.41
3662 3816 2.920724 TAAGGTACAACAGCACTGCA 57.079 45.000 3.30 0.00 0.00 4.41
3663 3817 4.766404 AATTAAGGTACAACAGCACTGC 57.234 40.909 0.00 0.00 0.00 4.40
3664 3818 6.072112 ACAAATTAAGGTACAACAGCACTG 57.928 37.500 0.00 0.00 0.00 3.66
3665 3819 6.709018 AACAAATTAAGGTACAACAGCACT 57.291 33.333 0.00 0.00 0.00 4.40
3684 3838 7.020602 CACGACAAATGCATCAGTAATAACAA 58.979 34.615 0.00 0.00 0.00 2.83
3698 3852 1.277495 GCAGCAACCACGACAAATGC 61.277 55.000 0.00 0.00 37.28 3.56
3708 3862 0.455410 GAACAACACAGCAGCAACCA 59.545 50.000 0.00 0.00 0.00 3.67
3717 3871 4.428209 AGAGCGAGATATGAACAACACAG 58.572 43.478 0.00 0.00 0.00 3.66
3751 3905 6.803154 AATAAGGTTAGTGTGCTTTCAGTC 57.197 37.500 0.00 0.00 0.00 3.51
3808 3966 2.652348 TGTTTGGATTGTAGGGGGACAT 59.348 45.455 0.00 0.00 0.00 3.06
3851 4009 5.416083 CAAGTGACCAGAATACGGATACAA 58.584 41.667 0.00 0.00 0.00 2.41



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

AutoCloner maintained by Alex Coulton.