Multiple sequence alignment - TraesCS2A01G208300

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 TraesCS2A01G208300 chr2A 100.000 3173 0 0 547 3719 189600712 189603884 0.000000e+00 5860
1 TraesCS2A01G208300 chr2A 100.000 240 0 0 1 240 189600166 189600405 9.480000e-121 444
2 TraesCS2A01G208300 chr2D 94.434 3216 99 31 547 3719 177093085 177096263 0.000000e+00 4874
3 TraesCS2A01G208300 chr2D 92.672 232 17 0 1 232 177092737 177092968 5.950000e-88 335
4 TraesCS2A01G208300 chr2B 93.320 2410 57 37 547 2891 234084629 234086999 0.000000e+00 3463
5 TraesCS2A01G208300 chr2B 86.845 783 45 31 2911 3676 234086985 234087726 0.000000e+00 822


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 TraesCS2A01G208300 chr2A 189600166 189603884 3718 False 3152.0 5860 100.0000 1 3719 2 chr2A.!!$F1 3718
1 TraesCS2A01G208300 chr2D 177092737 177096263 3526 False 2604.5 4874 93.5530 1 3719 2 chr2D.!!$F1 3718
2 TraesCS2A01G208300 chr2B 234084629 234087726 3097 False 2142.5 3463 90.0825 547 3676 2 chr2B.!!$F1 3129

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
79 80 1.125093 TTCAAAGGCGAGGTGAGGGA 61.125 55.000 0.00 0.00 0.00 4.20 F
133 134 1.376037 CTCCCTCTGAAACCGCCAC 60.376 63.158 0.00 0.00 0.00 5.01 F
1054 1056 1.658095 GCTACGAGTACGAGTTCGACT 59.342 52.381 8.72 7.33 43.02 4.18 F
2189 2230 0.108585 ACCACCACCTGTCATGTCAC 59.891 55.000 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1056 0.685097 CTCGTGAAGGGGTTCTCCAA 59.315 55.000 0.0 0.0 37.22 3.53 R
1646 1666 1.254284 ACTCCTCGTCCCTCTGCAAG 61.254 60.000 0.0 0.0 0.00 4.01 R
2372 2423 1.277557 CTTCTCCTGGACAGAGGGTTG 59.722 57.143 0.0 0.0 33.41 3.77 R
3630 3728 0.034863 TGGACCCGGCAATTACCTTC 60.035 55.000 0.0 0.0 0.00 3.46 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
21 22 3.919216 GGATGGATGGATCTTGACTACG 58.081 50.000 0.00 0.00 0.00 3.51
34 35 5.607477 TCTTGACTACGAACAACTGGATTT 58.393 37.500 0.00 0.00 0.00 2.17
51 52 5.972935 TGGATTTAGTTGACGATTGAGCTA 58.027 37.500 0.00 0.00 0.00 3.32
79 80 1.125093 TTCAAAGGCGAGGTGAGGGA 61.125 55.000 0.00 0.00 0.00 4.20
83 84 3.151022 GGCGAGGTGAGGGAGAGG 61.151 72.222 0.00 0.00 0.00 3.69
85 86 2.443016 CGAGGTGAGGGAGAGGGG 60.443 72.222 0.00 0.00 0.00 4.79
133 134 1.376037 CTCCCTCTGAAACCGCCAC 60.376 63.158 0.00 0.00 0.00 5.01
134 135 1.831652 CTCCCTCTGAAACCGCCACT 61.832 60.000 0.00 0.00 0.00 4.00
171 172 4.635223 CATCCGCATGATCTCCTTCTTTA 58.365 43.478 0.00 0.00 30.57 1.85
206 207 5.433081 CTAAGAATTAGCATCATCTCGCG 57.567 43.478 0.00 0.00 42.45 5.87
223 224 2.826128 TCGCGATAGAGATTTGCCCTAT 59.174 45.455 3.71 0.00 41.02 2.57
577 578 4.492294 GCGTCGACATTTTTAGCAAGAATC 59.508 41.667 17.16 0.00 0.00 2.52
580 581 5.795441 GTCGACATTTTTAGCAAGAATCACC 59.205 40.000 11.55 0.00 0.00 4.02
736 737 3.467803 CACCAGAAACTTTCTTCCTCGT 58.532 45.455 0.92 0.00 38.11 4.18
737 738 3.495001 CACCAGAAACTTTCTTCCTCGTC 59.505 47.826 0.92 0.00 38.11 4.20
819 821 7.425224 TCTTTACAAAAAGAACCCCAAATCA 57.575 32.000 0.00 0.00 46.32 2.57
1054 1056 1.658095 GCTACGAGTACGAGTTCGACT 59.342 52.381 8.72 7.33 43.02 4.18
1623 1643 4.016444 TGGGGATTAGTTGTCAATCAAGC 58.984 43.478 0.00 0.00 36.66 4.01
1626 1646 4.437390 GGGATTAGTTGTCAATCAAGCGTG 60.437 45.833 0.00 0.00 36.66 5.34
1681 1701 2.095843 GTTCATGTTCGACGCGGC 59.904 61.111 12.47 6.41 0.00 6.53
1850 1870 2.045143 GTCGACCTCCTCCTCCGT 60.045 66.667 3.51 0.00 0.00 4.69
2189 2230 0.108585 ACCACCACCTGTCATGTCAC 59.891 55.000 0.00 0.00 0.00 3.67
2334 2385 6.566753 GCTGATAAGCTTTCTTGTTTTCTCGT 60.567 38.462 3.20 0.00 33.85 4.18
2359 2410 2.351726 AGTTGATAATTTCGTGCGCTCC 59.648 45.455 9.73 0.00 0.00 4.70
2372 2423 1.216122 GCGCTCCTCTCACAATGATC 58.784 55.000 0.00 0.00 0.00 2.92
2685 2749 3.569194 TTACTCTTGCCCTGTTGTTCA 57.431 42.857 0.00 0.00 0.00 3.18
2742 2809 2.381109 TCGACTCGAGGCGAAGTAG 58.619 57.895 39.57 11.86 34.74 2.57
2743 2810 0.390866 TCGACTCGAGGCGAAGTAGT 60.391 55.000 39.57 4.06 34.74 2.73
2744 2811 1.134995 TCGACTCGAGGCGAAGTAGTA 60.135 52.381 39.57 16.77 34.74 1.82
2745 2812 1.258458 CGACTCGAGGCGAAGTAGTAG 59.742 57.143 36.99 1.48 34.74 2.57
2867 2934 0.109458 TTGCGGCAGTCGTAGTAGTG 60.109 55.000 1.67 0.00 41.72 2.74
2868 2935 1.226603 GCGGCAGTCGTAGTAGTGG 60.227 63.158 0.00 0.00 41.72 4.00
2869 2936 1.930908 GCGGCAGTCGTAGTAGTGGT 61.931 60.000 0.00 0.00 41.72 4.16
2870 2937 1.372582 CGGCAGTCGTAGTAGTGGTA 58.627 55.000 0.00 0.00 0.00 3.25
2871 2938 1.329906 CGGCAGTCGTAGTAGTGGTAG 59.670 57.143 0.00 0.00 0.00 3.18
2872 2939 1.065251 GGCAGTCGTAGTAGTGGTAGC 59.935 57.143 0.00 0.00 0.00 3.58
2905 2972 4.014406 AGGCTGGTATTTTCCCGTAAAAG 58.986 43.478 0.00 0.00 40.32 2.27
2994 3061 4.996758 GGTGCTGCAAAATAAGACCAAAAT 59.003 37.500 2.77 0.00 0.00 1.82
3022 3090 7.164122 TGTGCTCATTACTGATCTTCTCTTTT 58.836 34.615 0.00 0.00 0.00 2.27
3027 3095 6.820656 TCATTACTGATCTTCTCTTTTCTGCC 59.179 38.462 0.00 0.00 0.00 4.85
3035 3103 2.767505 TCTCTTTTCTGCCCGTTTCTC 58.232 47.619 0.00 0.00 0.00 2.87
3057 3125 7.851508 TCTCTTTTGAAAAGTCTTCATGTACG 58.148 34.615 16.41 0.00 0.00 3.67
3058 3126 7.494625 TCTCTTTTGAAAAGTCTTCATGTACGT 59.505 33.333 16.41 0.00 0.00 3.57
3059 3127 7.627340 TCTTTTGAAAAGTCTTCATGTACGTC 58.373 34.615 16.41 0.00 0.00 4.34
3060 3128 5.570262 TTGAAAAGTCTTCATGTACGTCG 57.430 39.130 0.00 0.00 0.00 5.12
3061 3129 3.985279 TGAAAAGTCTTCATGTACGTCGG 59.015 43.478 0.00 0.00 0.00 4.79
3062 3130 3.928727 AAAGTCTTCATGTACGTCGGA 57.071 42.857 0.00 0.00 0.00 4.55
3063 3131 4.451629 AAAGTCTTCATGTACGTCGGAT 57.548 40.909 0.00 0.00 0.00 4.18
3065 3133 4.451629 AGTCTTCATGTACGTCGGATTT 57.548 40.909 0.00 0.00 0.00 2.17
3090 3183 4.277515 TCTGGAAACATCTGAGGTTGAG 57.722 45.455 8.60 5.77 41.51 3.02
3120 3213 1.000731 CGTGTACCGGTAGAAAACCCA 59.999 52.381 16.41 4.48 46.62 4.51
3121 3214 2.547642 CGTGTACCGGTAGAAAACCCAA 60.548 50.000 16.41 0.00 46.62 4.12
3122 3215 2.807967 GTGTACCGGTAGAAAACCCAAC 59.192 50.000 16.41 1.71 46.62 3.77
3123 3216 2.224499 TGTACCGGTAGAAAACCCAACC 60.224 50.000 16.41 0.00 46.62 3.77
3124 3217 0.111061 ACCGGTAGAAAACCCAACCC 59.889 55.000 4.49 0.00 46.62 4.11
3136 3229 1.153429 CCAACCCTAGCAGTACGCC 60.153 63.158 6.15 0.00 44.04 5.68
3169 3262 5.122082 GGGCTCTGTAGATACGTATGAGTAC 59.878 48.000 13.97 11.69 0.00 2.73
3201 3294 6.314917 AGAAAGAAAGAAAATAAGCCAGGGA 58.685 36.000 0.00 0.00 0.00 4.20
3240 3333 3.936772 AAATGCCACGTGCCGGGAT 62.937 57.895 10.91 0.00 40.16 3.85
3376 3471 2.100631 GCATGGCGCTGTAGACGTT 61.101 57.895 7.64 0.00 37.77 3.99
3421 3517 4.520179 TCCTACTGTACGAAGAGTGCATA 58.480 43.478 0.00 0.00 44.27 3.14
3520 3616 3.876300 GACGCAAACGGCTCTCAT 58.124 55.556 0.00 0.00 46.72 2.90
3521 3617 1.421485 GACGCAAACGGCTCTCATG 59.579 57.895 0.00 0.00 46.72 3.07
3522 3618 1.291877 GACGCAAACGGCTCTCATGT 61.292 55.000 0.00 0.00 46.72 3.21
3523 3619 1.291877 ACGCAAACGGCTCTCATGTC 61.292 55.000 0.00 0.00 46.04 3.06
3524 3620 1.016130 CGCAAACGGCTCTCATGTCT 61.016 55.000 0.00 0.00 41.67 3.41
3565 3661 0.179000 GACCACCATGCCTGTAGGAG 59.821 60.000 1.17 0.00 37.39 3.69
3609 3707 0.746659 GCTTACATGTGGGCCCAATC 59.253 55.000 30.64 16.86 0.00 2.67
3707 3805 2.268076 GCTTTGCTTTCCAGGGCGA 61.268 57.895 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.112634 GCACATAGCTCAATCGTCAACTA 58.887 43.478 0.00 0.00 41.15 2.24
99 100 4.451150 AGGCGGCGAGATTTGCGA 62.451 61.111 12.98 0.00 0.00 5.10
152 153 5.118990 TCTTTAAAGAAGGAGATCATGCGG 58.881 41.667 15.57 0.00 30.73 5.69
559 560 7.702348 GGTATGGTGATTCTTGCTAAAAATGTC 59.298 37.037 0.00 0.00 0.00 3.06
577 578 3.135225 TGTGAAGAAACGTGGTATGGTG 58.865 45.455 0.00 0.00 0.00 4.17
639 640 1.134560 AGACCAGACGATTTACTCCGC 59.865 52.381 0.00 0.00 0.00 5.54
692 693 1.454479 CCCACCTGTCATGGATGCC 60.454 63.158 0.00 0.00 39.87 4.40
736 737 1.207791 GGCATGGAGGAAAGAGAGGA 58.792 55.000 0.00 0.00 0.00 3.71
737 738 0.182299 GGGCATGGAGGAAAGAGAGG 59.818 60.000 0.00 0.00 0.00 3.69
1054 1056 0.685097 CTCGTGAAGGGGTTCTCCAA 59.315 55.000 0.00 0.00 37.22 3.53
1554 1574 5.807011 CGAAAAGGAAAAGGGCAATAATCAG 59.193 40.000 0.00 0.00 0.00 2.90
1623 1643 3.331630 TACGCACGCCAACACACG 61.332 61.111 0.00 0.00 0.00 4.49
1646 1666 1.254284 ACTCCTCGTCCCTCTGCAAG 61.254 60.000 0.00 0.00 0.00 4.01
2106 2126 8.825667 AGAACAAAAATGTGCGGTTTTATAAT 57.174 26.923 0.00 0.00 0.00 1.28
2189 2230 3.521308 GAGTGTGTTTGGCGTGGCG 62.521 63.158 0.00 0.00 0.00 5.69
2334 2385 2.601314 CGCACGAAATTATCAACTCCGA 59.399 45.455 0.00 0.00 0.00 4.55
2359 2410 4.190001 CAGAGGGTTGATCATTGTGAGAG 58.810 47.826 0.00 0.00 0.00 3.20
2372 2423 1.277557 CTTCTCCTGGACAGAGGGTTG 59.722 57.143 0.00 0.00 33.41 3.77
2705 2772 8.391106 CGAGTCGAGAAGATTAAAATGGAAAAT 58.609 33.333 6.73 0.00 0.00 1.82
2735 2802 1.759994 CATCGCTGCCTACTACTTCG 58.240 55.000 0.00 0.00 0.00 3.79
2772 2839 4.207891 AGTAAATGACAGCTACCACCAG 57.792 45.455 0.00 0.00 0.00 4.00
2905 2972 2.424956 CCACCAGCCTAGCATCTTTTTC 59.575 50.000 0.00 0.00 0.00 2.29
2994 3061 6.097981 AGAGAAGATCAGTAATGAGCACATGA 59.902 38.462 11.37 0.00 36.79 3.07
3022 3090 2.631160 TCAAAAGAGAAACGGGCAGA 57.369 45.000 0.00 0.00 0.00 4.26
3027 3095 6.551736 TGAAGACTTTTCAAAAGAGAAACGG 58.448 36.000 17.05 0.00 37.24 4.44
3035 3103 6.570058 CGACGTACATGAAGACTTTTCAAAAG 59.430 38.462 8.42 8.42 31.55 2.27
3056 3124 3.002862 TGTTTCCAGAACAAAATCCGACG 59.997 43.478 0.00 0.00 0.00 5.12
3057 3125 4.561735 TGTTTCCAGAACAAAATCCGAC 57.438 40.909 0.00 0.00 0.00 4.79
3058 3126 5.048782 CAGATGTTTCCAGAACAAAATCCGA 60.049 40.000 0.00 0.00 33.42 4.55
3059 3127 5.048782 TCAGATGTTTCCAGAACAAAATCCG 60.049 40.000 0.00 0.00 33.42 4.18
3060 3128 6.331369 TCAGATGTTTCCAGAACAAAATCC 57.669 37.500 0.00 0.00 33.42 3.01
3061 3129 6.015940 ACCTCAGATGTTTCCAGAACAAAATC 60.016 38.462 0.00 0.00 33.42 2.17
3062 3130 5.835280 ACCTCAGATGTTTCCAGAACAAAAT 59.165 36.000 0.00 0.00 33.42 1.82
3063 3131 5.200483 ACCTCAGATGTTTCCAGAACAAAA 58.800 37.500 0.00 0.00 33.42 2.44
3065 3133 4.437682 ACCTCAGATGTTTCCAGAACAA 57.562 40.909 0.00 0.00 33.42 2.83
3120 3213 4.123571 TGGCGTACTGCTAGGGTT 57.876 55.556 9.06 0.00 45.43 4.11
3136 3229 1.115467 CTACAGAGCCCAGTACCCTG 58.885 60.000 0.00 0.00 38.50 4.45
3174 3267 7.933577 CCCTGGCTTATTTTCTTTCTTTCTTTT 59.066 33.333 0.00 0.00 0.00 2.27
3198 3291 1.450025 GTTTCTCCGTTGACCATCCC 58.550 55.000 0.00 0.00 0.00 3.85
3201 3294 0.321298 CCCGTTTCTCCGTTGACCAT 60.321 55.000 0.00 0.00 0.00 3.55
3234 3327 3.083349 TGCCAGTCTCCATCCCGG 61.083 66.667 0.00 0.00 0.00 5.73
3240 3333 2.926779 AGCTGCTGCCAGTCTCCA 60.927 61.111 12.44 0.00 41.26 3.86
3261 3354 3.928992 GTCTGCCCGTAAAGGTAAAGTAC 59.071 47.826 0.00 0.00 38.74 2.73
3376 3471 5.131067 AGGAGTAATACTACTGACGCATGA 58.869 41.667 3.99 0.00 38.17 3.07
3385 3480 7.288852 TCGTACAGTAGGAGGAGTAATACTACT 59.711 40.741 4.54 4.54 43.53 2.57
3389 3484 6.989169 TCTTCGTACAGTAGGAGGAGTAATAC 59.011 42.308 10.24 0.00 0.00 1.89
3421 3517 0.039074 GCAGTGTCACGAGTAGCACT 60.039 55.000 0.00 6.19 42.18 4.40
3521 3617 1.134995 TCGTGCCTGATGTCATGAGAC 60.135 52.381 0.20 0.00 45.19 3.36
3522 3618 1.135721 CTCGTGCCTGATGTCATGAGA 59.864 52.381 0.20 0.00 44.82 3.27
3523 3619 1.568606 CTCGTGCCTGATGTCATGAG 58.431 55.000 0.00 0.00 39.20 2.90
3524 3620 0.460811 GCTCGTGCCTGATGTCATGA 60.461 55.000 0.00 0.00 0.00 3.07
3630 3728 0.034863 TGGACCCGGCAATTACCTTC 60.035 55.000 0.00 0.00 0.00 3.46
3631 3729 0.323087 GTGGACCCGGCAATTACCTT 60.323 55.000 0.00 0.00 0.00 3.50
3632 3730 1.301954 GTGGACCCGGCAATTACCT 59.698 57.895 0.00 0.00 0.00 3.08
3633 3731 2.110352 CGTGGACCCGGCAATTACC 61.110 63.158 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.