Multiple sequence alignment - TraesCS2D01G295700

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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 TraesCS2D01G295700 chr2D 100.000 2979 0 0 1 2979 377504933 377501955 0.000000e+00 5502
1 TraesCS2D01G295700 chr2B 93.410 2883 83 26 1 2845 449121986 449119173 0.000000e+00 4172
2 TraesCS2D01G295700 chr2A 91.454 2387 89 44 513 2834 511924009 511921673 0.000000e+00 3171
3 TraesCS2D01G295700 chr2A 94.361 532 21 4 1 527 511924555 511924028 0.000000e+00 808
4 TraesCS2D01G295700 chr5D 79.710 345 70 0 1536 1880 528230433 528230089 1.770000e-62 250
5 TraesCS2D01G295700 chr5A 79.646 339 69 0 1536 1874 656210527 656210189 8.250000e-61 244
6 TraesCS2D01G295700 chr5B 79.191 346 70 2 1536 1880 664998549 664998205 3.840000e-59 239


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 TraesCS2D01G295700 chr2D 377501955 377504933 2978 True 5502.0 5502 100.0000 1 2979 1 chr2D.!!$R1 2978
1 TraesCS2D01G295700 chr2B 449119173 449121986 2813 True 4172.0 4172 93.4100 1 2845 1 chr2B.!!$R1 2844
2 TraesCS2D01G295700 chr2A 511921673 511924555 2882 True 1989.5 3171 92.9075 1 2834 2 chr2A.!!$R1 2833

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
613 674 0.592637 TCGCAATTCACAAGCACCAG 59.407 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 2495 1.003233 GTTGGCCTGTCACTCTCCC 60.003 63.158 3.32 0.0 0.0 4.3 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
134 152 1.513158 CACGAGAGATCGGGCACTT 59.487 57.895 2.46 0.00 37.45 3.16
215 233 3.245443 TGGGAGAAGCTAGCTAGGGATAG 60.245 52.174 19.70 0.00 34.84 2.08
216 234 3.361786 GGAGAAGCTAGCTAGGGATAGG 58.638 54.545 19.70 0.00 32.60 2.57
217 235 3.010808 GGAGAAGCTAGCTAGGGATAGGA 59.989 52.174 19.70 0.00 32.60 2.94
308 329 3.787001 CGACCTTGCCTCCCTCCC 61.787 72.222 0.00 0.00 0.00 4.30
309 330 2.285743 GACCTTGCCTCCCTCCCT 60.286 66.667 0.00 0.00 0.00 4.20
310 331 2.285743 ACCTTGCCTCCCTCCCTC 60.286 66.667 0.00 0.00 0.00 4.30
311 332 3.093172 CCTTGCCTCCCTCCCTCC 61.093 72.222 0.00 0.00 0.00 4.30
377 398 3.560068 AGCGAAGAAGTAACCAGTGTTTG 59.440 43.478 0.00 0.00 35.87 2.93
464 487 5.649557 TGATTGACAGACAAACCACAAAAG 58.350 37.500 0.00 0.00 42.03 2.27
466 489 2.757868 TGACAGACAAACCACAAAAGGG 59.242 45.455 0.00 0.00 0.00 3.95
473 498 2.955660 CAAACCACAAAAGGGTCAGCTA 59.044 45.455 0.00 0.00 37.77 3.32
474 499 3.525800 AACCACAAAAGGGTCAGCTAT 57.474 42.857 0.00 0.00 37.77 2.97
476 501 4.650972 ACCACAAAAGGGTCAGCTATTA 57.349 40.909 0.00 0.00 31.49 0.98
527 585 1.388547 TGCAAGACACCAACCTTCAC 58.611 50.000 0.00 0.00 0.00 3.18
554 615 5.906772 AAAGGTCCTACAAGAGAAGGAAA 57.093 39.130 0.00 0.00 43.44 3.13
560 621 6.126911 GGTCCTACAAGAGAAGGAAATCTGAT 60.127 42.308 0.00 0.00 43.44 2.90
611 672 2.253603 GAATCGCAATTCACAAGCACC 58.746 47.619 0.00 0.00 40.90 5.01
612 673 1.246649 ATCGCAATTCACAAGCACCA 58.753 45.000 0.00 0.00 0.00 4.17
613 674 0.592637 TCGCAATTCACAAGCACCAG 59.407 50.000 0.00 0.00 0.00 4.00
614 675 0.592637 CGCAATTCACAAGCACCAGA 59.407 50.000 0.00 0.00 0.00 3.86
615 676 1.001487 CGCAATTCACAAGCACCAGAA 60.001 47.619 0.00 0.00 0.00 3.02
616 677 2.669364 GCAATTCACAAGCACCAGAAG 58.331 47.619 0.00 0.00 0.00 2.85
617 678 2.608752 GCAATTCACAAGCACCAGAAGG 60.609 50.000 0.00 0.00 42.21 3.46
678 739 2.989840 GGCGATCTCGGATTAACAGATG 59.010 50.000 1.34 0.00 40.23 2.90
806 867 5.483937 ACCCCCAAAAGATAATCAACCTTTC 59.516 40.000 0.00 0.00 30.62 2.62
967 1034 1.603172 CCCTCACTCGAAGACACACAC 60.603 57.143 0.00 0.00 0.00 3.82
968 1035 1.067060 CCTCACTCGAAGACACACACA 59.933 52.381 0.00 0.00 0.00 3.72
1231 1299 4.646492 AGGTTGCACATCTCAAACTTCTTT 59.354 37.500 0.00 0.00 38.21 2.52
1270 1338 1.202651 AGTTCACAGTTTGGTCCTCGG 60.203 52.381 0.00 0.00 0.00 4.63
1372 1448 7.018826 GCAGAGCTACTATAGTTAGTGAATCG 58.981 42.308 11.40 0.00 39.08 3.34
1405 1481 9.959749 CTAGTAGGAGTATGAGAGAATGTTTTC 57.040 37.037 0.00 0.00 0.00 2.29
1492 1583 9.658475 TTTGTCACGAAATAAAGTACATTTCTG 57.342 29.630 12.65 10.40 39.29 3.02
1756 1855 1.640069 CATGAAGCAGGACATCGCG 59.360 57.895 0.00 0.00 0.00 5.87
2137 2251 6.259387 TGAATCTGTGCAGAATAATGCTACTG 59.741 38.462 5.95 0.00 46.63 2.74
2292 2406 0.741927 TGCATCTCAGTGTCCGCATG 60.742 55.000 0.00 0.00 0.00 4.06
2295 2409 2.599645 ATCTCAGTGTCCGCATGGCC 62.600 60.000 0.00 0.00 34.14 5.36
2300 2414 3.696676 TGTCCGCATGGCCGTACA 61.697 61.111 0.00 0.00 34.14 2.90
2301 2415 3.192922 GTCCGCATGGCCGTACAC 61.193 66.667 0.00 0.00 34.14 2.90
2302 2416 3.696676 TCCGCATGGCCGTACACA 61.697 61.111 0.00 0.00 34.14 3.72
2303 2417 3.496131 CCGCATGGCCGTACACAC 61.496 66.667 0.00 0.00 0.00 3.82
2451 2570 4.702081 GCGTCACGTCAGCTCCGT 62.702 66.667 0.00 2.22 39.52 4.69
2452 2571 2.865308 CGTCACGTCAGCTCCGTA 59.135 61.111 7.57 0.00 36.65 4.02
2453 2572 1.511464 CGTCACGTCAGCTCCGTAC 60.511 63.158 7.57 6.39 36.65 3.67
2454 2573 1.154073 GTCACGTCAGCTCCGTACC 60.154 63.158 7.57 0.00 36.65 3.34
2516 2635 0.606604 TCAGCGGGTAGACTGAAACC 59.393 55.000 0.00 0.00 39.89 3.27
2693 2814 2.069273 CCGCGTCTGAAATCTGAAACT 58.931 47.619 4.92 0.00 0.00 2.66
2746 2867 4.006532 GCGTCACGACACTTGTGA 57.993 55.556 0.00 0.00 43.68 3.58
2758 2879 2.837498 CACTTGTGATGAGTGTCCACA 58.163 47.619 0.00 0.00 39.66 4.17
2860 2981 4.778143 GGTGATTCGGGCGGTGCT 62.778 66.667 0.00 0.00 0.00 4.40
2861 2982 2.746277 GTGATTCGGGCGGTGCTT 60.746 61.111 0.00 0.00 0.00 3.91
2862 2983 2.745884 TGATTCGGGCGGTGCTTG 60.746 61.111 0.00 0.00 0.00 4.01
2863 2984 2.435938 GATTCGGGCGGTGCTTGA 60.436 61.111 0.00 0.00 0.00 3.02
2864 2985 2.746277 ATTCGGGCGGTGCTTGAC 60.746 61.111 0.00 0.00 0.00 3.18
2868 2989 4.643387 GGGCGGTGCTTGACCAGT 62.643 66.667 0.00 0.00 46.55 4.00
2869 2990 3.050275 GGCGGTGCTTGACCAGTC 61.050 66.667 0.00 0.00 46.55 3.51
2870 2991 2.280797 GCGGTGCTTGACCAGTCA 60.281 61.111 0.00 0.00 46.55 3.41
2871 2992 1.891919 GCGGTGCTTGACCAGTCAA 60.892 57.895 12.40 12.40 46.55 3.18
2872 2993 1.941812 CGGTGCTTGACCAGTCAAC 59.058 57.895 9.12 7.44 46.55 3.18
2873 2994 1.507141 CGGTGCTTGACCAGTCAACC 61.507 60.000 9.12 9.19 46.55 3.77
2874 2995 1.507141 GGTGCTTGACCAGTCAACCG 61.507 60.000 9.12 2.68 45.34 4.44
2875 2996 0.814010 GTGCTTGACCAGTCAACCGT 60.814 55.000 9.12 0.00 43.90 4.83
2876 2997 0.107410 TGCTTGACCAGTCAACCGTT 60.107 50.000 9.12 0.00 43.90 4.44
2877 2998 0.307760 GCTTGACCAGTCAACCGTTG 59.692 55.000 9.12 4.78 43.90 4.10
2878 2999 1.948104 CTTGACCAGTCAACCGTTGA 58.052 50.000 9.99 9.99 43.90 3.18
2879 3000 2.494059 CTTGACCAGTCAACCGTTGAT 58.506 47.619 16.80 1.01 43.90 2.57
2880 3001 2.631160 TGACCAGTCAACCGTTGATT 57.369 45.000 16.80 10.21 42.47 2.57
2881 3002 2.925724 TGACCAGTCAACCGTTGATTT 58.074 42.857 16.80 6.36 42.47 2.17
2882 3003 4.074627 TGACCAGTCAACCGTTGATTTA 57.925 40.909 16.80 0.00 42.47 1.40
2883 3004 3.810941 TGACCAGTCAACCGTTGATTTAC 59.189 43.478 16.80 5.11 42.47 2.01
2884 3005 2.803956 ACCAGTCAACCGTTGATTTACG 59.196 45.455 16.80 5.68 42.47 3.18
2885 3006 2.803956 CCAGTCAACCGTTGATTTACGT 59.196 45.455 16.80 0.00 42.47 3.57
2886 3007 3.989167 CCAGTCAACCGTTGATTTACGTA 59.011 43.478 16.80 0.00 42.47 3.57
2887 3008 4.448395 CCAGTCAACCGTTGATTTACGTAA 59.552 41.667 16.80 3.29 42.47 3.18
2888 3009 5.050227 CCAGTCAACCGTTGATTTACGTAAA 60.050 40.000 22.12 22.12 42.47 2.01
2889 3010 6.420588 CAGTCAACCGTTGATTTACGTAAAA 58.579 36.000 23.49 6.59 42.47 1.52
2890 3011 6.906143 CAGTCAACCGTTGATTTACGTAAAAA 59.094 34.615 23.49 12.26 42.47 1.94
2925 3046 9.994432 AAAAATTCGTTAATTGAAAAATGTGCA 57.006 22.222 0.00 0.00 35.46 4.57
2927 3048 9.596677 AAATTCGTTAATTGAAAAATGTGCATG 57.403 25.926 0.00 0.00 35.46 4.06
2928 3049 6.702972 TCGTTAATTGAAAAATGTGCATGG 57.297 33.333 0.00 0.00 0.00 3.66
2929 3050 6.219473 TCGTTAATTGAAAAATGTGCATGGT 58.781 32.000 0.00 0.00 0.00 3.55
2930 3051 6.703607 TCGTTAATTGAAAAATGTGCATGGTT 59.296 30.769 0.00 0.00 0.00 3.67
2931 3052 7.225538 TCGTTAATTGAAAAATGTGCATGGTTT 59.774 29.630 0.00 0.00 0.00 3.27
2932 3053 7.854916 CGTTAATTGAAAAATGTGCATGGTTTT 59.145 29.630 0.00 0.00 0.00 2.43
2933 3054 9.513727 GTTAATTGAAAAATGTGCATGGTTTTT 57.486 25.926 14.97 14.97 37.64 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.572243 CGCGTACTAGTAGCATAGCAC 58.428 52.381 18.33 2.65 0.00 4.40
39 40 1.069432 GCGCGTACTAGTAGCATAGCA 60.069 52.381 8.43 0.00 0.00 3.49
40 41 1.604396 GCGCGTACTAGTAGCATAGC 58.396 55.000 8.43 12.46 0.00 2.97
41 42 1.534163 TGGCGCGTACTAGTAGCATAG 59.466 52.381 8.43 8.30 0.00 2.23
42 43 1.265095 GTGGCGCGTACTAGTAGCATA 59.735 52.381 8.43 5.44 0.00 3.14
118 136 1.880340 GCAAGTGCCCGATCTCTCG 60.880 63.158 0.00 0.00 44.62 4.04
215 233 1.836802 AGCACCAGAGAAATCTCCTCC 59.163 52.381 6.81 0.00 43.88 4.30
216 234 2.235898 ACAGCACCAGAGAAATCTCCTC 59.764 50.000 6.81 0.00 43.88 3.71
217 235 2.027377 CACAGCACCAGAGAAATCTCCT 60.027 50.000 6.81 0.00 43.88 3.69
289 310 4.475135 GAGGGAGGCAAGGTCGGC 62.475 72.222 0.00 0.00 0.00 5.54
296 317 4.760220 GGGGAGGGAGGGAGGCAA 62.760 72.222 0.00 0.00 0.00 4.52
308 329 4.320456 CGGCATGGATCCGGGGAG 62.320 72.222 7.39 0.00 42.99 4.30
311 332 4.996434 GAGCGGCATGGATCCGGG 62.996 72.222 7.39 2.37 46.51 5.73
393 416 7.414222 AATTTCATACTACCAGGAGTTACGA 57.586 36.000 0.00 0.00 0.00 3.43
394 417 7.762615 TGAAATTTCATACTACCAGGAGTTACG 59.237 37.037 16.91 0.00 31.01 3.18
395 418 9.099454 CTGAAATTTCATACTACCAGGAGTTAC 57.901 37.037 20.76 0.00 36.46 2.50
404 427 4.495844 GCGGTGCTGAAATTTCATACTACC 60.496 45.833 20.76 21.16 36.46 3.18
453 476 2.159179 AGCTGACCCTTTTGTGGTTT 57.841 45.000 0.00 0.00 35.85 3.27
464 487 6.168270 ACTTCTGAGAATAATAGCTGACCC 57.832 41.667 0.00 0.00 0.00 4.46
466 489 8.172352 TCCTACTTCTGAGAATAATAGCTGAC 57.828 38.462 0.00 0.00 0.00 3.51
473 498 7.468906 GCACGTACTCCTACTTCTGAGAATAAT 60.469 40.741 0.00 0.00 32.84 1.28
474 499 6.183360 GCACGTACTCCTACTTCTGAGAATAA 60.183 42.308 0.00 0.00 32.84 1.40
476 501 4.096682 GCACGTACTCCTACTTCTGAGAAT 59.903 45.833 0.00 0.00 32.84 2.40
527 585 6.014499 TCCTTCTCTTGTAGGACCTTTTACTG 60.014 42.308 0.00 0.00 35.28 2.74
554 615 1.632409 AGGTGGTCAAGTGCATCAGAT 59.368 47.619 0.00 0.00 0.00 2.90
560 621 1.148273 GGTCAGGTGGTCAAGTGCA 59.852 57.895 0.00 0.00 0.00 4.57
611 672 0.535780 TGGTGTGCTTCTGCCTTCTG 60.536 55.000 0.00 0.00 38.71 3.02
612 673 0.250640 CTGGTGTGCTTCTGCCTTCT 60.251 55.000 0.00 0.00 38.71 2.85
613 674 0.250467 TCTGGTGTGCTTCTGCCTTC 60.250 55.000 0.00 0.00 38.71 3.46
614 675 0.536006 GTCTGGTGTGCTTCTGCCTT 60.536 55.000 0.00 0.00 38.71 4.35
615 676 1.072159 GTCTGGTGTGCTTCTGCCT 59.928 57.895 0.00 0.00 38.71 4.75
616 677 0.952984 GAGTCTGGTGTGCTTCTGCC 60.953 60.000 0.00 0.00 38.71 4.85
617 678 0.250038 TGAGTCTGGTGTGCTTCTGC 60.250 55.000 0.00 0.00 40.20 4.26
678 739 5.299782 CGGTATGGAGCTTACCTATCTATCC 59.700 48.000 10.62 0.00 37.54 2.59
806 867 2.126888 GGTGTGGCGCATGTTTCG 60.127 61.111 10.83 0.00 0.00 3.46
967 1034 2.203139 TGGGCTTCGGTGTGTGTG 60.203 61.111 0.00 0.00 0.00 3.82
968 1035 2.111043 CTGGGCTTCGGTGTGTGT 59.889 61.111 0.00 0.00 0.00 3.72
1231 1299 5.762711 TGAACTGTCCGAGATGAATGAAAAA 59.237 36.000 0.00 0.00 0.00 1.94
1346 1422 7.308049 CGATTCACTAACTATAGTAGCTCTGCA 60.308 40.741 5.65 0.00 40.44 4.41
1372 1448 5.553123 TCTCATACTCCTACTAGCTAGCAC 58.447 45.833 20.91 0.00 0.00 4.40
1405 1481 5.363868 TCCCTCATACTGATGTTACTCTTGG 59.636 44.000 0.00 0.00 34.41 3.61
1491 1582 8.926092 ATACTGCTTCAGATACTATGTAGTCA 57.074 34.615 0.29 0.00 35.23 3.41
2162 2276 7.260387 TGATACTCAGGGGTAACAATAACAA 57.740 36.000 0.00 0.00 39.74 2.83
2167 2281 7.673926 ACAAATTTGATACTCAGGGGTAACAAT 59.326 33.333 24.64 0.00 35.50 2.71
2234 2348 5.221130 ACTCTGCTTTTACAAGTAGACGAC 58.779 41.667 5.43 0.00 44.30 4.34
2235 2349 5.449107 ACTCTGCTTTTACAAGTAGACGA 57.551 39.130 5.43 0.00 44.30 4.20
2236 2350 6.346678 GGAAACTCTGCTTTTACAAGTAGACG 60.347 42.308 5.43 5.39 44.30 4.18
2292 2406 1.007502 TACGTGTGTGTGTACGGCC 60.008 57.895 0.00 0.00 44.07 6.13
2381 2495 1.003233 GTTGGCCTGTCACTCTCCC 60.003 63.158 3.32 0.00 0.00 4.30
2450 2569 3.060000 GCCCTTTGCACGGGGTAC 61.060 66.667 19.24 4.24 44.25 3.34
2693 2814 3.714963 CACTGCATGCGCACGTCA 61.715 61.111 14.90 10.24 45.36 4.35
2746 2867 0.891373 CTCCGTCTGTGGACACTCAT 59.109 55.000 3.91 0.00 42.21 2.90
2758 2879 1.751162 CCTTCTCTCGCCTCCGTCT 60.751 63.158 0.00 0.00 35.54 4.18
2845 2966 2.745884 CAAGCACCGCCCGAATCA 60.746 61.111 0.00 0.00 0.00 2.57
2846 2967 2.435938 TCAAGCACCGCCCGAATC 60.436 61.111 0.00 0.00 0.00 2.52
2847 2968 2.746277 GTCAAGCACCGCCCGAAT 60.746 61.111 0.00 0.00 0.00 3.34
2859 2980 8.669712 CGTAAATCAACGGTTGACTGGTCAAG 62.670 46.154 24.56 8.81 43.48 3.02
2860 2981 2.631160 ATCAACGGTTGACTGGTCAA 57.369 45.000 24.56 11.53 46.27 3.18
2861 2982 2.631160 AATCAACGGTTGACTGGTCA 57.369 45.000 24.56 2.21 43.48 4.02
2862 2983 3.120786 CGTAAATCAACGGTTGACTGGTC 60.121 47.826 24.56 13.23 43.48 4.02
2863 2984 2.803956 CGTAAATCAACGGTTGACTGGT 59.196 45.455 24.56 12.73 43.48 4.00
2864 2985 3.449322 CGTAAATCAACGGTTGACTGG 57.551 47.619 24.56 9.64 43.48 4.00
2899 3020 9.994432 TGCACATTTTTCAATTAACGAATTTTT 57.006 22.222 0.00 0.00 32.73 1.94
2901 3022 9.596677 CATGCACATTTTTCAATTAACGAATTT 57.403 25.926 0.00 0.00 32.73 1.82
2902 3023 8.229137 CCATGCACATTTTTCAATTAACGAATT 58.771 29.630 0.00 0.00 35.56 2.17
2903 3024 7.387397 ACCATGCACATTTTTCAATTAACGAAT 59.613 29.630 0.00 0.00 0.00 3.34
2904 3025 6.703607 ACCATGCACATTTTTCAATTAACGAA 59.296 30.769 0.00 0.00 0.00 3.85
2905 3026 6.219473 ACCATGCACATTTTTCAATTAACGA 58.781 32.000 0.00 0.00 0.00 3.85
2906 3027 6.464895 ACCATGCACATTTTTCAATTAACG 57.535 33.333 0.00 0.00 0.00 3.18
2907 3028 9.513727 AAAAACCATGCACATTTTTCAATTAAC 57.486 25.926 10.00 0.00 31.52 2.01


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

AutoCloner maintained by Alex Coulton.