Multiple sequence alignment - TraesCS2D01G289400

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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 TraesCS2D01G289400 chr2D 100.000 3110 0 0 1 3110 371691024 371687915 0.000000e+00 5744.0
1 TraesCS2D01G289400 chr2D 84.889 225 30 4 2887 3110 75375994 75375773 1.120000e-54 224.0
2 TraesCS2D01G289400 chr2D 94.340 53 3 0 2885 2937 75376078 75376026 7.150000e-12 82.4
3 TraesCS2D01G289400 chr2A 92.159 2844 125 37 275 3072 502323480 502320689 0.000000e+00 3927.0
4 TraesCS2D01G289400 chr2A 82.222 270 8 13 11 241 502323741 502323473 2.450000e-46 196.0
5 TraesCS2D01G289400 chr2B 91.126 2930 108 42 1 2847 440766490 440763630 0.000000e+00 3831.0
6 TraesCS2D01G289400 chr4A 87.838 222 23 4 2887 3107 31578730 31578512 1.110000e-64 257.0
7 TraesCS2D01G289400 chr7D 84.015 269 34 7 2842 3107 169436981 169437243 1.850000e-62 250.0
8 TraesCS2D01G289400 chr7D 87.273 220 24 3 2889 3107 33224732 33224516 6.660000e-62 248.0
9 TraesCS2D01G289400 chr7D 82.394 284 30 11 2840 3107 602173961 602174240 2.410000e-56 230.0
10 TraesCS2D01G289400 chr4D 78.676 272 41 9 2850 3110 502078104 502077839 6.900000e-37 165.0
11 TraesCS2D01G289400 chr3D 78.112 233 31 8 2889 3107 481918889 481918663 2.520000e-26 130.0
12 TraesCS2D01G289400 chr5B 91.892 74 5 1 2887 2959 644464537 644464610 5.490000e-18 102.0


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 TraesCS2D01G289400 chr2D 371687915 371691024 3109 True 5744.0 5744 100.0000 1 3110 1 chr2D.!!$R1 3109
1 TraesCS2D01G289400 chr2A 502320689 502323741 3052 True 2061.5 3927 87.1905 11 3072 2 chr2A.!!$R1 3061
2 TraesCS2D01G289400 chr2B 440763630 440766490 2860 True 3831.0 3831 91.1260 1 2847 1 chr2B.!!$R1 2846

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
41 42 0.109551 CGTCGTGCTCTGATCACTGT 60.110 55.0 9.65 0.0 32.54 3.55 F
475 530 0.523072 GTGCAATCACGCATGGTCTT 59.477 50.0 0.00 0.0 45.26 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1381 2.281484 GTCTTGCCCTTGTGCGGA 60.281 61.111 0.0 0.0 0.00 5.54 R
2367 2472 0.539986 TCTCTATTTCCACCACGGGC 59.460 55.000 0.0 0.0 34.36 6.13 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
41 42 0.109551 CGTCGTGCTCTGATCACTGT 60.110 55.000 9.65 0.00 32.54 3.55
43 44 2.408050 GTCGTGCTCTGATCACTGTTT 58.592 47.619 9.65 0.00 32.54 2.83
185 225 3.570540 TGGACAAAAACCATGACCATCA 58.429 40.909 0.00 0.00 37.63 3.07
194 234 6.942532 AAACCATGACCATCATATGTGTAC 57.057 37.500 1.90 0.00 34.28 2.90
273 313 1.222300 TGCAACGCAGAAACATACGT 58.778 45.000 0.00 0.00 41.16 3.57
274 314 2.405172 TGCAACGCAGAAACATACGTA 58.595 42.857 0.00 0.00 37.87 3.57
275 315 2.156117 TGCAACGCAGAAACATACGTAC 59.844 45.455 0.00 0.00 37.87 3.67
276 316 2.778641 GCAACGCAGAAACATACGTACG 60.779 50.000 15.01 15.01 37.87 3.67
354 401 1.083657 CGCGTGCCGTGTAATATGC 60.084 57.895 0.00 0.00 32.40 3.14
436 491 7.615365 AGTGGTAATTTTCATCAAGCAGGATAA 59.385 33.333 0.00 0.00 0.00 1.75
444 499 9.679661 TTTTCATCAAGCAGGATAAATGTACTA 57.320 29.630 0.00 0.00 0.00 1.82
445 500 8.893219 TTCATCAAGCAGGATAAATGTACTAG 57.107 34.615 0.00 0.00 0.00 2.57
475 530 0.523072 GTGCAATCACGCATGGTCTT 59.477 50.000 0.00 0.00 45.26 3.01
872 939 3.825623 CATCCCCCAAGCTCCCCC 61.826 72.222 0.00 0.00 0.00 5.40
948 1015 2.047465 AGCAACTGAGCCGCTCTG 60.047 61.111 21.91 21.91 35.91 3.35
983 1050 0.729116 CGGCACAGCATTACCAAGAG 59.271 55.000 0.00 0.00 0.00 2.85
1200 1282 1.770324 CTCCAAGTCCAGCCCCTTT 59.230 57.895 0.00 0.00 0.00 3.11
1299 1381 2.769621 TCTGCCATGGCGATCCCT 60.770 61.111 30.87 0.00 45.51 4.20
1467 1549 1.151908 CCTCTACCCCTCCTCCTCG 59.848 68.421 0.00 0.00 0.00 4.63
1512 1594 2.206900 TCTCTGGCCAGTGGGGAA 59.793 61.111 31.58 11.07 40.01 3.97
1593 1675 4.292178 CGGAGGCTGGAGGCGATC 62.292 72.222 0.00 0.00 46.23 3.69
1992 2074 2.281484 GCGAGGGTTTCTGGCACA 60.281 61.111 0.00 0.00 45.05 4.57
2135 2235 4.105733 TTGGATTGCAGCTGCGCG 62.106 61.111 32.11 0.00 45.83 6.86
2192 2292 6.357198 GCTCTTCTTCTCGAACTATACTACG 58.643 44.000 0.00 0.00 0.00 3.51
2193 2293 6.018832 GCTCTTCTTCTCGAACTATACTACGT 60.019 42.308 0.00 0.00 0.00 3.57
2194 2294 7.168972 GCTCTTCTTCTCGAACTATACTACGTA 59.831 40.741 0.00 0.00 0.00 3.57
2195 2295 8.346476 TCTTCTTCTCGAACTATACTACGTAC 57.654 38.462 0.00 0.00 0.00 3.67
2244 2344 2.127708 ACTCCTGTTCTTGGTTCTGGT 58.872 47.619 0.00 0.00 0.00 4.00
2245 2345 3.314693 ACTCCTGTTCTTGGTTCTGGTA 58.685 45.455 0.00 0.00 0.00 3.25
2250 2352 4.576463 CCTGTTCTTGGTTCTGGTATATGC 59.424 45.833 0.00 0.00 0.00 3.14
2367 2472 3.319137 TCGAGATTTTCTCCTGTGGTG 57.681 47.619 0.00 0.00 40.34 4.17
2368 2473 1.734465 CGAGATTTTCTCCTGTGGTGC 59.266 52.381 0.00 0.00 40.34 5.01
2369 2474 2.087646 GAGATTTTCTCCTGTGGTGCC 58.912 52.381 0.00 0.00 37.55 5.01
2370 2475 1.177401 GATTTTCTCCTGTGGTGCCC 58.823 55.000 0.00 0.00 0.00 5.36
2400 2505 9.994432 GTGGAAATAGAGATGTTTTATGTTGAG 57.006 33.333 0.00 0.00 0.00 3.02
2514 2630 6.814644 TGTGCCTTGATTCATTTTTCATGATC 59.185 34.615 0.00 0.00 0.00 2.92
2517 2633 7.342541 TGCCTTGATTCATTTTTCATGATCCTA 59.657 33.333 0.00 0.00 0.00 2.94
2581 2699 1.808891 CGGACCCGTCAAAAGTGAGTT 60.809 52.381 0.00 0.00 33.27 3.01
2625 2743 1.465354 CGTCTACAACCGTCTTCCTCG 60.465 57.143 0.00 0.00 0.00 4.63
2677 2797 4.547966 GCAATGTAAAACAAACACACGCAG 60.548 41.667 0.00 0.00 0.00 5.18
2715 2835 5.814314 TGCAATGTAAAATAAACACACGC 57.186 34.783 0.00 0.00 0.00 5.34
2716 2836 5.281727 TGCAATGTAAAATAAACACACGCA 58.718 33.333 0.00 0.00 33.79 5.24
2937 3058 4.263506 CCATTTCTAGCCGATCCCCTAAAT 60.264 45.833 0.00 0.00 0.00 1.40
2941 3062 6.503560 TTCTAGCCGATCCCCTAAATTTAA 57.496 37.500 0.00 0.00 0.00 1.52
2942 3063 5.861727 TCTAGCCGATCCCCTAAATTTAAC 58.138 41.667 0.00 0.00 0.00 2.01
2984 3105 1.790755 TGCGTCACATACTCAACCAC 58.209 50.000 0.00 0.00 0.00 4.16
2985 3106 1.076332 GCGTCACATACTCAACCACC 58.924 55.000 0.00 0.00 0.00 4.61
2986 3107 1.346365 CGTCACATACTCAACCACCG 58.654 55.000 0.00 0.00 0.00 4.94
2987 3108 1.068125 CGTCACATACTCAACCACCGA 60.068 52.381 0.00 0.00 0.00 4.69
2988 3109 2.608506 CGTCACATACTCAACCACCGAA 60.609 50.000 0.00 0.00 0.00 4.30
2989 3110 3.395639 GTCACATACTCAACCACCGAAA 58.604 45.455 0.00 0.00 0.00 3.46
2990 3111 3.185797 GTCACATACTCAACCACCGAAAC 59.814 47.826 0.00 0.00 0.00 2.78
2991 3112 3.135225 CACATACTCAACCACCGAAACA 58.865 45.455 0.00 0.00 0.00 2.83
2992 3113 3.059188 CACATACTCAACCACCGAAACAC 60.059 47.826 0.00 0.00 0.00 3.32
2993 3114 2.983907 TACTCAACCACCGAAACACA 57.016 45.000 0.00 0.00 0.00 3.72
2994 3115 2.341846 ACTCAACCACCGAAACACAT 57.658 45.000 0.00 0.00 0.00 3.21
2995 3116 2.650322 ACTCAACCACCGAAACACATT 58.350 42.857 0.00 0.00 0.00 2.71
2996 3117 3.020984 ACTCAACCACCGAAACACATTT 58.979 40.909 0.00 0.00 0.00 2.32
2997 3118 3.445805 ACTCAACCACCGAAACACATTTT 59.554 39.130 0.00 0.00 0.00 1.82
2998 3119 4.035278 TCAACCACCGAAACACATTTTC 57.965 40.909 0.00 0.00 0.00 2.29
2999 3120 3.697045 TCAACCACCGAAACACATTTTCT 59.303 39.130 0.00 0.00 0.00 2.52
3000 3121 4.158764 TCAACCACCGAAACACATTTTCTT 59.841 37.500 0.00 0.00 0.00 2.52
3001 3122 5.357314 TCAACCACCGAAACACATTTTCTTA 59.643 36.000 0.00 0.00 0.00 2.10
3002 3123 5.177725 ACCACCGAAACACATTTTCTTAC 57.822 39.130 0.00 0.00 0.00 2.34
3003 3124 4.885325 ACCACCGAAACACATTTTCTTACT 59.115 37.500 0.00 0.00 0.00 2.24
3004 3125 5.358725 ACCACCGAAACACATTTTCTTACTT 59.641 36.000 0.00 0.00 0.00 2.24
3005 3126 6.127563 ACCACCGAAACACATTTTCTTACTTT 60.128 34.615 0.00 0.00 0.00 2.66
3006 3127 6.754675 CCACCGAAACACATTTTCTTACTTTT 59.245 34.615 0.00 0.00 0.00 2.27
3007 3128 7.276878 CCACCGAAACACATTTTCTTACTTTTT 59.723 33.333 0.00 0.00 0.00 1.94
3072 3193 1.608025 CGCCACTAGAGCAAGACCAAA 60.608 52.381 0.00 0.00 0.00 3.28
3073 3194 2.504367 GCCACTAGAGCAAGACCAAAA 58.496 47.619 0.00 0.00 0.00 2.44
3074 3195 2.884639 GCCACTAGAGCAAGACCAAAAA 59.115 45.455 0.00 0.00 0.00 1.94
3098 3219 9.581099 AAAAACAAGAACGACAATTAGACATTT 57.419 25.926 0.00 0.00 0.00 2.32
3099 3220 9.581099 AAAACAAGAACGACAATTAGACATTTT 57.419 25.926 0.00 0.00 0.00 1.82
3101 3222 9.878599 AACAAGAACGACAATTAGACATTTTAG 57.121 29.630 0.00 0.00 0.00 1.85
3102 3223 9.268268 ACAAGAACGACAATTAGACATTTTAGA 57.732 29.630 0.00 0.00 0.00 2.10
3105 3226 9.706691 AGAACGACAATTAGACATTTTAGAAGA 57.293 29.630 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 225 3.466836 CGGCAGTGATTGGTACACATAT 58.533 45.455 0.00 0.00 39.29 1.78
194 234 2.294791 TGTTTTAACCGGCAGTGATTGG 59.705 45.455 0.00 0.00 0.00 3.16
273 313 1.729517 CATTCATTGGTGTCGTGCGTA 59.270 47.619 0.00 0.00 0.00 4.42
274 314 0.516877 CATTCATTGGTGTCGTGCGT 59.483 50.000 0.00 0.00 0.00 5.24
275 315 0.795698 TCATTCATTGGTGTCGTGCG 59.204 50.000 0.00 0.00 0.00 5.34
276 316 2.031245 TGTTCATTCATTGGTGTCGTGC 60.031 45.455 0.00 0.00 0.00 5.34
369 416 1.136110 AGTGGGAAAAGGTTTGCGTTG 59.864 47.619 0.00 0.00 0.00 4.10
374 421 1.480137 TGCACAGTGGGAAAAGGTTTG 59.520 47.619 0.00 0.00 0.00 2.93
414 462 9.807649 ACATTTATCCTGCTTGATGAAAATTAC 57.192 29.630 0.00 0.00 0.00 1.89
444 499 0.999406 GATTGCACGTGCGATGTACT 59.001 50.000 40.67 22.66 44.75 2.73
445 500 0.718904 TGATTGCACGTGCGATGTAC 59.281 50.000 40.67 28.12 44.75 2.90
475 530 2.523168 TGCCACTGGGACGAGACA 60.523 61.111 0.00 0.00 35.59 3.41
670 726 1.553654 GTCATCGCATCGCACGTAC 59.446 57.895 0.00 0.00 0.00 3.67
671 727 1.587876 GGTCATCGCATCGCACGTA 60.588 57.895 0.00 0.00 0.00 3.57
672 728 2.885644 GGTCATCGCATCGCACGT 60.886 61.111 0.00 0.00 0.00 4.49
778 839 4.154347 GAGGAGCGGAGTGGCAGG 62.154 72.222 0.00 0.00 34.64 4.85
779 840 4.154347 GGAGGAGCGGAGTGGCAG 62.154 72.222 0.00 0.00 34.64 4.85
782 843 2.765807 ATGGGAGGAGCGGAGTGG 60.766 66.667 0.00 0.00 0.00 4.00
783 844 2.818132 GATGGGAGGAGCGGAGTG 59.182 66.667 0.00 0.00 0.00 3.51
784 845 2.648613 ATCGATGGGAGGAGCGGAGT 62.649 60.000 0.00 0.00 0.00 3.85
785 846 1.905843 ATCGATGGGAGGAGCGGAG 60.906 63.158 0.00 0.00 0.00 4.63
786 847 2.198703 ATCGATGGGAGGAGCGGA 59.801 61.111 0.00 0.00 0.00 5.54
787 848 2.341543 CATCGATGGGAGGAGCGG 59.658 66.667 17.96 0.00 0.00 5.52
788 849 2.356793 GCATCGATGGGAGGAGCG 60.357 66.667 26.00 0.00 0.00 5.03
789 850 1.005156 GAGCATCGATGGGAGGAGC 60.005 63.158 26.00 10.36 0.00 4.70
790 851 0.602562 GAGAGCATCGATGGGAGGAG 59.397 60.000 26.00 0.00 42.67 3.69
791 852 0.829602 GGAGAGCATCGATGGGAGGA 60.830 60.000 26.00 0.00 42.67 3.71
921 988 2.008329 GCTCAGTTGCTCTCTTGATGG 58.992 52.381 0.00 0.00 0.00 3.51
948 1015 4.933064 CGGATCTGGGACGCGAGC 62.933 72.222 15.93 3.71 0.00 5.03
955 1022 3.785859 GCTGTGCCGGATCTGGGA 61.786 66.667 22.38 17.35 0.00 4.37
997 1079 1.451028 GCGCTTTCTCCTCCATGCT 60.451 57.895 0.00 0.00 0.00 3.79
1299 1381 2.281484 GTCTTGCCCTTGTGCGGA 60.281 61.111 0.00 0.00 0.00 5.54
1975 2057 2.281484 TGTGCCAGAAACCCTCGC 60.281 61.111 0.00 0.00 0.00 5.03
2192 2292 7.441760 TCATACTAGTAGAAGCAGCAGTAGTAC 59.558 40.741 8.85 0.00 34.90 2.73
2193 2293 7.506971 TCATACTAGTAGAAGCAGCAGTAGTA 58.493 38.462 8.85 7.35 35.95 1.82
2194 2294 6.358178 TCATACTAGTAGAAGCAGCAGTAGT 58.642 40.000 8.85 0.00 33.90 2.73
2195 2295 6.869315 TCATACTAGTAGAAGCAGCAGTAG 57.131 41.667 8.85 0.00 0.00 2.57
2244 2344 3.506398 TCAGGACTCGAATGGGCATATA 58.494 45.455 0.00 0.00 0.00 0.86
2245 2345 2.301296 CTCAGGACTCGAATGGGCATAT 59.699 50.000 0.00 0.00 0.00 1.78
2250 2352 1.472376 GCTTCTCAGGACTCGAATGGG 60.472 57.143 0.00 0.00 0.00 4.00
2367 2472 0.539986 TCTCTATTTCCACCACGGGC 59.460 55.000 0.00 0.00 34.36 6.13
2368 2473 2.170607 ACATCTCTATTTCCACCACGGG 59.829 50.000 0.00 0.00 34.36 5.28
2369 2474 3.543680 ACATCTCTATTTCCACCACGG 57.456 47.619 0.00 0.00 0.00 4.94
2370 2475 5.880054 AAAACATCTCTATTTCCACCACG 57.120 39.130 0.00 0.00 0.00 4.94
2400 2505 2.096909 CGTCTCCAACACACGAATGAAC 60.097 50.000 0.00 0.00 35.49 3.18
2514 2630 4.999950 CCCGTAGTATAGTGTGGTAGTAGG 59.000 50.000 0.00 0.00 0.00 3.18
2517 2633 4.202441 CACCCGTAGTATAGTGTGGTAGT 58.798 47.826 0.00 0.00 0.00 2.73
2540 2658 3.181510 CGGTTGTAGATGCTTTAACAGGC 60.182 47.826 0.00 0.00 0.00 4.85
2581 2699 3.091545 GACATTTGAGATTTGAGGGGCA 58.908 45.455 0.00 0.00 0.00 5.36
2712 2832 2.108178 ATTTTTACGTTGCGTTGCGT 57.892 40.000 0.00 5.73 41.54 5.24
2713 2833 4.086227 TGTTTATTTTTACGTTGCGTTGCG 60.086 37.500 0.00 0.00 41.54 4.85
2714 2834 5.118307 GTGTTTATTTTTACGTTGCGTTGC 58.882 37.500 0.00 0.00 41.54 4.17
2715 2835 6.108471 GTGTGTTTATTTTTACGTTGCGTTG 58.892 36.000 0.00 0.00 41.54 4.10
2716 2836 5.053156 CGTGTGTTTATTTTTACGTTGCGTT 60.053 36.000 0.00 0.00 41.54 4.84
2806 2927 9.483916 TCGATAGTTCAAACTTTTAGAACATGA 57.516 29.630 0.00 0.00 43.00 3.07
2905 3026 3.961480 GGCTAGAAATGGCCAAAACTT 57.039 42.857 10.96 0.05 46.84 2.66
2913 3034 0.606673 GGGGATCGGCTAGAAATGGC 60.607 60.000 0.00 0.00 0.00 4.40
3005 3126 9.190858 CTCCAATGTCGTTGAATGAAATAAAAA 57.809 29.630 6.35 0.00 40.37 1.94
3006 3127 8.356657 ACTCCAATGTCGTTGAATGAAATAAAA 58.643 29.630 6.35 0.00 40.37 1.52
3007 3128 7.881142 ACTCCAATGTCGTTGAATGAAATAAA 58.119 30.769 6.35 0.00 40.37 1.40
3008 3129 7.447374 ACTCCAATGTCGTTGAATGAAATAA 57.553 32.000 6.35 0.00 40.37 1.40
3052 3173 0.037326 TTGGTCTTGCTCTAGTGGCG 60.037 55.000 0.00 0.00 0.00 5.69
3072 3193 9.581099 AAATGTCTAATTGTCGTTCTTGTTTTT 57.419 25.926 0.00 0.00 0.00 1.94
3073 3194 9.581099 AAAATGTCTAATTGTCGTTCTTGTTTT 57.419 25.926 0.00 0.00 0.00 2.43
3075 3196 9.878599 CTAAAATGTCTAATTGTCGTTCTTGTT 57.121 29.630 0.00 0.00 0.00 2.83
3076 3197 9.268268 TCTAAAATGTCTAATTGTCGTTCTTGT 57.732 29.630 0.00 0.00 0.00 3.16
3079 3200 9.706691 TCTTCTAAAATGTCTAATTGTCGTTCT 57.293 29.630 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.