Multiple sequence alignment - TraesCS2D01G266200

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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 TraesCS2D01G266200 chr2D 100.000 3479 0 0 1 3479 324863983 324860505 0 6425
1 TraesCS2D01G266200 chr2D 91.608 715 44 9 1 712 428621826 428622527 0 974
2 TraesCS2D01G266200 chr2D 90.443 722 60 6 1 722 275227271 275227983 0 942
3 TraesCS2D01G266200 chr2B 95.794 2734 91 8 754 3479 393861080 393858363 0 4390
4 TraesCS2D01G266200 chr2A 96.162 1850 56 4 719 2566 393339292 393341128 0 3009
5 TraesCS2D01G266200 chr2A 92.375 918 47 8 2565 3479 393341186 393342083 0 1286
6 TraesCS2D01G266200 chr3B 91.330 1857 133 20 778 2617 642487124 642485279 0 2512
7 TraesCS2D01G266200 chr3D 91.653 1821 123 15 765 2568 481517084 481515276 0 2494
8 TraesCS2D01G266200 chr3A 90.356 1856 153 16 778 2618 624530274 624528430 0 2412
9 TraesCS2D01G266200 chr1B 91.978 723 50 7 1 718 677029007 677028288 0 1007
10 TraesCS2D01G266200 chrUn 92.000 725 44 8 1 723 95416692 95417404 0 1005
11 TraesCS2D01G266200 chr5D 91.643 718 51 4 1 717 16588631 16589340 0 985
12 TraesCS2D01G266200 chr5D 90.456 723 60 8 4 725 438193222 438192508 0 944
13 TraesCS2D01G266200 chr1D 91.226 718 50 7 1 717 56231960 56232665 0 965
14 TraesCS2D01G266200 chr4B 90.411 730 61 9 1 725 114953734 114953009 0 952
15 TraesCS2D01G266200 chr5B 90.483 725 61 7 1 721 78441633 78440913 0 950
16 TraesCS2D01G266200 chr6A 96.491 456 13 3 2452 2905 4814987 4814533 0 750


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 TraesCS2D01G266200 chr2D 324860505 324863983 3478 True 6425.0 6425 100.0000 1 3479 1 chr2D.!!$R1 3478
1 TraesCS2D01G266200 chr2D 428621826 428622527 701 False 974.0 974 91.6080 1 712 1 chr2D.!!$F2 711
2 TraesCS2D01G266200 chr2D 275227271 275227983 712 False 942.0 942 90.4430 1 722 1 chr2D.!!$F1 721
3 TraesCS2D01G266200 chr2B 393858363 393861080 2717 True 4390.0 4390 95.7940 754 3479 1 chr2B.!!$R1 2725
4 TraesCS2D01G266200 chr2A 393339292 393342083 2791 False 2147.5 3009 94.2685 719 3479 2 chr2A.!!$F1 2760
5 TraesCS2D01G266200 chr3B 642485279 642487124 1845 True 2512.0 2512 91.3300 778 2617 1 chr3B.!!$R1 1839
6 TraesCS2D01G266200 chr3D 481515276 481517084 1808 True 2494.0 2494 91.6530 765 2568 1 chr3D.!!$R1 1803
7 TraesCS2D01G266200 chr3A 624528430 624530274 1844 True 2412.0 2412 90.3560 778 2618 1 chr3A.!!$R1 1840
8 TraesCS2D01G266200 chr1B 677028288 677029007 719 True 1007.0 1007 91.9780 1 718 1 chr1B.!!$R1 717
9 TraesCS2D01G266200 chrUn 95416692 95417404 712 False 1005.0 1005 92.0000 1 723 1 chrUn.!!$F1 722
10 TraesCS2D01G266200 chr5D 16588631 16589340 709 False 985.0 985 91.6430 1 717 1 chr5D.!!$F1 716
11 TraesCS2D01G266200 chr5D 438192508 438193222 714 True 944.0 944 90.4560 4 725 1 chr5D.!!$R1 721
12 TraesCS2D01G266200 chr1D 56231960 56232665 705 False 965.0 965 91.2260 1 717 1 chr1D.!!$F1 716
13 TraesCS2D01G266200 chr4B 114953009 114953734 725 True 952.0 952 90.4110 1 725 1 chr4B.!!$R1 724
14 TraesCS2D01G266200 chr5B 78440913 78441633 720 True 950.0 950 90.4830 1 721 1 chr5B.!!$R1 720

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
149 160 0.690762 ACTACTCGCACCAACCCAAT 59.309 50.0 0.0 0.0 0.00 3.16 F
446 469 0.753111 CCATGGCAACTAGGGAAGGC 60.753 60.0 0.0 0.0 37.61 4.35 F
1002 1045 2.054232 AGCATTGGAGAGCTTGGATG 57.946 50.0 0.0 0.0 38.01 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1144 1.538204 GGCGCCGATTGTCTTGAGATA 60.538 52.381 12.58 0.0 0.0 1.98 R
1739 1784 1.680207 GCTTCTCCTTGATGATTGCCC 59.320 52.381 0.00 0.0 0.0 5.36 R
2605 2720 0.938637 CTGCGCGTTGCCAAATTTCA 60.939 50.000 8.43 0.0 45.6 2.69 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
149 160 0.690762 ACTACTCGCACCAACCCAAT 59.309 50.000 0.00 0.00 0.00 3.16
175 186 4.644685 AGAAGCTTAGCTCAACTCTAGGAG 59.355 45.833 7.36 0.00 38.25 3.69
208 219 1.195442 TCTGGCGTATGTTGGTGGGA 61.195 55.000 0.00 0.00 0.00 4.37
266 278 1.834188 TGACAGCGTGGATCTAGTCA 58.166 50.000 0.00 0.00 34.02 3.41
446 469 0.753111 CCATGGCAACTAGGGAAGGC 60.753 60.000 0.00 0.00 37.61 4.35
573 596 3.576356 GTCGATCGCCCGGACGTA 61.576 66.667 10.78 0.00 0.00 3.57
767 791 9.525826 GGTGAGGATGGATTAATTAATCATCTT 57.474 33.333 30.09 25.16 42.92 2.40
830 866 2.754472 TCCATCGTAAGCATGATTCCG 58.246 47.619 0.00 0.00 37.18 4.30
843 879 4.321230 GCATGATTCCGTCCAATAATTCCC 60.321 45.833 0.00 0.00 0.00 3.97
1002 1045 2.054232 AGCATTGGAGAGCTTGGATG 57.946 50.000 0.00 0.00 38.01 3.51
1284 1328 2.365105 CTCCCCACGGCCTTCCTA 60.365 66.667 0.00 0.00 0.00 2.94
1909 1954 1.899437 CGCCAGCCTCCTTACCTTCA 61.899 60.000 0.00 0.00 0.00 3.02
1969 2014 0.463654 AGTCGTGGCAGAGCAACAAA 60.464 50.000 0.00 0.00 30.74 2.83
2425 2470 2.068821 GCTCAGGGGCTCCTCATCA 61.069 63.158 0.00 0.00 42.67 3.07
2433 2478 1.134401 GGGCTCCTCATCAACATCGAA 60.134 52.381 0.00 0.00 0.00 3.71
2456 2503 3.476552 CAATAGACACAACCACCACAGT 58.523 45.455 0.00 0.00 0.00 3.55
2483 2530 3.677700 GCAGGCATCAGCAAATGATTTCA 60.678 43.478 2.77 0.00 46.97 2.69
2486 2533 4.933400 AGGCATCAGCAAATGATTTCAAAC 59.067 37.500 2.77 0.00 46.97 2.93
2605 2720 8.031277 GCCAAGTATTTCTCACATTCTTGAAAT 58.969 33.333 0.00 0.00 40.69 2.17
2756 2871 1.826385 GGCATAACCAGCAACACTCT 58.174 50.000 0.00 0.00 38.86 3.24
2842 2957 6.512297 GGATTTTCTCCTCTACTAGAGCAAG 58.488 44.000 7.50 7.28 40.98 4.01
2890 3006 3.312421 CAGAACAAGCAGAAGACGGAAAA 59.688 43.478 0.00 0.00 0.00 2.29
2897 3013 4.137543 AGCAGAAGACGGAAAATTCACTT 58.862 39.130 0.00 0.00 0.00 3.16
2963 3079 5.977129 ACACTTCGATGATTTTGGAAAACAC 59.023 36.000 5.16 0.00 0.00 3.32
2964 3080 5.976534 CACTTCGATGATTTTGGAAAACACA 59.023 36.000 5.16 0.00 0.00 3.72
2965 3081 5.977129 ACTTCGATGATTTTGGAAAACACAC 59.023 36.000 5.16 0.00 0.00 3.82
2966 3082 5.506686 TCGATGATTTTGGAAAACACACA 57.493 34.783 0.00 0.00 0.00 3.72
2967 3083 5.518812 TCGATGATTTTGGAAAACACACAG 58.481 37.500 0.00 0.00 0.00 3.66
2968 3084 4.148696 CGATGATTTTGGAAAACACACAGC 59.851 41.667 0.00 0.00 0.00 4.40
2969 3085 4.734398 TGATTTTGGAAAACACACAGCT 57.266 36.364 0.00 0.00 0.00 4.24
2970 3086 4.681744 TGATTTTGGAAAACACACAGCTC 58.318 39.130 0.00 0.00 0.00 4.09
2971 3087 4.159321 TGATTTTGGAAAACACACAGCTCA 59.841 37.500 0.00 0.00 0.00 4.26
2972 3088 4.527509 TTTTGGAAAACACACAGCTCAA 57.472 36.364 0.00 0.00 0.00 3.02
2973 3089 4.527509 TTTGGAAAACACACAGCTCAAA 57.472 36.364 0.00 0.00 0.00 2.69
2974 3090 3.502191 TGGAAAACACACAGCTCAAAC 57.498 42.857 0.00 0.00 0.00 2.93
2975 3091 2.822561 TGGAAAACACACAGCTCAAACA 59.177 40.909 0.00 0.00 0.00 2.83
3016 3145 5.163258 ACCAGACATGTAAAATTTTGGGCAA 60.163 36.000 13.76 0.00 0.00 4.52
3225 3355 9.931210 GAAGTAATTCTACAAAAATACCATCGG 57.069 33.333 0.00 0.00 0.00 4.18
3227 3357 8.889717 AGTAATTCTACAAAAATACCATCGGTG 58.110 33.333 0.00 0.00 36.19 4.94
3243 3373 1.670811 CGGTGCCATGGTAATGACTTC 59.329 52.381 14.67 0.00 35.67 3.01
3245 3375 3.356290 GGTGCCATGGTAATGACTTCTT 58.644 45.455 14.67 0.00 35.67 2.52
3419 3550 4.623595 CACAAGTATATACACGTGCACACA 59.376 41.667 17.22 0.00 31.98 3.72
3454 3590 7.126061 TCTGGAAGAAGATCTGTAGACCATAA 58.874 38.462 0.00 0.00 42.31 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 160 3.169099 AGAGTTGAGCTAAGCTTCTGGA 58.831 45.455 0.00 0.00 39.88 3.86
175 186 2.289320 ACGCCAGATCTGCCATATTCTC 60.289 50.000 17.76 0.00 0.00 2.87
239 251 0.821301 TCCACGCTGTCATGGCAAAA 60.821 50.000 0.00 0.00 35.81 2.44
266 278 0.620556 AGATTGCCCACGAAGATGGT 59.379 50.000 0.00 0.00 38.16 3.55
398 421 3.686045 GATCCCTAGCGCCTCCCG 61.686 72.222 2.29 0.00 40.75 5.14
440 463 1.144936 CCTCCATCGTCTGCCTTCC 59.855 63.158 0.00 0.00 0.00 3.46
446 469 0.106167 TCCCCTACCTCCATCGTCTG 60.106 60.000 0.00 0.00 0.00 3.51
727 751 6.210584 TCCATCCTCACCTAAAAATTTTGACC 59.789 38.462 3.73 0.00 0.00 4.02
740 764 8.898728 AGATGATTAATTAATCCATCCTCACCT 58.101 33.333 27.53 9.13 40.98 4.00
767 791 2.365293 TGAGCAGCTACAGAGACAACAA 59.635 45.455 0.00 0.00 0.00 2.83
830 866 9.750125 GTTTATTTCTGATGGGAATTATTGGAC 57.250 33.333 0.00 0.00 0.00 4.02
1002 1045 3.895998 AGCCTCCATTTCCATCTTCTTC 58.104 45.455 0.00 0.00 0.00 2.87
1100 1144 1.538204 GGCGCCGATTGTCTTGAGATA 60.538 52.381 12.58 0.00 0.00 1.98
1297 1341 2.367567 TGGCGAAGAGGAACTTGTTAGT 59.632 45.455 0.00 0.00 41.55 2.24
1299 1343 2.870435 GCTGGCGAAGAGGAACTTGTTA 60.870 50.000 0.00 0.00 41.55 2.41
1739 1784 1.680207 GCTTCTCCTTGATGATTGCCC 59.320 52.381 0.00 0.00 0.00 5.36
1969 2014 2.348998 CTTGCTCCTGGCGACCTT 59.651 61.111 0.00 0.00 45.43 3.50
2425 2470 4.454504 GGTTGTGTCTATTGGTTCGATGTT 59.545 41.667 0.00 0.00 0.00 2.71
2433 2478 2.173782 TGTGGTGGTTGTGTCTATTGGT 59.826 45.455 0.00 0.00 0.00 3.67
2483 2530 5.741011 TCGGATCAGGCTACTAAATTGTTT 58.259 37.500 0.00 0.00 0.00 2.83
2486 2533 5.991606 TCATTCGGATCAGGCTACTAAATTG 59.008 40.000 0.00 0.00 0.00 2.32
2605 2720 0.938637 CTGCGCGTTGCCAAATTTCA 60.939 50.000 8.43 0.00 45.60 2.69
2756 2871 2.230992 GCACTTGCCATGTTTACCATCA 59.769 45.455 0.00 0.00 34.31 3.07
2842 2957 1.546029 GGTGGAATTTGGTTGAGAGCC 59.454 52.381 0.00 0.00 0.00 4.70
2890 3006 3.117131 CCAGGGGCCCTATAAAAGTGAAT 60.117 47.826 28.28 0.00 29.64 2.57
2897 3013 1.518367 CAGTCCAGGGGCCCTATAAA 58.482 55.000 28.28 8.11 29.64 1.40
2950 3066 4.734398 TGAGCTGTGTGTTTTCCAAAAT 57.266 36.364 0.00 0.00 0.00 1.82
2963 3079 0.956633 ATGCTGGTGTTTGAGCTGTG 59.043 50.000 0.00 0.00 36.11 3.66
2964 3080 1.610522 GAATGCTGGTGTTTGAGCTGT 59.389 47.619 0.00 0.00 36.11 4.40
2965 3081 1.610038 TGAATGCTGGTGTTTGAGCTG 59.390 47.619 0.00 0.00 36.11 4.24
2966 3082 1.884579 CTGAATGCTGGTGTTTGAGCT 59.115 47.619 0.00 0.00 36.11 4.09
2967 3083 1.668047 GCTGAATGCTGGTGTTTGAGC 60.668 52.381 0.00 0.00 38.95 4.26
2968 3084 2.342910 GCTGAATGCTGGTGTTTGAG 57.657 50.000 0.00 0.00 38.95 3.02
3016 3145 8.854117 GCTTAGAATAATGGATGAACTTGGAAT 58.146 33.333 0.00 0.00 0.00 3.01
3068 3197 7.036220 CGCAATATCACCCTATTAACTAGAGG 58.964 42.308 0.00 0.00 0.00 3.69
3225 3355 4.009675 TCAAGAAGTCATTACCATGGCAC 58.990 43.478 13.04 0.77 37.49 5.01
3227 3357 4.641989 ACATCAAGAAGTCATTACCATGGC 59.358 41.667 13.04 0.00 34.94 4.40
3330 3460 4.689612 TCTTACTTGATCATAGGTGGCC 57.310 45.455 0.00 0.00 0.00 5.36
3388 3519 7.680350 GCACGTGTATATACTTGTGTCCTTCTA 60.680 40.741 25.36 0.24 35.74 2.10
3393 3524 4.266976 GTGCACGTGTATATACTTGTGTCC 59.733 45.833 25.36 17.64 35.74 4.02
3419 3550 2.435805 TCTTCTTCCAGAACAGTGCACT 59.564 45.455 15.25 15.25 29.89 4.40


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

AutoCloner maintained by Alex Coulton.