Multiple sequence alignment - TraesCS2D01G393200

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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 TraesCS2D01G393200 chr2D 100.000 3057 0 0 828 3884 502108894 502111950 0.000000e+00 5646
1 TraesCS2D01G393200 chr2D 100.000 617 0 0 1 617 502108067 502108683 0.000000e+00 1140
2 TraesCS2D01G393200 chr2B 95.110 3088 102 19 830 3884 589211584 589214655 0.000000e+00 4820
3 TraesCS2D01G393200 chr2B 88.264 605 27 25 1 590 589210768 589211343 0.000000e+00 684
4 TraesCS2D01G393200 chr2A 94.042 3105 88 37 830 3884 647345110 647348167 0.000000e+00 4619
5 TraesCS2D01G393200 chr2A 84.520 646 55 20 1 617 647344292 647344921 7.180000e-167 597
6 TraesCS2D01G393200 chr1D 94.216 536 24 3 2681 3216 215044105 215043577 0.000000e+00 811
7 TraesCS2D01G393200 chr1D 88.976 127 13 1 2715 2841 113492871 113492996 5.200000e-34 156
8 TraesCS2D01G393200 chr5D 93.600 125 8 0 2715 2839 321681930 321682054 1.840000e-43 187
9 TraesCS2D01G393200 chr6D 88.976 127 14 0 2715 2841 185870425 185870299 1.440000e-34 158
10 TraesCS2D01G393200 chr4D 78.992 238 32 8 2714 2943 435186147 435185920 3.130000e-31 147
11 TraesCS2D01G393200 chr4A 79.310 203 30 7 2716 2910 36538936 36538738 8.760000e-27 132


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 TraesCS2D01G393200 chr2D 502108067 502111950 3883 False 3393 5646 100.000 1 3884 2 chr2D.!!$F1 3883
1 TraesCS2D01G393200 chr2B 589210768 589214655 3887 False 2752 4820 91.687 1 3884 2 chr2B.!!$F1 3883
2 TraesCS2D01G393200 chr2A 647344292 647348167 3875 False 2608 4619 89.281 1 3884 2 chr2A.!!$F1 3883
3 TraesCS2D01G393200 chr1D 215043577 215044105 528 True 811 811 94.216 2681 3216 1 chr1D.!!$R1 535

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
176 201 0.326927 TCCTTCCCTTTCGCCGAATT 59.673 50.000 0.00 0.00 0.00 2.17 F
327 365 0.515717 CGTTCGAAATTCACGCGACC 60.516 55.000 15.93 0.00 33.33 4.79 F
892 960 1.135315 CATTTGCGTTCGGAGCCAG 59.865 57.895 0.00 0.00 0.00 4.85 F
905 973 1.614413 GGAGCCAGGAGTAGTATTCCG 59.386 57.143 6.08 2.18 39.77 4.30 F
2572 2659 2.032620 ACTACGGAGCCATTCTCGATT 58.967 47.619 0.00 0.00 42.82 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1809 1.446272 CGAGGAAGAAGCCGTGGAC 60.446 63.158 0.00 0.0 0.00 4.02 R
1984 2071 2.676265 GGGACCCGGTATGGTGCTT 61.676 63.158 0.00 0.0 45.31 3.91 R
2544 2631 0.530744 TGGCTCCGTAGTGCAAGTAG 59.469 55.000 0.00 0.0 34.10 2.57 R
2799 2886 1.079405 TTGATTCACGACGAGGCCC 60.079 57.895 0.00 0.0 0.00 5.80 R
3502 3618 2.839486 TTTCGTGCACCATCTCTTCT 57.161 45.000 12.15 0.0 0.00 2.85 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
66 72 4.015406 CACAGCCCTACCGCCACA 62.015 66.667 0.00 0.00 0.00 4.17
101 126 2.325509 AAATTGTTTCGCACCGCTAC 57.674 45.000 0.00 0.00 0.00 3.58
103 128 2.373540 ATTGTTTCGCACCGCTACTA 57.626 45.000 0.00 0.00 0.00 1.82
104 129 1.705256 TTGTTTCGCACCGCTACTAG 58.295 50.000 0.00 0.00 0.00 2.57
105 130 0.734942 TGTTTCGCACCGCTACTAGC 60.735 55.000 0.00 0.00 38.02 3.42
106 131 0.458025 GTTTCGCACCGCTACTAGCT 60.458 55.000 6.50 0.00 39.60 3.32
107 132 0.457853 TTTCGCACCGCTACTAGCTG 60.458 55.000 6.50 2.36 39.60 4.24
108 133 1.592400 TTCGCACCGCTACTAGCTGT 61.592 55.000 6.50 3.00 39.28 4.40
109 134 0.745486 TCGCACCGCTACTAGCTGTA 60.745 55.000 4.94 0.00 36.51 2.74
125 150 4.995124 AGCTGTAGTACTAACACCAATCG 58.005 43.478 3.61 0.00 0.00 3.34
136 161 7.513371 ACTAACACCAATCGGTTGATAAAAA 57.487 32.000 10.75 0.00 46.31 1.94
176 201 0.326927 TCCTTCCCTTTCGCCGAATT 59.673 50.000 0.00 0.00 0.00 2.17
267 292 3.607661 GATCTCCCGCCCTCCGAC 61.608 72.222 0.00 0.00 40.02 4.79
296 321 2.268076 ACCCGCAAACATCACCTGC 61.268 57.895 0.00 0.00 0.00 4.85
297 322 2.568090 CCGCAAACATCACCTGCC 59.432 61.111 0.00 0.00 32.27 4.85
299 324 2.126346 GCAAACATCACCTGCCGC 60.126 61.111 0.00 0.00 0.00 6.53
302 327 2.629656 AAACATCACCTGCCGCTGC 61.630 57.895 0.00 0.00 38.26 5.25
325 363 0.706184 CTCGTTCGAAATTCACGCGA 59.294 50.000 15.93 1.71 33.85 5.87
327 365 0.515717 CGTTCGAAATTCACGCGACC 60.516 55.000 15.93 0.00 33.33 4.79
349 387 2.584418 CTCGCATCGCAGGTGAGG 60.584 66.667 0.00 0.00 38.82 3.86
352 390 4.101448 GCATCGCAGGTGAGGGGT 62.101 66.667 0.00 0.00 0.00 4.95
353 391 2.124983 CATCGCAGGTGAGGGGTG 60.125 66.667 0.00 0.00 0.00 4.61
354 392 3.402681 ATCGCAGGTGAGGGGTGG 61.403 66.667 0.00 0.00 0.00 4.61
355 393 4.954118 TCGCAGGTGAGGGGTGGT 62.954 66.667 0.00 0.00 0.00 4.16
374 415 4.994471 TGCTGTGCCGTGGAGCTG 62.994 66.667 0.00 0.00 33.66 4.24
584 639 1.488393 TCACACCATTCACTCACCACA 59.512 47.619 0.00 0.00 0.00 4.17
890 958 2.202479 GCATTTGCGTTCGGAGCC 60.202 61.111 0.00 0.00 0.00 4.70
891 959 2.976840 GCATTTGCGTTCGGAGCCA 61.977 57.895 0.00 0.00 0.00 4.75
892 960 1.135315 CATTTGCGTTCGGAGCCAG 59.865 57.895 0.00 0.00 0.00 4.85
893 961 2.040544 ATTTGCGTTCGGAGCCAGG 61.041 57.895 0.00 0.00 0.00 4.45
894 962 2.463589 ATTTGCGTTCGGAGCCAGGA 62.464 55.000 0.00 0.00 0.00 3.86
895 963 3.589654 TTGCGTTCGGAGCCAGGAG 62.590 63.158 0.00 0.00 0.00 3.69
905 973 1.614413 GGAGCCAGGAGTAGTATTCCG 59.386 57.143 6.08 2.18 39.77 4.30
1722 1809 2.501222 CCGTCGAACTCGTCCACG 60.501 66.667 0.00 2.28 40.80 4.94
2241 2328 3.068691 TCCCTAGCAGCGACGCTT 61.069 61.111 21.97 9.72 43.56 4.68
2351 2438 2.440980 GGCATCCAAGCTGGGGTC 60.441 66.667 7.48 0.00 38.32 4.46
2572 2659 2.032620 ACTACGGAGCCATTCTCGATT 58.967 47.619 0.00 0.00 42.82 3.34
2909 2996 4.256090 GGTCGCGCCATCATTGCC 62.256 66.667 13.61 0.00 37.17 4.52
2910 2997 3.507924 GTCGCGCCATCATTGCCA 61.508 61.111 0.00 0.00 0.00 4.92
2911 2998 2.516695 TCGCGCCATCATTGCCAT 60.517 55.556 0.00 0.00 0.00 4.40
2912 2999 2.120282 TCGCGCCATCATTGCCATT 61.120 52.632 0.00 0.00 0.00 3.16
2913 3000 1.947146 CGCGCCATCATTGCCATTG 60.947 57.895 0.00 0.00 0.00 2.82
2914 3001 2.241880 GCGCCATCATTGCCATTGC 61.242 57.895 0.00 0.00 38.26 3.56
2965 3052 3.813724 GCACCCGTCCTCTATTTTTATCC 59.186 47.826 0.00 0.00 0.00 2.59
3013 3103 5.335191 GGTGTGATGAGTTTGTTCTTGATCC 60.335 44.000 0.00 0.00 0.00 3.36
3126 3216 0.179020 TGTCACCTGTTGCTTGGAGG 60.179 55.000 0.00 0.00 0.00 4.30
3146 3236 2.610727 GGAGTTGTAGATAGCATCGGCC 60.611 54.545 0.00 0.00 42.56 6.13
3321 3414 1.068055 CGTGCTACTTTCGGGTGTACT 60.068 52.381 0.00 0.00 0.00 2.73
3365 3469 8.295288 GGTCATGCTTGTACGTAATACTAGTAT 58.705 37.037 9.71 9.71 40.64 2.12
3502 3618 1.004745 GTTGGAAGGATGGCTGGAAGA 59.995 52.381 0.00 0.00 34.07 2.87
3810 3940 2.223377 GGTCACCAATGTCGAACTTGTC 59.777 50.000 0.00 0.00 0.00 3.18
3839 3969 2.436646 CCATTTCCTGCGTCGCCT 60.437 61.111 15.88 0.00 0.00 5.52
3871 4001 3.067742 TCGCTGGTATCAGTTACTTAGCC 59.932 47.826 4.60 0.00 42.78 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 126 6.200100 CGATTGGTGTTAGTACTACAGCTAG 58.800 44.000 23.04 13.99 42.77 3.42
103 128 4.142227 CCGATTGGTGTTAGTACTACAGCT 60.142 45.833 23.04 12.34 42.77 4.24
104 129 4.110482 CCGATTGGTGTTAGTACTACAGC 58.890 47.826 19.22 19.22 42.67 4.40
136 161 1.494721 ACAGATGGCGGGGTATCAATT 59.505 47.619 0.00 0.00 0.00 2.32
144 169 1.452108 GAAGGAACAGATGGCGGGG 60.452 63.158 0.00 0.00 0.00 5.73
176 201 1.048601 AGAAGTCGCAGTCCCTTTCA 58.951 50.000 0.00 0.00 0.00 2.69
299 324 0.798776 AATTTCGAACGAGGCAGCAG 59.201 50.000 0.00 0.00 0.00 4.24
302 327 1.201812 CGTGAATTTCGAACGAGGCAG 60.202 52.381 0.00 0.00 39.64 4.85
305 330 0.246757 CGCGTGAATTTCGAACGAGG 60.247 55.000 10.57 0.00 39.64 4.63
308 343 0.515717 GGTCGCGTGAATTTCGAACG 60.516 55.000 5.77 0.00 40.22 3.95
353 391 4.927782 TCCACGGCACAGCACACC 62.928 66.667 0.00 0.00 0.00 4.16
354 392 3.349006 CTCCACGGCACAGCACAC 61.349 66.667 0.00 0.00 0.00 3.82
464 509 3.756727 GGCTCTGCCTTGCCTTGC 61.757 66.667 0.73 0.00 46.69 4.01
584 639 1.746220 TGCTAAAATAAATGCGCGGGT 59.254 42.857 8.83 0.00 0.00 5.28
827 895 4.083484 GCTATAAACGGGTGCCATTCATAC 60.083 45.833 0.00 0.00 0.00 2.39
828 896 4.069304 GCTATAAACGGGTGCCATTCATA 58.931 43.478 0.00 0.00 0.00 2.15
890 958 1.269831 GGCAGCGGAATACTACTCCTG 60.270 57.143 0.00 0.00 0.00 3.86
891 959 1.041437 GGCAGCGGAATACTACTCCT 58.959 55.000 0.00 0.00 0.00 3.69
892 960 0.033642 GGGCAGCGGAATACTACTCC 59.966 60.000 0.00 0.00 0.00 3.85
893 961 0.033642 GGGGCAGCGGAATACTACTC 59.966 60.000 0.00 0.00 0.00 2.59
894 962 0.398664 AGGGGCAGCGGAATACTACT 60.399 55.000 0.00 0.00 0.00 2.57
895 963 0.249911 CAGGGGCAGCGGAATACTAC 60.250 60.000 0.00 0.00 0.00 2.73
985 1060 3.869272 CATGCAGGCGAGGCGAAC 61.869 66.667 0.00 0.00 0.00 3.95
1104 1179 4.394712 CGCTTGAGAACCCCGCCT 62.395 66.667 0.00 0.00 0.00 5.52
1163 1238 2.435586 GCTCCTGCTGCATGACGT 60.436 61.111 1.31 0.00 36.03 4.34
1658 1745 7.977853 TGTAGTTGTTCTTATTATTCGGAGTCC 59.022 37.037 0.00 0.00 0.00 3.85
1668 1755 3.861113 CCGCGCTGTAGTTGTTCTTATTA 59.139 43.478 5.56 0.00 0.00 0.98
1722 1809 1.446272 CGAGGAAGAAGCCGTGGAC 60.446 63.158 0.00 0.00 0.00 4.02
1984 2071 2.676265 GGGACCCGGTATGGTGCTT 61.676 63.158 0.00 0.00 45.31 3.91
2544 2631 0.530744 TGGCTCCGTAGTGCAAGTAG 59.469 55.000 0.00 0.00 34.10 2.57
2572 2659 1.228033 TGACCGTCGAGTCCAGTGA 60.228 57.895 10.19 0.00 35.83 3.41
2679 2766 3.282745 GAAGACCTCGCACCGCTCA 62.283 63.158 0.00 0.00 0.00 4.26
2799 2886 1.079405 TTGATTCACGACGAGGCCC 60.079 57.895 0.00 0.00 0.00 5.80
2909 2996 1.597797 ATTGTCTGGTGCCGGCAATG 61.598 55.000 34.66 23.34 32.28 2.82
2910 2997 0.899717 AATTGTCTGGTGCCGGCAAT 60.900 50.000 34.66 16.99 33.69 3.56
2911 2998 1.530419 AATTGTCTGGTGCCGGCAA 60.530 52.632 34.66 16.92 0.00 4.52
2912 2999 2.115052 AATTGTCTGGTGCCGGCA 59.885 55.556 29.03 29.03 0.00 5.69
2913 3000 2.568090 CAATTGTCTGGTGCCGGC 59.432 61.111 22.73 22.73 0.00 6.13
2914 3001 1.526575 AAGCAATTGTCTGGTGCCGG 61.527 55.000 7.40 0.00 39.13 6.13
2965 3052 6.308766 CCTTGCCAATCGAACAAATAAGAAAG 59.691 38.462 0.00 0.00 0.00 2.62
3013 3103 4.735822 CGCTACAGCTAAGCTTTACTACTG 59.264 45.833 3.20 8.18 36.40 2.74
3077 3167 5.643664 ACAACGACAATCAGTAGCGTAATA 58.356 37.500 0.00 0.00 34.46 0.98
3126 3216 2.678324 GGCCGATGCTATCTACAACTC 58.322 52.381 0.00 0.00 37.74 3.01
3146 3236 4.129737 ACGCGGTGGAGTGGATCG 62.130 66.667 12.47 0.00 0.00 3.69
3165 3255 4.992319 TGTACAAGTGTATGTAGCCACAAC 59.008 41.667 0.00 0.00 38.42 3.32
3321 3414 3.317711 TGACCAACTACTTTTACCGACGA 59.682 43.478 0.00 0.00 0.00 4.20
3392 3505 3.306703 TGTTCAACGAACTACAAACCGTC 59.693 43.478 8.23 0.00 42.39 4.79
3393 3506 3.260740 TGTTCAACGAACTACAAACCGT 58.739 40.909 8.23 0.00 42.39 4.83
3402 3515 4.836125 AGCAATCAATGTTCAACGAACT 57.164 36.364 8.23 0.00 42.39 3.01
3502 3618 2.839486 TTTCGTGCACCATCTCTTCT 57.161 45.000 12.15 0.00 0.00 2.85
3810 3940 3.441163 CAGGAAATGGCAATCACAATCG 58.559 45.455 0.00 0.00 0.00 3.34
3839 3969 4.521639 ACTGATACCAGCGAATCCGTAATA 59.478 41.667 0.00 0.00 44.16 0.98


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

AutoCloner maintained by Alex Coulton.