Multiple sequence alignment - TraesCS3A01G204000

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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 TraesCS3A01G204000 chr3A 100.000 3110 0 0 1 3110 354854515 354851406 0.000000e+00 5744
1 TraesCS3A01G204000 chr3A 89.137 313 29 5 2581 2890 171717890 171718200 4.870000e-103 385
2 TraesCS3A01G204000 chr3A 89.899 297 27 3 2581 2875 60138890 60139185 2.260000e-101 379
3 TraesCS3A01G204000 chr3A 88.818 313 29 6 2582 2890 453568418 453568108 2.260000e-101 379
4 TraesCS3A01G204000 chr3B 96.038 2196 68 12 923 3106 366392613 366394801 0.000000e+00 3555
5 TraesCS3A01G204000 chr3D 96.324 2149 55 11 892 3028 259434174 259436310 0.000000e+00 3509
6 TraesCS3A01G204000 chr1A 94.190 895 51 1 1 894 82179977 82179083 0.000000e+00 1363
7 TraesCS3A01G204000 chr1A 88.780 205 17 6 2906 3108 156540255 156540055 2.400000e-61 246
8 TraesCS3A01G204000 chr2B 87.987 899 93 7 1 896 554306213 554307099 0.000000e+00 1048
9 TraesCS3A01G204000 chr5A 89.206 315 29 5 2579 2890 363546929 363547241 3.760000e-104 388
10 TraesCS3A01G204000 chr5A 89.103 312 29 5 2582 2890 151723551 151723242 1.750000e-102 383
11 TraesCS3A01G204000 chr5A 89.103 312 29 5 2582 2890 151730668 151730359 1.750000e-102 383
12 TraesCS3A01G204000 chr5A 88.818 313 28 7 2582 2890 363554049 363554358 8.140000e-101 377
13 TraesCS3A01G204000 chr5A 86.977 215 24 4 2891 3104 328788475 328788264 4.010000e-59 239
14 TraesCS3A01G204000 chr4D 89.655 203 17 4 2906 3108 364515749 364515551 3.980000e-64 255
15 TraesCS3A01G204000 chr2A 88.725 204 18 5 2906 3108 103260570 103260769 8.620000e-61 244
16 TraesCS3A01G204000 chr2A 77.329 322 47 20 592 896 16755282 16754970 1.920000e-37 167
17 TraesCS3A01G204000 chr7D 86.818 220 23 6 2891 3108 164653557 164653342 1.110000e-59 241
18 TraesCS3A01G204000 chr7D 86.574 216 26 3 2891 3105 310616265 310616478 5.190000e-58 235
19 TraesCS3A01G204000 chr4B 86.818 220 23 5 2891 3108 424889621 424889406 1.110000e-59 241
20 TraesCS3A01G204000 chr2D 87.097 217 22 6 2891 3105 236072260 236072472 1.110000e-59 241


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 TraesCS3A01G204000 chr3A 354851406 354854515 3109 True 5744 5744 100.000 1 3110 1 chr3A.!!$R1 3109
1 TraesCS3A01G204000 chr3B 366392613 366394801 2188 False 3555 3555 96.038 923 3106 1 chr3B.!!$F1 2183
2 TraesCS3A01G204000 chr3D 259434174 259436310 2136 False 3509 3509 96.324 892 3028 1 chr3D.!!$F1 2136
3 TraesCS3A01G204000 chr1A 82179083 82179977 894 True 1363 1363 94.190 1 894 1 chr1A.!!$R1 893
4 TraesCS3A01G204000 chr2B 554306213 554307099 886 False 1048 1048 87.987 1 896 1 chr2B.!!$F1 895

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
121 124 0.603975 GCCGGATCTATTGCTGTCCC 60.604 60.000 5.05 0.0 0.0 4.46 F
384 388 0.790207 CATCACGACGGTTGTTCCTG 59.210 55.000 0.00 0.0 0.0 3.86 F
630 634 2.018086 GGGGGATTGGGGATGGGAA 61.018 63.158 0.00 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1217 1.071071 CTTCACGGTCCCTGGTGTTAA 59.929 52.381 0.0 0.0 35.67 2.01 R
1206 1219 1.450211 CTTCACGGTCCCTGGTGTT 59.550 57.895 0.0 0.0 35.67 3.32 R
2547 2562 0.105778 CAGGGAGGGCTTCGAGATTC 59.894 60.000 0.0 0.0 0.00 2.52 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
33 34 1.546773 GCAACACCTGAACCCATACCA 60.547 52.381 0.00 0.00 0.00 3.25
113 116 1.472662 CCCACCTCGCCGGATCTATT 61.473 60.000 5.05 0.00 36.31 1.73
116 119 1.115930 ACCTCGCCGGATCTATTGCT 61.116 55.000 5.05 0.00 36.31 3.91
120 123 0.946221 CGCCGGATCTATTGCTGTCC 60.946 60.000 5.05 0.00 0.00 4.02
121 124 0.603975 GCCGGATCTATTGCTGTCCC 60.604 60.000 5.05 0.00 0.00 4.46
170 173 2.046280 AGCCTTCAACCCTACCTTCT 57.954 50.000 0.00 0.00 0.00 2.85
178 181 5.014534 TCAACCCTACCTTCTACCAGTAA 57.985 43.478 0.00 0.00 0.00 2.24
240 243 2.487986 GCAACTCCCTAATCCATCCCAG 60.488 54.545 0.00 0.00 0.00 4.45
260 263 2.546368 AGAAATAACGCGTGCTTCAACA 59.454 40.909 14.98 0.00 0.00 3.33
278 281 1.028330 CAATCCACCATGTGCTCGCT 61.028 55.000 0.00 0.00 31.34 4.93
285 288 2.419673 CACCATGTGCTCGCTGATTTAA 59.580 45.455 0.00 0.00 0.00 1.52
310 314 3.807622 ACGAAAAGCAGAAAATCGAGACA 59.192 39.130 0.07 0.00 37.27 3.41
372 376 1.006086 CCAATGCGCTAACATCACGA 58.994 50.000 9.73 0.00 0.00 4.35
384 388 0.790207 CATCACGACGGTTGTTCCTG 59.210 55.000 0.00 0.00 0.00 3.86
422 426 3.952508 TGCTTCCCTTCTGCCGCA 61.953 61.111 0.00 0.00 0.00 5.69
442 446 2.124819 CTGCTCCTCTTGCCGCAT 60.125 61.111 0.00 0.00 0.00 4.73
630 634 2.018086 GGGGGATTGGGGATGGGAA 61.018 63.158 0.00 0.00 0.00 3.97
870 874 2.176792 GCGGCTGCAAACTAGCAC 59.823 61.111 14.08 0.00 42.88 4.40
874 878 2.667318 GCTGCAAACTAGCACGCGA 61.667 57.895 15.93 0.00 40.11 5.87
902 906 7.704899 CACTTTTTAGGTTTTAGGTTGGAACAG 59.295 37.037 0.00 0.00 42.39 3.16
903 907 7.616542 ACTTTTTAGGTTTTAGGTTGGAACAGA 59.383 33.333 0.00 0.00 42.39 3.41
915 919 9.847224 TTAGGTTGGAACAGATAATTTAGATCC 57.153 33.333 0.00 0.00 42.39 3.36
969 973 2.536997 ATAAGCCGCACACTCCACCC 62.537 60.000 0.00 0.00 0.00 4.61
1206 1219 1.448893 GCCCACGGCGATGACTTTA 60.449 57.895 16.62 0.00 39.62 1.85
1388 1401 2.359975 GCCCTTGAAGGTCCGTGG 60.360 66.667 10.82 0.00 31.93 4.94
1839 1852 3.483085 GCTGAATTTCGGTGTACTTACGC 60.483 47.826 7.07 0.00 36.03 4.42
2158 2171 9.798994 TTTTCTCTTCAAGTATAGGTAATCGTC 57.201 33.333 0.00 0.00 0.00 4.20
2264 2277 6.515043 GTGATACACATGCAAATAATTGCC 57.485 37.500 12.85 0.00 46.03 4.52
2395 2410 8.211629 ACTAGGTTTTTGTATCTCAGTTTGTCT 58.788 33.333 0.00 0.00 0.00 3.41
2547 2562 6.728200 TGAGAAGAACTTGTTAGTTTGCATG 58.272 36.000 0.00 0.00 44.51 4.06
2719 2734 8.110860 TGAAAGTTGAATGAGAGGGAATAAAC 57.889 34.615 0.00 0.00 0.00 2.01
2817 2832 7.271511 AGTGAAGATGATATGACTTCTTCCAC 58.728 38.462 17.86 15.97 43.78 4.02
2912 2927 2.033372 TGACGCCCCGACTTAATCATA 58.967 47.619 0.00 0.00 0.00 2.15
2913 2928 2.631062 TGACGCCCCGACTTAATCATAT 59.369 45.455 0.00 0.00 0.00 1.78
2915 2930 4.464951 TGACGCCCCGACTTAATCATATAT 59.535 41.667 0.00 0.00 0.00 0.86
2916 2931 4.755411 ACGCCCCGACTTAATCATATATG 58.245 43.478 6.36 6.36 0.00 1.78
2917 2932 3.555956 CGCCCCGACTTAATCATATATGC 59.444 47.826 7.92 0.00 0.00 3.14
2947 2972 2.716504 CACGATTAAGATCAGCGACTCG 59.283 50.000 0.00 0.00 32.33 4.18
2948 2973 2.355132 ACGATTAAGATCAGCGACTCGT 59.645 45.455 0.00 0.00 33.69 4.18
2978 3003 8.072321 AGATATCACAACACAACTCTAGACAT 57.928 34.615 5.32 0.00 0.00 3.06
3031 3056 3.151022 CAGGGTCCTCGAGGGCTC 61.151 72.222 33.64 31.59 41.76 4.70
3059 3084 8.749841 ATACATAATCTCGAATACACAAGAGC 57.250 34.615 0.00 0.00 0.00 4.09
3065 3090 1.735700 CGAATACACAAGAGCCAGCGA 60.736 52.381 0.00 0.00 0.00 4.93
3068 3093 2.248280 TACACAAGAGCCAGCGAAAA 57.752 45.000 0.00 0.00 0.00 2.29
3087 3112 6.955963 GCGAAAACAACAATATCTGAGTACAG 59.044 38.462 0.00 0.00 44.66 2.74
3108 3133 9.530633 GTACAGACATAAGGTAAATAAGTCTGG 57.469 37.037 19.77 6.23 46.00 3.86
3109 3134 7.048512 ACAGACATAAGGTAAATAAGTCTGGC 58.951 38.462 19.77 0.00 46.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.376625 TCTAGTTTTGTGAATGACTTGCCT 58.623 37.500 0.00 0.00 0.00 4.75
116 119 2.203938 GTGAGGGAGGGTGGGACA 60.204 66.667 0.00 0.00 0.00 4.02
120 123 1.925455 ATGGTGTGAGGGAGGGTGG 60.925 63.158 0.00 0.00 0.00 4.61
121 124 1.300963 CATGGTGTGAGGGAGGGTG 59.699 63.158 0.00 0.00 0.00 4.61
170 173 2.811136 CGCAAGGGTTTGGTTACTGGTA 60.811 50.000 0.00 0.00 34.79 3.25
178 181 2.123897 AGTGCGCAAGGGTTTGGT 60.124 55.556 14.00 0.00 34.79 3.67
240 243 2.911120 TGTTGAAGCACGCGTTATTTC 58.089 42.857 10.22 14.25 0.00 2.17
260 263 1.028330 CAGCGAGCACATGGTGGATT 61.028 55.000 0.00 0.00 33.64 3.01
278 281 5.759506 TTCTGCTTTTCGTGGTTAAATCA 57.240 34.783 0.00 0.00 0.00 2.57
285 288 2.875933 TCGATTTTCTGCTTTTCGTGGT 59.124 40.909 0.00 0.00 0.00 4.16
310 314 3.319972 GCAATCCTTGGTATGCACATCAT 59.680 43.478 12.10 0.00 38.63 2.45
355 359 0.645355 CGTCGTGATGTTAGCGCATT 59.355 50.000 11.47 0.00 0.00 3.56
362 366 2.036217 AGGAACAACCGTCGTGATGTTA 59.964 45.455 8.54 0.00 44.74 2.41
372 376 0.814010 GACACAGCAGGAACAACCGT 60.814 55.000 0.00 0.00 44.74 4.83
422 426 2.348998 CGGCAAGAGGAGCAGGTT 59.651 61.111 0.00 0.00 0.00 3.50
442 446 0.691078 GTGGAGGATAGCCAGGGTCA 60.691 60.000 0.00 0.00 35.77 4.02
510 514 0.470456 AAGAGGGGTGTACGGTGACA 60.470 55.000 0.00 0.00 0.00 3.58
514 518 2.590114 GGCAAGAGGGGTGTACGGT 61.590 63.158 0.00 0.00 0.00 4.83
870 874 3.343380 AAAACCTAAAAAGTGGTCGCG 57.657 42.857 0.00 0.00 35.17 5.87
874 878 6.196434 TCCAACCTAAAACCTAAAAAGTGGT 58.804 36.000 0.00 0.00 38.35 4.16
902 906 9.945904 AAAATACTCCCTCGGATCTAAATTATC 57.054 33.333 0.00 0.00 0.00 1.75
914 918 6.995511 TCATTTTGTAAAATACTCCCTCGG 57.004 37.500 2.54 0.00 36.52 4.63
915 919 7.432252 GCATTCATTTTGTAAAATACTCCCTCG 59.568 37.037 2.54 0.00 36.52 4.63
969 973 2.062971 AGTAATCTGCTGCCCAATGG 57.937 50.000 0.00 0.00 0.00 3.16
1064 1068 3.450096 AGTACCAACGAAGGTAGGAATCC 59.550 47.826 10.28 0.00 44.43 3.01
1203 1216 1.129917 TCACGGTCCCTGGTGTTAAA 58.870 50.000 0.00 0.00 35.67 1.52
1204 1217 1.071071 CTTCACGGTCCCTGGTGTTAA 59.929 52.381 0.00 0.00 35.67 2.01
1206 1219 1.450211 CTTCACGGTCCCTGGTGTT 59.550 57.895 0.00 0.00 35.67 3.32
1370 1383 2.750350 CACGGACCTTCAAGGGCT 59.250 61.111 9.91 0.00 45.15 5.19
1839 1852 7.770433 TCCACATAAAAGGATGAAGACATACAG 59.230 37.037 0.00 0.00 39.65 2.74
2135 2148 7.774157 ACAGACGATTACCTATACTTGAAGAGA 59.226 37.037 0.00 0.00 0.00 3.10
2138 2151 8.838365 ACTACAGACGATTACCTATACTTGAAG 58.162 37.037 0.00 0.00 0.00 3.02
2264 2277 7.803189 ACATTTGACAACTAGATTAACAAAGCG 59.197 33.333 0.00 2.04 32.19 4.68
2272 2285 8.684386 TTGGTTGACATTTGACAACTAGATTA 57.316 30.769 19.79 2.88 45.33 1.75
2395 2410 8.355913 TGTACAGTTTTGCACATTCAAATGATA 58.644 29.630 9.62 0.00 39.67 2.15
2547 2562 0.105778 CAGGGAGGGCTTCGAGATTC 59.894 60.000 0.00 0.00 0.00 2.52
2786 2801 8.224025 AGAAGTCATATCATCTTCACTCTAGGA 58.776 37.037 11.24 0.00 39.69 2.94
2817 2832 8.956533 TTCAAACCCCTTTTCATTTCTTTAAG 57.043 30.769 0.00 0.00 0.00 1.85
2912 2927 2.780065 ATCGTGCGCATTTTGCATAT 57.220 40.000 15.91 0.00 45.36 1.78
2913 2928 2.558265 AATCGTGCGCATTTTGCATA 57.442 40.000 15.91 0.00 45.36 3.14
2915 2930 2.095516 TCTTAATCGTGCGCATTTTGCA 60.096 40.909 15.91 0.00 45.36 4.08
2916 2931 2.514902 TCTTAATCGTGCGCATTTTGC 58.485 42.857 15.91 0.00 40.69 3.68
2917 2932 4.341935 TGATCTTAATCGTGCGCATTTTG 58.658 39.130 15.91 4.26 34.39 2.44
2932 2957 0.738975 CCCACGAGTCGCTGATCTTA 59.261 55.000 13.59 0.00 0.00 2.10
2947 2972 5.003804 AGTTGTGTTGTGATATCTTCCCAC 58.996 41.667 3.98 6.72 0.00 4.61
2948 2973 5.013079 AGAGTTGTGTTGTGATATCTTCCCA 59.987 40.000 3.98 0.00 0.00 4.37
3031 3056 9.394477 TCTTGTGTATTCGAGATTATGTATTCG 57.606 33.333 0.00 0.00 34.56 3.34
3059 3084 5.106555 ACTCAGATATTGTTGTTTTCGCTGG 60.107 40.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.