Multiple sequence alignment - TraesCS2A01G140600

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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 TraesCS2A01G140600 chr2A 100.000 3383 0 0 1 3383 85614595 85611213 0.000000e+00 6248
1 TraesCS2A01G140600 chr2A 96.694 3085 78 20 1 3077 85928022 85924954 0.000000e+00 5110
2 TraesCS2A01G140600 chr2A 96.595 3084 81 20 1 3077 85812113 85809047 0.000000e+00 5092
3 TraesCS2A01G140600 chr2A 91.710 965 54 17 2084 3030 84144624 84145580 0.000000e+00 1315
4 TraesCS2A01G140600 chr4A 96.757 3084 77 19 1 3077 349807649 349804582 0.000000e+00 5120
5 TraesCS2A01G140600 chrUn 99.368 1583 9 1 1 1582 354326938 354325356 0.000000e+00 2867
6 TraesCS2A01G140600 chrUn 93.750 80 5 0 3170 3249 394570473 394570552 1.650000e-23 121
7 TraesCS2A01G140600 chrUn 93.750 80 5 0 3170 3249 430913531 430913610 1.650000e-23 121
8 TraesCS2A01G140600 chr2D 94.274 1240 40 10 869 2084 84938032 84936800 0.000000e+00 1868
9 TraesCS2A01G140600 chr2D 94.113 1240 42 2 869 2084 85408829 85407597 0.000000e+00 1857
10 TraesCS2A01G140600 chr2D 88.835 1245 79 20 2084 3315 85250908 85249711 0.000000e+00 1474
11 TraesCS2A01G140600 chr2D 91.106 922 33 3 869 1766 85251896 85251000 0.000000e+00 1203
12 TraesCS2A01G140600 chr2D 86.697 436 23 13 2950 3383 84935536 84935134 5.150000e-123 451
13 TraesCS2A01G140600 chr2D 86.697 436 23 12 2950 3383 85406332 85405930 5.150000e-123 451
14 TraesCS2A01G140600 chr2D 85.316 395 40 12 2950 3343 84777964 84777587 3.160000e-105 392
15 TraesCS2A01G140600 chr2D 88.346 266 15 6 622 874 84780829 84780567 4.240000e-79 305
16 TraesCS2A01G140600 chr2D 88.889 126 10 3 24 145 84784982 84784857 5.850000e-33 152
17 TraesCS2A01G140600 chr2B 96.570 1137 21 9 2090 3210 136813857 136812723 0.000000e+00 1868
18 TraesCS2A01G140600 chr2B 94.037 1241 43 2 868 2084 137622536 137621303 0.000000e+00 1853
19 TraesCS2A01G140600 chr2B 93.710 1240 47 3 869 2084 136639018 136637786 0.000000e+00 1829
20 TraesCS2A01G140600 chr2B 93.387 1240 51 2 869 2084 137014843 137013611 0.000000e+00 1807
21 TraesCS2A01G140600 chr2B 93.306 1240 52 3 869 2084 136815186 136813954 0.000000e+00 1801
22 TraesCS2A01G140600 chr2B 95.583 1132 15 11 2090 3208 137621205 137620096 0.000000e+00 1781
23 TraesCS2A01G140600 chr2B 95.079 1138 32 11 2087 3210 137013550 137012423 0.000000e+00 1770
24 TraesCS2A01G140600 chr2B 90.909 1243 78 19 2090 3315 136637689 136636465 0.000000e+00 1637
25 TraesCS2A01G140600 chr2B 92.968 967 42 14 2084 3030 135464707 135465667 0.000000e+00 1386
26 TraesCS2A01G140600 chr2B 91.788 962 58 13 2084 3030 182132934 182131979 0.000000e+00 1319
27 TraesCS2A01G140600 chr2B 86.667 465 43 9 1 446 136639960 136639496 6.520000e-137 497
28 TraesCS2A01G140600 chr2B 90.659 364 14 13 522 874 136639497 136639143 1.840000e-127 466
29 TraesCS2A01G140600 chr2B 94.915 118 3 1 3266 3383 137012412 137012298 7.460000e-42 182
30 TraesCS2A01G140600 chr2B 94.624 93 5 0 3266 3358 137620083 137619991 9.780000e-31 145
31 TraesCS2A01G140600 chr2B 84.177 158 12 7 541 688 137015186 137015032 1.270000e-29 141
32 TraesCS2A01G140600 chr2B 84.177 158 12 7 541 688 137622879 137622725 1.270000e-29 141
33 TraesCS2A01G140600 chr7A 92.400 921 33 3 870 1766 618195380 618194473 0.000000e+00 1279
34 TraesCS2A01G140600 chr7A 88.479 1085 73 29 2084 3149 618194378 618193327 0.000000e+00 1264
35 TraesCS2A01G140600 chr5A 88.670 406 32 10 146 539 416027101 416026698 1.830000e-132 483
36 TraesCS2A01G140600 chr5A 87.023 262 16 12 626 871 375377685 375377426 2.570000e-71 279
37 TraesCS2A01G140600 chr3D 85.086 409 44 11 146 540 184141157 184141562 5.260000e-108 401
38 TraesCS2A01G140600 chr5D 84.951 412 43 10 146 540 456802902 456803311 1.890000e-107 399
39 TraesCS2A01G140600 chr5D 86.416 346 16 10 558 874 283110898 283110555 1.930000e-92 350
40 TraesCS2A01G140600 chr3A 84.352 409 46 14 146 540 481087858 481087454 5.300000e-103 385
41 TraesCS2A01G140600 chr5B 84.136 353 18 22 558 874 321478750 321478400 1.180000e-79 307


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 TraesCS2A01G140600 chr2A 85611213 85614595 3382 True 6248.00 6248 100.00000 1 3383 1 chr2A.!!$R1 3382
1 TraesCS2A01G140600 chr2A 85924954 85928022 3068 True 5110.00 5110 96.69400 1 3077 1 chr2A.!!$R3 3076
2 TraesCS2A01G140600 chr2A 85809047 85812113 3066 True 5092.00 5092 96.59500 1 3077 1 chr2A.!!$R2 3076
3 TraesCS2A01G140600 chr2A 84144624 84145580 956 False 1315.00 1315 91.71000 2084 3030 1 chr2A.!!$F1 946
4 TraesCS2A01G140600 chr4A 349804582 349807649 3067 True 5120.00 5120 96.75700 1 3077 1 chr4A.!!$R1 3076
5 TraesCS2A01G140600 chrUn 354325356 354326938 1582 True 2867.00 2867 99.36800 1 1582 1 chrUn.!!$R1 1581
6 TraesCS2A01G140600 chr2D 85249711 85251896 2185 True 1338.50 1474 89.97050 869 3315 2 chr2D.!!$R4 2446
7 TraesCS2A01G140600 chr2D 84935134 84938032 2898 True 1159.50 1868 90.48550 869 3383 2 chr2D.!!$R3 2514
8 TraesCS2A01G140600 chr2D 85405930 85408829 2899 True 1154.00 1857 90.40500 869 3383 2 chr2D.!!$R5 2514
9 TraesCS2A01G140600 chr2D 84777587 84780829 3242 True 348.50 392 86.83100 622 3343 2 chr2D.!!$R2 2721
10 TraesCS2A01G140600 chr2B 136812723 136815186 2463 True 1834.50 1868 94.93800 869 3210 2 chr2B.!!$R3 2341
11 TraesCS2A01G140600 chr2B 135464707 135465667 960 False 1386.00 1386 92.96800 2084 3030 1 chr2B.!!$F1 946
12 TraesCS2A01G140600 chr2B 182131979 182132934 955 True 1319.00 1319 91.78800 2084 3030 1 chr2B.!!$R1 946
13 TraesCS2A01G140600 chr2B 136636465 136639960 3495 True 1107.25 1829 90.48625 1 3315 4 chr2B.!!$R2 3314
14 TraesCS2A01G140600 chr2B 137619991 137622879 2888 True 980.00 1853 92.10525 541 3358 4 chr2B.!!$R5 2817
15 TraesCS2A01G140600 chr2B 137012298 137015186 2888 True 975.00 1807 91.88950 541 3383 4 chr2B.!!$R4 2842
16 TraesCS2A01G140600 chr7A 618193327 618195380 2053 True 1271.50 1279 90.43950 870 3149 2 chr7A.!!$R1 2279

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
485 505 6.621316 TTAAGCATCCGAAGTGTGTTTTTA 57.379 33.333 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2676 3399 7.062749 AGAGTTCACTAACCAATGTTACTCA 57.937 36.0 0.0 0.0 36.15 3.41 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
485 505 6.621316 TTAAGCATCCGAAGTGTGTTTTTA 57.379 33.333 0.00 0.00 0.00 1.52
2676 3399 4.196971 AGTTAAAGTTGCAGTTTCCGACT 58.803 39.130 0.00 1.98 39.89 4.18
3002 3906 8.414003 GGAACAGTTCTTGGTTAGAAGATTTTT 58.586 33.333 13.13 0.00 43.39 1.94
3249 4165 4.026744 TGGAGTGGAATTTTTGTGTGGAA 58.973 39.130 0.00 0.00 0.00 3.53
3250 4166 4.467795 TGGAGTGGAATTTTTGTGTGGAAA 59.532 37.500 0.00 0.00 0.00 3.13
3251 4167 5.049828 GGAGTGGAATTTTTGTGTGGAAAG 58.950 41.667 0.00 0.00 0.00 2.62
3252 4168 4.441792 AGTGGAATTTTTGTGTGGAAAGC 58.558 39.130 0.00 0.00 0.00 3.51
3253 4169 3.245048 GTGGAATTTTTGTGTGGAAAGCG 59.755 43.478 0.00 0.00 0.00 4.68
3254 4170 3.131223 TGGAATTTTTGTGTGGAAAGCGA 59.869 39.130 0.00 0.00 0.00 4.93
3255 4171 3.489416 GGAATTTTTGTGTGGAAAGCGAC 59.511 43.478 0.00 0.00 0.00 5.19
3257 4173 5.506649 GGAATTTTTGTGTGGAAAGCGACTA 60.507 40.000 0.00 0.00 0.00 2.59
3260 4176 1.990799 TGTGTGGAAAGCGACTATCG 58.009 50.000 0.00 0.00 43.89 2.92
3264 4180 2.230508 TGTGGAAAGCGACTATCGAGTT 59.769 45.455 1.69 0.00 43.74 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 297 4.735662 TCTATAGCGCAAAACAAAACGT 57.264 36.364 11.47 0.00 0.00 3.99
492 512 4.922206 TCCAGTGCTCTTGGTATTTGAAT 58.078 39.130 2.43 0.00 0.00 2.57
520 540 2.094675 ACGAAAAATGCCTGCAGCTAT 58.905 42.857 8.66 1.22 44.23 2.97
2676 3399 7.062749 AGAGTTCACTAACCAATGTTACTCA 57.937 36.000 0.00 0.00 36.15 3.41
2794 3670 2.741228 GCACAAATTCAGGCCAACAACA 60.741 45.455 5.01 0.00 0.00 3.33
3249 4165 2.656560 AGCAAACTCGATAGTCGCTT 57.343 45.000 0.00 0.00 40.21 4.68
3250 4166 3.315470 TGATAGCAAACTCGATAGTCGCT 59.685 43.478 6.83 6.83 40.21 4.93
3251 4167 3.629058 TGATAGCAAACTCGATAGTCGC 58.371 45.455 0.00 0.00 40.21 5.19
3252 4168 5.274718 ACTTGATAGCAAACTCGATAGTCG 58.725 41.667 0.00 0.00 35.83 4.18
3253 4169 7.063544 ACAAACTTGATAGCAAACTCGATAGTC 59.936 37.037 0.00 0.00 33.75 2.59
3254 4170 6.874134 ACAAACTTGATAGCAAACTCGATAGT 59.126 34.615 0.00 0.00 37.65 2.12
3255 4171 7.063426 TGACAAACTTGATAGCAAACTCGATAG 59.937 37.037 0.00 0.00 32.73 2.08
3257 4173 5.700832 TGACAAACTTGATAGCAAACTCGAT 59.299 36.000 0.00 0.00 32.73 3.59
3260 4176 8.454106 ACATATGACAAACTTGATAGCAAACTC 58.546 33.333 10.38 0.00 32.73 3.01
3264 4180 8.673711 GGTTACATATGACAAACTTGATAGCAA 58.326 33.333 10.38 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.