Multiple sequence alignment - TraesCS3B01G249100

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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 TraesCS3B01G249100 chr3B 100.000 3184 0 0 1 3184 397261246 397264429 0.000000e+00 5880
1 TraesCS3B01G249100 chr3B 92.978 1780 112 7 626 2399 245471673 245469901 0.000000e+00 2582
2 TraesCS3B01G249100 chr3B 92.415 936 66 3 4 934 422104427 422105362 0.000000e+00 1330
3 TraesCS3B01G249100 chr3B 93.434 792 47 3 2397 3184 245469760 245468970 0.000000e+00 1170
4 TraesCS3B01G249100 chr2A 92.139 2417 149 23 4 2399 302440239 302437843 0.000000e+00 3373
5 TraesCS3B01G249100 chr2A 93.467 796 40 8 2397 3184 259173909 259174700 0.000000e+00 1171
6 TraesCS3B01G249100 chr2A 93.342 796 41 7 2397 3184 348627166 348627957 0.000000e+00 1166
7 TraesCS3B01G249100 chr2A 94.150 547 29 3 4 548 348626129 348626674 0.000000e+00 830
8 TraesCS3B01G249100 chr2A 94.118 544 25 5 2646 3184 300547202 300547743 0.000000e+00 821
9 TraesCS3B01G249100 chr2A 91.900 321 23 1 2397 2714 300546881 300547201 2.250000e-121 446
10 TraesCS3B01G249100 chr7B 91.962 2426 158 26 1 2399 428787541 428785126 0.000000e+00 3365
11 TraesCS3B01G249100 chr7B 91.355 937 74 6 4 935 478020378 478021312 0.000000e+00 1275
12 TraesCS3B01G249100 chr7B 93.432 609 33 5 4 608 40703702 40704307 0.000000e+00 896
13 TraesCS3B01G249100 chr5B 91.660 2422 166 25 4 2399 291602043 291604454 0.000000e+00 3321
14 TraesCS3B01G249100 chr5B 92.290 428 26 6 2762 3184 496647323 496647748 4.540000e-168 601
15 TraesCS3B01G249100 chr5A 91.608 2419 159 28 4 2399 222766246 222768643 0.000000e+00 3302
16 TraesCS3B01G249100 chr6B 92.924 2247 130 18 164 2399 637183881 637181653 0.000000e+00 3241
17 TraesCS3B01G249100 chr6B 94.417 609 30 3 4 608 283253349 283253957 0.000000e+00 933
18 TraesCS3B01G249100 chr4B 90.961 2434 172 23 1 2399 360895360 360897780 0.000000e+00 3232
19 TraesCS3B01G249100 chr4B 94.264 2092 109 9 312 2399 205682161 205680077 0.000000e+00 3188
20 TraesCS3B01G249100 chr4B 94.892 646 24 4 2396 3032 205679935 205679290 0.000000e+00 1002
21 TraesCS3B01G249100 chr4B 91.866 627 46 4 2561 3184 360898197 360898821 0.000000e+00 870
22 TraesCS3B01G249100 chr4A 93.112 1539 86 13 871 2399 535944466 535942938 0.000000e+00 2237
23 TraesCS3B01G249100 chr2D 92.674 1324 68 8 4 1320 245569764 245571065 0.000000e+00 1881
24 TraesCS3B01G249100 chr6A 92.695 794 48 6 2397 3184 409744564 409745353 0.000000e+00 1136
25 TraesCS3B01G249100 chr3D 94.922 709 32 4 4 708 208626257 208626965 0.000000e+00 1107
26 TraesCS3B01G249100 chr1A 93.007 429 23 5 2762 3184 382776285 382776712 1.250000e-173 619
27 TraesCS3B01G249100 chr1B 91.803 427 30 4 2762 3184 82618043 82618468 9.840000e-165 590
28 TraesCS3B01G249100 chr1B 94.097 288 17 0 2427 2714 82617465 82617752 3.770000e-119 438
29 TraesCS3B01G249100 chr2B 94.097 288 17 0 2427 2714 93132999 93132712 3.770000e-119 438


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 TraesCS3B01G249100 chr3B 397261246 397264429 3183 False 5880.0 5880 100.0000 1 3184 1 chr3B.!!$F1 3183
1 TraesCS3B01G249100 chr3B 245468970 245471673 2703 True 1876.0 2582 93.2060 626 3184 2 chr3B.!!$R1 2558
2 TraesCS3B01G249100 chr3B 422104427 422105362 935 False 1330.0 1330 92.4150 4 934 1 chr3B.!!$F2 930
3 TraesCS3B01G249100 chr2A 302437843 302440239 2396 True 3373.0 3373 92.1390 4 2399 1 chr2A.!!$R1 2395
4 TraesCS3B01G249100 chr2A 259173909 259174700 791 False 1171.0 1171 93.4670 2397 3184 1 chr2A.!!$F1 787
5 TraesCS3B01G249100 chr2A 348626129 348627957 1828 False 998.0 1166 93.7460 4 3184 2 chr2A.!!$F3 3180
6 TraesCS3B01G249100 chr2A 300546881 300547743 862 False 633.5 821 93.0090 2397 3184 2 chr2A.!!$F2 787
7 TraesCS3B01G249100 chr7B 428785126 428787541 2415 True 3365.0 3365 91.9620 1 2399 1 chr7B.!!$R1 2398
8 TraesCS3B01G249100 chr7B 478020378 478021312 934 False 1275.0 1275 91.3550 4 935 1 chr7B.!!$F2 931
9 TraesCS3B01G249100 chr7B 40703702 40704307 605 False 896.0 896 93.4320 4 608 1 chr7B.!!$F1 604
10 TraesCS3B01G249100 chr5B 291602043 291604454 2411 False 3321.0 3321 91.6600 4 2399 1 chr5B.!!$F1 2395
11 TraesCS3B01G249100 chr5A 222766246 222768643 2397 False 3302.0 3302 91.6080 4 2399 1 chr5A.!!$F1 2395
12 TraesCS3B01G249100 chr6B 637181653 637183881 2228 True 3241.0 3241 92.9240 164 2399 1 chr6B.!!$R1 2235
13 TraesCS3B01G249100 chr6B 283253349 283253957 608 False 933.0 933 94.4170 4 608 1 chr6B.!!$F1 604
14 TraesCS3B01G249100 chr4B 205679290 205682161 2871 True 2095.0 3188 94.5780 312 3032 2 chr4B.!!$R1 2720
15 TraesCS3B01G249100 chr4B 360895360 360898821 3461 False 2051.0 3232 91.4135 1 3184 2 chr4B.!!$F1 3183
16 TraesCS3B01G249100 chr4A 535942938 535944466 1528 True 2237.0 2237 93.1120 871 2399 1 chr4A.!!$R1 1528
17 TraesCS3B01G249100 chr2D 245569764 245571065 1301 False 1881.0 1881 92.6740 4 1320 1 chr2D.!!$F1 1316
18 TraesCS3B01G249100 chr6A 409744564 409745353 789 False 1136.0 1136 92.6950 2397 3184 1 chr6A.!!$F1 787
19 TraesCS3B01G249100 chr3D 208626257 208626965 708 False 1107.0 1107 94.9220 4 708 1 chr3D.!!$F1 704
20 TraesCS3B01G249100 chr1B 82617465 82618468 1003 False 514.0 590 92.9500 2427 3184 2 chr1B.!!$F1 757

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
899 988 1.338973 ACAGTTTGACCTCGACGCTTA 59.661 47.619 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2726 3163 0.106819 GTTCCCAGGCTCATCTGCAT 60.107 55.0 0.0 0.0 33.64 3.96 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
96 100 4.627611 CATGATCACATGTTCCCTTCAC 57.372 45.455 0.00 0.00 46.01 3.18
651 736 3.150949 CACTGGTGAGGTCTGGCA 58.849 61.111 0.00 0.00 0.00 4.92
682 767 4.770795 TCCTCTTTTTATGTAGCCTCTGC 58.229 43.478 0.00 0.00 37.95 4.26
704 789 1.691976 TCGAAGTTCACCTCCATGTGT 59.308 47.619 3.32 0.00 37.51 3.72
899 988 1.338973 ACAGTTTGACCTCGACGCTTA 59.661 47.619 0.00 0.00 0.00 3.09
1016 1105 2.146342 CGCAATGTACATGGAGATCCC 58.854 52.381 14.78 0.00 34.29 3.85
1175 1264 5.848406 TGTTCACTGGTTTTGTTTTCACTT 58.152 33.333 0.00 0.00 0.00 3.16
2174 2281 2.388494 TAGCTCACTATGACGCCGCG 62.388 60.000 12.14 12.14 0.00 6.46
2197 2304 0.732880 CACTAGCACGAAGGACACCG 60.733 60.000 0.00 0.00 0.00 4.94
2198 2305 1.805945 CTAGCACGAAGGACACCGC 60.806 63.158 0.00 0.00 0.00 5.68
2222 2329 5.114780 CAGGTTGAGGATGAAGTACATGAG 58.885 45.833 0.00 0.00 39.56 2.90
2239 2346 0.247736 GAGGCAGACAATGAGGACGT 59.752 55.000 0.00 0.00 0.00 4.34
2548 2801 3.024547 ACATCGCCATAGTGAGTACAGT 58.975 45.455 0.00 0.00 35.57 3.55
2637 3005 1.435105 CTGAGAGAAGCATCGCCGA 59.565 57.895 0.00 0.00 0.00 5.54
2743 3180 1.703014 GGATGCAGATGAGCCTGGGA 61.703 60.000 0.00 0.00 34.82 4.37
2948 3643 1.129811 GATAAGTCCAAAACCCGCACG 59.870 52.381 0.00 0.00 0.00 5.34
3085 3787 1.656095 GTGAACGCTCATACACTCTGC 59.344 52.381 0.00 0.00 33.05 4.26
3166 3869 8.343366 AGAAAAACTAGAACTTCAAAATCGACC 58.657 33.333 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 141 1.141657 TGCCACTTCTCTTGCACTTCT 59.858 47.619 0.00 0.00 0.00 2.85
142 146 2.346766 TCTTTGCCACTTCTCTTGCA 57.653 45.000 0.00 0.00 0.00 4.08
234 238 2.134346 CAAGTTTGTTGAAATGGGGCG 58.866 47.619 0.00 0.00 0.00 6.13
651 736 6.607600 GCTACATAAAAAGAGGAAGGGGAAAT 59.392 38.462 0.00 0.00 0.00 2.17
682 767 1.336887 ACATGGAGGTGAACTTCGACG 60.337 52.381 0.00 0.00 0.00 5.12
704 789 1.605058 GGGAGCTACGAGTGGAGCAA 61.605 60.000 1.86 0.00 41.36 3.91
749 834 3.000041 GGTTGAACTGATATCGTGCACA 59.000 45.455 18.64 4.45 0.00 4.57
899 988 3.920817 TCCTTGTGGGACTGCCAT 58.079 55.556 0.00 0.00 39.58 4.40
1016 1105 1.000274 TGCCATCATCGTACTCCATCG 60.000 52.381 0.00 0.00 0.00 3.84
1089 1178 4.758251 TCATGCACCCGCGTCCAG 62.758 66.667 4.92 0.00 42.97 3.86
1127 1216 1.593296 GGAGTAAGCGGTGGTCGACT 61.593 60.000 16.46 0.00 42.43 4.18
1128 1217 1.153881 GGAGTAAGCGGTGGTCGAC 60.154 63.158 7.13 7.13 42.43 4.20
1175 1264 0.099968 CGACGAGGAATAGGCGTGAA 59.900 55.000 0.00 0.00 38.51 3.18
1376 1465 4.101741 ACTGAACTGAGAGCACCTAGTTTT 59.898 41.667 2.98 0.00 33.83 2.43
1415 1505 8.669801 GCATGTTATATGTATTTTTCACGAACG 58.330 33.333 0.00 0.00 0.00 3.95
1621 1720 4.277476 TCCTCACCACAAAAGAACACATT 58.723 39.130 0.00 0.00 0.00 2.71
1840 1942 9.517609 AACATTATACTAGAAAACGTGAGCTAG 57.482 33.333 13.94 13.94 37.08 3.42
1890 1993 7.336427 ACTCGTACTAATCTAGCTAACACAACT 59.664 37.037 0.00 0.00 0.00 3.16
2071 2177 6.493458 AGAGAAAAGAGCAGTAGAGAGAAACT 59.507 38.462 0.00 0.00 0.00 2.66
2174 2281 1.476891 TGTCCTTCGTGCTAGTGATCC 59.523 52.381 0.00 0.00 0.00 3.36
2197 2304 2.027192 TGTACTTCATCCTCAACCTGGC 60.027 50.000 0.00 0.00 0.00 4.85
2198 2305 3.981071 TGTACTTCATCCTCAACCTGG 57.019 47.619 0.00 0.00 0.00 4.45
2222 2329 0.741221 GGACGTCCTCATTGTCTGCC 60.741 60.000 27.64 0.00 33.21 4.85
2390 2497 2.928116 CGGACTTCCTCAAATTCGTACC 59.072 50.000 0.00 0.00 0.00 3.34
2548 2801 2.092103 AGTACTTCCCAAGGTGTTGCAA 60.092 45.455 0.00 0.00 31.64 4.08
2637 3005 2.692557 CAGATCATCGAACTCTCCCAGT 59.307 50.000 0.00 0.00 36.64 4.00
2726 3163 0.106819 GTTCCCAGGCTCATCTGCAT 60.107 55.000 0.00 0.00 33.64 3.96
2743 3180 1.628846 AGTGAGTAGGGCATTTCGGTT 59.371 47.619 0.00 0.00 0.00 4.44
2812 3492 4.957954 ACCACGGGAGTATACTATGTGAAA 59.042 41.667 23.18 0.00 44.67 2.69
3034 3731 9.087424 AGTAATTGAACTTTTGAGCACTTTTTC 57.913 29.630 0.00 0.00 0.00 2.29
3072 3774 5.240891 TCTTTTGGAAGCAGAGTGTATGAG 58.759 41.667 0.00 0.00 32.75 2.90
3085 3787 4.843220 AATGTGCACTCTCTTTTGGAAG 57.157 40.909 19.41 0.00 0.00 3.46
3121 3823 4.781775 TCTGTCCTTGAACTTACCCAAA 57.218 40.909 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.