Multiple sequence alignment - TraesCS2B01G102100

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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 TraesCS2B01G102100 chr2B 100.000 2619 0 0 1 2619 63132209 63129591 0.000000e+00 4837
1 TraesCS2B01G102100 chr4B 95.413 2289 98 4 334 2619 74349132 74351416 0.000000e+00 3639
2 TraesCS2B01G102100 chr2D 95.363 2286 97 4 334 2619 644818111 644820387 0.000000e+00 3626
3 TraesCS2B01G102100 chr7D 95.144 2286 100 6 334 2619 29571376 29569102 0.000000e+00 3596
4 TraesCS2B01G102100 chr7D 96.119 335 11 1 1 335 29571839 29571507 1.770000e-151 545
5 TraesCS2B01G102100 chr5A 95.057 2286 105 3 334 2619 139476492 139474215 0.000000e+00 3589
6 TraesCS2B01G102100 chr5A 96.716 335 11 0 1 335 139476957 139476623 2.280000e-155 558
7 TraesCS2B01G102100 chr4D 95.059 2287 102 6 334 2619 403009343 403011619 0.000000e+00 3587
8 TraesCS2B01G102100 chr4D 97.015 335 10 0 1 335 403008878 403009212 4.890000e-157 564
9 TraesCS2B01G102100 chr1D 94.619 2286 112 6 334 2619 187808817 187811091 0.000000e+00 3530
10 TraesCS2B01G102100 chr3D 95.240 2038 90 5 584 2619 107214418 107216450 0.000000e+00 3219
11 TraesCS2B01G102100 chr3D 96.418 335 10 2 1 335 107205543 107205875 3.810000e-153 551
12 TraesCS2B01G102100 chr3D 94.118 255 8 1 334 588 107206005 107206252 5.290000e-102 381
13 TraesCS2B01G102100 chr7B 97.301 1371 35 1 1 1369 400419597 400418227 0.000000e+00 2326
14 TraesCS2B01G102100 chr7B 97.693 1257 28 1 1363 2619 400417620 400416365 0.000000e+00 2159
15 TraesCS2B01G102100 chr7B 98.503 668 10 0 1 668 400460714 400460047 0.000000e+00 1179
16 TraesCS2B01G102100 chr6D 93.165 1463 78 11 334 1781 433251236 433252691 0.000000e+00 2128
17 TraesCS2B01G102100 chr6A 96.555 987 33 1 1633 2619 615072488 615071503 0.000000e+00 1633
18 TraesCS2B01G102100 chr6A 96.736 337 8 2 1 335 615073963 615073628 2.280000e-155 558
19 TraesCS2B01G102100 chr5B 97.944 535 11 0 1 535 691751938 691751404 0.000000e+00 928
20 TraesCS2B01G102100 chr6B 97.598 333 8 0 3 335 128934676 128934344 2.920000e-159 571


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 TraesCS2B01G102100 chr2B 63129591 63132209 2618 True 4837.0 4837 100.0000 1 2619 1 chr2B.!!$R1 2618
1 TraesCS2B01G102100 chr4B 74349132 74351416 2284 False 3639.0 3639 95.4130 334 2619 1 chr4B.!!$F1 2285
2 TraesCS2B01G102100 chr2D 644818111 644820387 2276 False 3626.0 3626 95.3630 334 2619 1 chr2D.!!$F1 2285
3 TraesCS2B01G102100 chr7D 29569102 29571839 2737 True 2070.5 3596 95.6315 1 2619 2 chr7D.!!$R1 2618
4 TraesCS2B01G102100 chr5A 139474215 139476957 2742 True 2073.5 3589 95.8865 1 2619 2 chr5A.!!$R1 2618
5 TraesCS2B01G102100 chr4D 403008878 403011619 2741 False 2075.5 3587 96.0370 1 2619 2 chr4D.!!$F1 2618
6 TraesCS2B01G102100 chr1D 187808817 187811091 2274 False 3530.0 3530 94.6190 334 2619 1 chr1D.!!$F1 2285
7 TraesCS2B01G102100 chr3D 107214418 107216450 2032 False 3219.0 3219 95.2400 584 2619 1 chr3D.!!$F1 2035
8 TraesCS2B01G102100 chr3D 107205543 107206252 709 False 466.0 551 95.2680 1 588 2 chr3D.!!$F2 587
9 TraesCS2B01G102100 chr7B 400416365 400419597 3232 True 2242.5 2326 97.4970 1 2619 2 chr7B.!!$R2 2618
10 TraesCS2B01G102100 chr7B 400460047 400460714 667 True 1179.0 1179 98.5030 1 668 1 chr7B.!!$R1 667
11 TraesCS2B01G102100 chr6D 433251236 433252691 1455 False 2128.0 2128 93.1650 334 1781 1 chr6D.!!$F1 1447
12 TraesCS2B01G102100 chr6A 615071503 615073963 2460 True 1095.5 1633 96.6455 1 2619 2 chr6A.!!$R1 2618
13 TraesCS2B01G102100 chr5B 691751404 691751938 534 True 928.0 928 97.9440 1 535 1 chr5B.!!$R1 534

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
984 1136 1.559682 CTTCCCCAGAATCTTTCCCGA 59.44 52.381 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 3366 0.906066 TAAGTGCCCCTTCATGCGTA 59.094 50.0 0.0 0.0 34.46 4.42 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
58 59 7.112452 ACAATGGTCCTTGGAAATTATTAGC 57.888 36.000 0.00 0.0 0.00 3.09
152 154 6.826727 AGGAAGGAAGATGGGGATATATGTA 58.173 40.000 0.00 0.0 0.00 2.29
153 155 6.905776 AGGAAGGAAGATGGGGATATATGTAG 59.094 42.308 0.00 0.0 0.00 2.74
396 536 9.522804 TTTGTTTATGTTTTGAGTGGTCAATAC 57.477 29.630 2.80 2.8 42.41 1.89
420 560 2.003937 TACCGCTGGCCACATATCTA 57.996 50.000 0.00 0.0 0.00 1.98
616 767 7.568199 AAAAGTATTGTCAGTGCTACAAACT 57.432 32.000 1.90 4.8 40.05 2.66
645 796 8.976986 AACTGATGAAAGAAGAACATATTTGC 57.023 30.769 0.00 0.0 0.00 3.68
655 806 8.353423 AGAAGAACATATTTGCACCTTATTGT 57.647 30.769 0.00 0.0 0.00 2.71
682 833 5.566826 GCTGACTATACACACAAGAACCTCA 60.567 44.000 0.00 0.0 0.00 3.86
951 1103 3.440522 CACGACCACTGAGATGTAGAAGA 59.559 47.826 0.00 0.0 0.00 2.87
984 1136 1.559682 CTTCCCCAGAATCTTTCCCGA 59.440 52.381 0.00 0.0 0.00 5.14
1085 1237 1.610624 GGACATGACATTGTGGTCGGT 60.611 52.381 0.00 0.0 40.72 4.69
1259 1414 1.294659 GAACTTGAGACTGCAGCCGG 61.295 60.000 15.27 0.0 0.00 6.13
1280 1435 0.472925 TCTGGAGCAAGGGTGGTGTA 60.473 55.000 0.00 0.0 35.00 2.90
1491 2261 3.795688 AGATGTCAGTGGTGGAAACAT 57.204 42.857 0.00 0.0 46.14 2.71
2166 2946 6.992123 TCAACTTAATACATAGCATGTCCTGG 59.008 38.462 5.25 0.0 43.67 4.45
2609 3389 2.223572 CGCATGAAGGGGCACTTAATTC 60.224 50.000 0.00 0.0 40.21 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.827284 AGGGGACAGACATTTTGTAAAGTG 59.173 41.667 0.00 0.00 0.00 3.16
152 154 3.377154 TCCTCCTATCTCCCTCTCTCT 57.623 52.381 0.00 0.00 0.00 3.10
153 155 3.245264 CCTTCCTCCTATCTCCCTCTCTC 60.245 56.522 0.00 0.00 0.00 3.20
246 252 7.187824 ACAGAGACATACATATTTGAGTGGT 57.812 36.000 0.00 0.00 0.00 4.16
396 536 0.392998 ATGTGGCCAGCGGTAAAGAG 60.393 55.000 5.11 0.00 0.00 2.85
655 806 5.470368 GTTCTTGTGTGTATAGTCAGCTGA 58.530 41.667 13.74 13.74 0.00 4.26
951 1103 0.846693 GGGGAAGCACCAGGACATAT 59.153 55.000 0.00 0.00 41.20 1.78
1004 1156 1.480137 CCAAAAACTGCCACCAGAACA 59.520 47.619 0.00 0.00 41.77 3.18
1141 1293 2.182030 GTGAGAAGAGGCGACCCG 59.818 66.667 0.00 0.00 35.76 5.28
1244 1399 1.301716 GAACCGGCTGCAGTCTCAA 60.302 57.895 17.70 0.00 0.00 3.02
1251 1406 4.704833 GCTCCAGAACCGGCTGCA 62.705 66.667 0.00 0.00 34.56 4.41
1259 1414 0.890996 CACCACCCTTGCTCCAGAAC 60.891 60.000 0.00 0.00 0.00 3.01
1491 2261 8.204160 CACCCTCAACATCTTCTATAACATGTA 58.796 37.037 0.00 0.00 0.00 2.29
1858 2638 1.229400 ACTGGCGGGGTTTCCTCTA 60.229 57.895 0.00 0.00 0.00 2.43
2166 2946 7.596248 AGTGAAGAAATGCATCATGTTTAACAC 59.404 33.333 0.00 2.70 0.00 3.32
2320 3100 5.004448 GTGATAGTGGATAGGATCGTCTCA 58.996 45.833 3.59 0.00 0.00 3.27
2586 3366 0.906066 TAAGTGCCCCTTCATGCGTA 59.094 50.000 0.00 0.00 34.46 4.42


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

AutoCloner maintained by Alex Coulton.