Multiple sequence alignment - TraesCS6A01G212400

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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 TraesCS6A01G212400 chr6A 100.000 3197 0 0 1 3197 385573390 385570194 0.000000e+00 5904
1 TraesCS6A01G212400 chr6A 98.172 547 9 1 2649 3195 580785524 580786069 0.000000e+00 953
2 TraesCS6A01G212400 chr6A 94.389 303 17 0 2274 2576 580785227 580785529 1.740000e-127 466
3 TraesCS6A01G212400 chr1A 95.195 3205 130 14 1 3195 503679170 503675980 0.000000e+00 5044
4 TraesCS6A01G212400 chr3A 93.998 3199 160 16 5 3193 734237802 734240978 0.000000e+00 4815
5 TraesCS6A01G212400 chr7D 92.828 3207 161 26 4 3195 158647643 158644491 0.000000e+00 4584
6 TraesCS6A01G212400 chr7D 92.503 2521 150 10 1 2507 435178679 435181174 0.000000e+00 3572
7 TraesCS6A01G212400 chr7D 91.976 2505 147 21 14 2507 577333915 577331454 0.000000e+00 3463
8 TraesCS6A01G212400 chr7D 92.647 1768 112 9 4 1768 65768271 65766519 0.000000e+00 2529
9 TraesCS6A01G212400 chr1B 92.490 3209 165 29 1 3195 671830302 671833448 0.000000e+00 4521
10 TraesCS6A01G212400 chr2A 94.496 2489 109 10 1 2477 731834175 731836647 0.000000e+00 3812
11 TraesCS6A01G212400 chr2A 92.787 1220 57 11 1093 2301 21732238 21731039 0.000000e+00 1736
12 TraesCS6A01G212400 chr2A 96.011 727 23 3 2470 3193 731836804 731837527 0.000000e+00 1177
13 TraesCS6A01G212400 chr3D 93.272 2512 142 19 4 2507 584383172 584380680 0.000000e+00 3677
14 TraesCS6A01G212400 chr7A 93.649 1858 85 10 730 2576 26229373 26227538 0.000000e+00 2747
15 TraesCS6A01G212400 chr7A 91.229 1904 105 35 608 2500 69160776 69158924 0.000000e+00 2534
16 TraesCS6A01G212400 chr7A 97.248 545 14 1 2649 3193 26227543 26227000 0.000000e+00 922
17 TraesCS6A01G212400 chr5D 91.864 1733 132 6 15 1743 556291023 556289296 0.000000e+00 2410
18 TraesCS6A01G212400 chr6D 87.223 1127 117 19 5 1114 74865398 74866514 0.000000e+00 1258
19 TraesCS6A01G212400 chr2B 96.793 686 18 2 2513 3195 733356174 733355490 0.000000e+00 1142
20 TraesCS6A01G212400 chr4D 95.773 686 25 2 2513 3195 251092894 251092210 0.000000e+00 1103
21 TraesCS6A01G212400 chr3B 93.914 608 23 3 2120 2713 801611728 801611121 0.000000e+00 905


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 TraesCS6A01G212400 chr6A 385570194 385573390 3196 True 5904.0 5904 100.0000 1 3197 1 chr6A.!!$R1 3196
1 TraesCS6A01G212400 chr6A 580785227 580786069 842 False 709.5 953 96.2805 2274 3195 2 chr6A.!!$F1 921
2 TraesCS6A01G212400 chr1A 503675980 503679170 3190 True 5044.0 5044 95.1950 1 3195 1 chr1A.!!$R1 3194
3 TraesCS6A01G212400 chr3A 734237802 734240978 3176 False 4815.0 4815 93.9980 5 3193 1 chr3A.!!$F1 3188
4 TraesCS6A01G212400 chr7D 158644491 158647643 3152 True 4584.0 4584 92.8280 4 3195 1 chr7D.!!$R2 3191
5 TraesCS6A01G212400 chr7D 435178679 435181174 2495 False 3572.0 3572 92.5030 1 2507 1 chr7D.!!$F1 2506
6 TraesCS6A01G212400 chr7D 577331454 577333915 2461 True 3463.0 3463 91.9760 14 2507 1 chr7D.!!$R3 2493
7 TraesCS6A01G212400 chr7D 65766519 65768271 1752 True 2529.0 2529 92.6470 4 1768 1 chr7D.!!$R1 1764
8 TraesCS6A01G212400 chr1B 671830302 671833448 3146 False 4521.0 4521 92.4900 1 3195 1 chr1B.!!$F1 3194
9 TraesCS6A01G212400 chr2A 731834175 731837527 3352 False 2494.5 3812 95.2535 1 3193 2 chr2A.!!$F1 3192
10 TraesCS6A01G212400 chr2A 21731039 21732238 1199 True 1736.0 1736 92.7870 1093 2301 1 chr2A.!!$R1 1208
11 TraesCS6A01G212400 chr3D 584380680 584383172 2492 True 3677.0 3677 93.2720 4 2507 1 chr3D.!!$R1 2503
12 TraesCS6A01G212400 chr7A 69158924 69160776 1852 True 2534.0 2534 91.2290 608 2500 1 chr7A.!!$R1 1892
13 TraesCS6A01G212400 chr7A 26227000 26229373 2373 True 1834.5 2747 95.4485 730 3193 2 chr7A.!!$R2 2463
14 TraesCS6A01G212400 chr5D 556289296 556291023 1727 True 2410.0 2410 91.8640 15 1743 1 chr5D.!!$R1 1728
15 TraesCS6A01G212400 chr6D 74865398 74866514 1116 False 1258.0 1258 87.2230 5 1114 1 chr6D.!!$F1 1109
16 TraesCS6A01G212400 chr2B 733355490 733356174 684 True 1142.0 1142 96.7930 2513 3195 1 chr2B.!!$R1 682
17 TraesCS6A01G212400 chr4D 251092210 251092894 684 True 1103.0 1103 95.7730 2513 3195 1 chr4D.!!$R1 682
18 TraesCS6A01G212400 chr3B 801611121 801611728 607 True 905.0 905 93.9140 2120 2713 1 chr3B.!!$R1 593

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
935 959 0.107643 TGGAGACGTTTGTGCCATGA 59.892 50.0 0.0 0.0 0.00 3.07 F
1577 1666 0.177373 GGTAAGCCAACCCTACCTCG 59.823 60.0 0.0 0.0 33.02 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2140 0.543749 GGCAGAGAGGTTAGCCACAT 59.456 55.0 0.0 0.0 46.26 3.21 R
2540 2842 1.067693 CGCTGCTATCGTGTTTGACA 58.932 50.0 0.0 0.0 0.00 3.58 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
126 127 8.489990 TTTGTCAATTGTGCATTAAATATGGG 57.510 30.769 5.13 0.00 0.00 4.00
217 219 4.048504 CCCATTTTTGTCACTCGGAAAAC 58.951 43.478 0.00 0.00 0.00 2.43
417 419 8.293114 TGTTTCTGAGAACACTTTTTCAAAAC 57.707 30.769 0.00 0.00 34.77 2.43
544 559 4.388469 CCCGTTTCAAAATGCGATCAAAAT 59.612 37.500 0.00 0.00 0.00 1.82
551 566 1.750193 ATGCGATCAAAATGACGGGT 58.250 45.000 0.00 0.00 0.00 5.28
935 959 0.107643 TGGAGACGTTTGTGCCATGA 59.892 50.000 0.00 0.00 0.00 3.07
948 972 2.874086 GTGCCATGAATCGATGACATGA 59.126 45.455 30.29 18.01 42.41 3.07
949 973 3.313249 GTGCCATGAATCGATGACATGAA 59.687 43.478 30.29 21.20 42.41 2.57
1014 1069 1.453745 CACCCATCCATTCCCCACG 60.454 63.158 0.00 0.00 0.00 4.94
1077 1136 1.615124 TTCCCCTTCCAGATCGCCA 60.615 57.895 0.00 0.00 0.00 5.69
1191 1256 3.505773 GCATCCATGGCCTCCCCT 61.506 66.667 6.96 0.00 0.00 4.79
1258 1323 2.752238 CGACGCTCCCCTCACTCT 60.752 66.667 0.00 0.00 0.00 3.24
1276 1341 0.984961 CTGGGCCTTCATCCTCTCCA 60.985 60.000 4.53 0.00 0.00 3.86
1395 1463 1.264749 ATCTAGCCCGTCAAGCACCA 61.265 55.000 0.00 0.00 0.00 4.17
1491 1559 1.364626 GACGCCTTCCTCGTCGACTA 61.365 60.000 14.70 0.95 45.19 2.59
1577 1666 0.177373 GGTAAGCCAACCCTACCTCG 59.823 60.000 0.00 0.00 33.02 4.63
1596 1691 2.695970 CCCTCTCCCTCTCCCTCGT 61.696 68.421 0.00 0.00 0.00 4.18
1598 1693 2.043852 TCTCCCTCTCCCTCGTGC 60.044 66.667 0.00 0.00 0.00 5.34
1991 2090 0.322816 ACATGCGTGAGGAATGGCTT 60.323 50.000 14.17 0.00 32.68 4.35
2041 2140 5.360144 GGTTGTAGCTCTAGGTCTATTGTGA 59.640 44.000 0.00 0.00 0.00 3.58
2049 2148 5.454966 TCTAGGTCTATTGTGATGTGGCTA 58.545 41.667 0.00 0.00 0.00 3.93
2086 2185 0.250684 TGGACGTCCGTGTGGTACTA 60.251 55.000 28.70 4.91 39.43 1.82
2239 2366 3.982516 TGGAGCATCTGGTTAGAGTAGT 58.017 45.455 0.00 0.00 36.14 2.73
2260 2398 9.036980 AGTAGTCATTTGATTACTCCAGTACTT 57.963 33.333 9.26 0.00 41.75 2.24
2309 2447 7.906199 ATGGAGTAGTTAGAGTAGCATCTTT 57.094 36.000 0.00 0.00 0.00 2.52
2337 2475 6.382869 AACTAAATGGATGATAGCTGTTGC 57.617 37.500 0.00 0.00 40.05 4.17
2388 2526 2.289694 GCAAGCAGTAGTTCCCTCTTCA 60.290 50.000 0.00 0.00 0.00 3.02
2416 2554 8.366671 TCTCTTCTTTCTTGCAGTAGTTTAAC 57.633 34.615 0.00 0.00 0.00 2.01
2501 2803 5.301551 TGAATCCAGTTACAACAAAGCATGT 59.698 36.000 0.00 0.00 46.82 3.21
2522 2824 6.614694 TGTCAGTAACAATAAAGCTCCCTA 57.385 37.500 0.00 0.00 34.03 3.53
2540 2842 7.454694 AGCTCCCTATAACCTTTTGTTTCATTT 59.545 33.333 0.00 0.00 38.42 2.32
2571 2873 4.615815 GCAGCGATGCCGAGGGAT 62.616 66.667 16.30 0.00 38.22 3.85
2609 2911 6.646653 CGTATGCATTCTAATGGTCACATACT 59.353 38.462 3.54 0.00 36.98 2.12
3055 3361 6.011628 TCTCCTCCATGGAAAGACCTATTTTT 60.012 38.462 17.00 0.00 45.63 1.94
3098 3404 2.552155 GGCAGACCATGTGAACAACCTA 60.552 50.000 0.00 0.00 35.26 3.08
3151 3457 3.402681 GGAGGTGCTGCAGGGCTA 61.403 66.667 17.12 0.00 0.00 3.93
3195 3501 3.382083 AACCAAATCGGCTTCCCTATT 57.618 42.857 0.00 0.00 39.03 1.73
3196 3502 4.513406 AACCAAATCGGCTTCCCTATTA 57.487 40.909 0.00 0.00 39.03 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 7.885922 TGTGAAGAACCTACCAAATATTTGCTA 59.114 33.333 20.67 11.85 36.86 3.49
392 394 7.923344 TGTTTTGAAAAAGTGTTCTCAGAAACA 59.077 29.630 0.00 0.00 36.82 2.83
551 566 3.220110 CCACTAGCTAGGAACGGTCATA 58.780 50.000 24.35 0.00 0.00 2.15
935 959 7.120285 GGATGGATATGTTTCATGTCATCGATT 59.880 37.037 0.00 0.00 32.89 3.34
948 972 5.554747 AGGAGATGGATGGATGGATATGTTT 59.445 40.000 0.00 0.00 0.00 2.83
949 973 5.106577 AGGAGATGGATGGATGGATATGTT 58.893 41.667 0.00 0.00 0.00 2.71
1014 1069 0.035343 GAGACAGGTAGGGGTTTGCC 60.035 60.000 0.00 0.00 0.00 4.52
1162 1227 2.662866 CATGGATGCTGATGGAAAGGT 58.337 47.619 0.00 0.00 0.00 3.50
1165 1230 1.405872 GCCATGGATGCTGATGGAAA 58.594 50.000 18.40 0.00 41.63 3.13
1191 1256 4.329545 GCGGTGAGGAAGGGTGCA 62.330 66.667 0.00 0.00 0.00 4.57
1194 1259 2.990479 GATGCGGTGAGGAAGGGT 59.010 61.111 0.00 0.00 0.00 4.34
1254 1319 0.043940 AGAGGATGAAGGCCCAGAGT 59.956 55.000 0.00 0.00 0.00 3.24
1258 1323 0.984961 CTGGAGAGGATGAAGGCCCA 60.985 60.000 0.00 0.00 0.00 5.36
1395 1463 3.194542 CCTCGAAGGAGAGACTTTGACAT 59.805 47.826 0.00 0.00 43.27 3.06
1456 1524 1.878656 CGTCGAAGAAGGCCTCCACT 61.879 60.000 5.23 3.10 39.69 4.00
1491 1559 0.321996 GCGGAACCAGAAGAGGAAGT 59.678 55.000 0.00 0.00 0.00 3.01
1577 1666 2.123033 GAGGGAGAGGGAGAGGGC 60.123 72.222 0.00 0.00 0.00 5.19
1596 1691 3.706373 GAACAGAGGAGCCGGGCA 61.706 66.667 23.09 0.00 0.00 5.36
1598 1693 2.837371 GAACGAACAGAGGAGCCGGG 62.837 65.000 2.18 0.00 0.00 5.73
1895 1994 2.223688 CCTAAGCTCCTCATCTGTGTCG 60.224 54.545 0.00 0.00 0.00 4.35
1991 2090 4.335874 ACAGTAACAATAACCGCACAACAA 59.664 37.500 0.00 0.00 0.00 2.83
2041 2140 0.543749 GGCAGAGAGGTTAGCCACAT 59.456 55.000 0.00 0.00 46.26 3.21
2049 2148 2.520536 AACCAGCGGCAGAGAGGTT 61.521 57.895 1.45 5.44 37.73 3.50
2111 2210 2.866156 CACACACACTGTTCATTCGAGT 59.134 45.455 0.00 0.00 0.00 4.18
2260 2398 5.351948 TGCAAGATGCCACTGTAACTATA 57.648 39.130 0.00 0.00 44.23 1.31
2309 2447 9.851686 AACAGCTATCATCCATTTAGTTAATCA 57.148 29.630 0.00 0.00 0.00 2.57
2322 2460 4.274459 CCAACTTAGCAACAGCTATCATCC 59.726 45.833 0.00 0.00 40.33 3.51
2337 2475 2.227388 CTGCTTGCAAGTCCCAACTTAG 59.773 50.000 26.55 7.74 43.99 2.18
2416 2554 5.256474 ACTCCACCAAAGACCAATCATAAG 58.744 41.667 0.00 0.00 0.00 1.73
2425 2563 5.313712 TCAAGAAATACTCCACCAAAGACC 58.686 41.667 0.00 0.00 0.00 3.85
2501 2803 8.208903 GGTTATAGGGAGCTTTATTGTTACTGA 58.791 37.037 0.00 0.00 0.00 3.41
2522 2824 9.442047 TGTTTGACAAATGAAACAAAAGGTTAT 57.558 25.926 3.49 0.00 38.73 1.89
2540 2842 1.067693 CGCTGCTATCGTGTTTGACA 58.932 50.000 0.00 0.00 0.00 3.58
2571 2873 1.731433 GCATACGCGTGTAGGGGAGA 61.731 60.000 24.59 0.00 33.08 3.71
2583 2885 3.559655 TGTGACCATTAGAATGCATACGC 59.440 43.478 0.00 0.00 35.08 4.42
3055 3361 5.048504 GCCACTTCAAAACAATCATCAGAGA 60.049 40.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.