Multiple sequence alignment - TraesCS1D01G131400

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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 TraesCS1D01G131400 chr1D 100.000 2637 0 0 1 2637 152625962 152628598 0.000000e+00 4870
1 TraesCS1D01G131400 chr1D 96.038 530 10 3 2108 2637 152482806 152483324 0.000000e+00 852
2 TraesCS1D01G131400 chr1D 97.288 295 7 1 1 295 152476562 152476855 1.410000e-137 499
3 TraesCS1D01G131400 chr6A 94.915 2635 92 14 1 2635 577151917 577154509 0.000000e+00 4085
4 TraesCS1D01G131400 chr5A 94.976 2548 79 11 1 2526 687969397 687971917 0.000000e+00 3951
5 TraesCS1D01G131400 chr5A 94.981 2331 94 10 316 2635 40241304 40238986 0.000000e+00 3635
6 TraesCS1D01G131400 chr5A 95.625 2217 67 6 310 2526 562122940 562120754 0.000000e+00 3530
7 TraesCS1D01G131400 chr5D 96.199 2368 79 8 269 2635 51585593 51583236 0.000000e+00 3864
8 TraesCS1D01G131400 chr5D 96.717 2315 68 6 321 2635 437728263 437725957 0.000000e+00 3847
9 TraesCS1D01G131400 chr5D 95.882 340 13 1 1 340 51585913 51585575 1.380000e-152 549
10 TraesCS1D01G131400 chr5D 94.194 310 17 1 1 310 92293790 92294098 3.070000e-129 472
11 TraesCS1D01G131400 chr5D 95.302 298 13 1 1 298 437728540 437728244 3.070000e-129 472
12 TraesCS1D01G131400 chr7D 94.793 2343 92 9 313 2635 107241847 107239515 0.000000e+00 3624
13 TraesCS1D01G131400 chr7D 95.987 299 11 1 1 299 509205906 509205609 3.950000e-133 484
14 TraesCS1D01G131400 chr7D 95.593 295 12 1 1 295 592037546 592037839 3.070000e-129 472
15 TraesCS1D01G131400 chr1A 95.038 2217 86 6 310 2526 16225042 16227234 0.000000e+00 3463
16 TraesCS1D01G131400 chr3A 92.029 2346 150 13 316 2637 604792362 604794694 0.000000e+00 3262
17 TraesCS1D01G131400 chr2B 94.148 1931 70 6 707 2637 32110224 32112111 0.000000e+00 2900
18 TraesCS1D01G131400 chr2B 93.550 1628 61 9 1013 2637 559330218 559328632 0.000000e+00 2385
19 TraesCS1D01G131400 chr5B 94.071 1501 73 9 1145 2637 163625277 163623785 0.000000e+00 2265
20 TraesCS1D01G131400 chr2D 96.417 307 10 1 1 307 165663875 165664180 3.030000e-139 505


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 TraesCS1D01G131400 chr1D 152625962 152628598 2636 False 4870.0 4870 100.0000 1 2637 1 chr1D.!!$F3 2636
1 TraesCS1D01G131400 chr1D 152482806 152483324 518 False 852.0 852 96.0380 2108 2637 1 chr1D.!!$F2 529
2 TraesCS1D01G131400 chr6A 577151917 577154509 2592 False 4085.0 4085 94.9150 1 2635 1 chr6A.!!$F1 2634
3 TraesCS1D01G131400 chr5A 687969397 687971917 2520 False 3951.0 3951 94.9760 1 2526 1 chr5A.!!$F1 2525
4 TraesCS1D01G131400 chr5A 40238986 40241304 2318 True 3635.0 3635 94.9810 316 2635 1 chr5A.!!$R1 2319
5 TraesCS1D01G131400 chr5A 562120754 562122940 2186 True 3530.0 3530 95.6250 310 2526 1 chr5A.!!$R2 2216
6 TraesCS1D01G131400 chr5D 51583236 51585913 2677 True 2206.5 3864 96.0405 1 2635 2 chr5D.!!$R1 2634
7 TraesCS1D01G131400 chr5D 437725957 437728540 2583 True 2159.5 3847 96.0095 1 2635 2 chr5D.!!$R2 2634
8 TraesCS1D01G131400 chr7D 107239515 107241847 2332 True 3624.0 3624 94.7930 313 2635 1 chr7D.!!$R1 2322
9 TraesCS1D01G131400 chr1A 16225042 16227234 2192 False 3463.0 3463 95.0380 310 2526 1 chr1A.!!$F1 2216
10 TraesCS1D01G131400 chr3A 604792362 604794694 2332 False 3262.0 3262 92.0290 316 2637 1 chr3A.!!$F1 2321
11 TraesCS1D01G131400 chr2B 32110224 32112111 1887 False 2900.0 2900 94.1480 707 2637 1 chr2B.!!$F1 1930
12 TraesCS1D01G131400 chr2B 559328632 559330218 1586 True 2385.0 2385 93.5500 1013 2637 1 chr2B.!!$R1 1624
13 TraesCS1D01G131400 chr5B 163623785 163625277 1492 True 2265.0 2265 94.0710 1145 2637 1 chr5B.!!$R1 1492

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
600 715 1.078214 TCGCTGGATCTTGCCCAAG 60.078 57.895 1.62 1.62 39.71 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2252 0.610232 ACAGCAACATGGCTTCCTCC 60.61 55.0 0.0 0.0 42.71 4.3 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
44 45 2.429058 CCTCAGTGTGGTGCAGCT 59.571 61.111 18.08 0.00 0.00 4.24
66 67 3.790416 TTGGGCCACTCCAGTGCAC 62.790 63.158 5.23 9.40 44.34 4.57
109 110 7.388776 TGTTGTCCTTTGTCTCATCATCTTAAG 59.611 37.037 0.00 0.00 0.00 1.85
213 214 9.922477 TCATGTTATATGATCCCTACCTAGTAG 57.078 37.037 0.00 0.00 36.04 2.57
220 221 5.326069 TGATCCCTACCTAGTAGCTTCATC 58.674 45.833 0.00 0.00 35.06 2.92
496 611 5.705905 GGCAATATATGGTAGTTTCCACTCC 59.294 44.000 0.00 0.00 40.51 3.85
497 612 5.705905 GCAATATATGGTAGTTTCCACTCCC 59.294 44.000 0.00 0.00 40.51 4.30
521 636 4.100963 TCACGCCCAAGATTAGTATGATGT 59.899 41.667 0.00 0.00 0.00 3.06
593 708 1.220206 CTGCACCTCGCTGGATCTT 59.780 57.895 1.32 0.00 43.06 2.40
600 715 1.078214 TCGCTGGATCTTGCCCAAG 60.078 57.895 1.62 1.62 39.71 3.61
857 1000 4.814147 CTCTGCTCATGTTGTTAGACAGA 58.186 43.478 0.00 0.00 32.19 3.41
992 1135 5.012239 CACTGAATCTGGGGAGAAAATCAA 58.988 41.667 0.00 0.00 0.00 2.57
1357 1500 7.469537 AACACAGAGAGTATTTACTACTGCT 57.530 36.000 16.98 2.03 40.88 4.24
1373 1516 4.756084 ACTGCTAACACAGAGATTTTGC 57.244 40.909 0.00 0.00 40.25 3.68
1400 1543 2.568956 TGCTACCTGATGAGTGCTTTCT 59.431 45.455 0.00 0.00 0.00 2.52
1449 1592 7.855409 TGCATAGATTTATTCGGTTTGAATTCG 59.145 33.333 0.04 0.00 45.06 3.34
1590 1756 2.485479 GCATTGGTACCCATCATCGAGT 60.485 50.000 10.07 0.00 31.53 4.18
1742 1908 3.181439 CCTTGGTTCCCTTTGTTCTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
1811 1977 3.431673 TGCCAGTTGAATGTATGGTCA 57.568 42.857 0.00 0.00 35.17 4.02
1813 1979 3.695556 TGCCAGTTGAATGTATGGTCATG 59.304 43.478 0.00 0.00 35.17 3.07
1814 1980 3.947196 GCCAGTTGAATGTATGGTCATGA 59.053 43.478 0.00 0.00 35.17 3.07
1815 1981 4.581824 GCCAGTTGAATGTATGGTCATGAT 59.418 41.667 0.00 0.00 35.17 2.45
1816 1982 5.764686 GCCAGTTGAATGTATGGTCATGATA 59.235 40.000 0.00 0.00 35.17 2.15
2017 2190 7.781324 ATACATGTCCTTTTCTTGAATGGTT 57.219 32.000 0.00 0.00 34.85 3.67
2039 2212 8.637986 TGGTTTGTTCATAATATATTTGCTCCC 58.362 33.333 2.68 0.00 0.00 4.30
2079 2252 7.215085 TCTCTGATTCATGTAACAGGATGATG 58.785 38.462 9.24 0.00 39.69 3.07
2230 2414 6.518032 GCATAGAAATATGAGAGAGTCCAGCA 60.518 42.308 0.00 0.00 0.00 4.41
2236 2420 1.261480 GAGAGAGTCCAGCAAGTCCA 58.739 55.000 0.00 0.00 0.00 4.02
2237 2421 1.204467 GAGAGAGTCCAGCAAGTCCAG 59.796 57.143 0.00 0.00 0.00 3.86
2238 2422 0.972883 GAGAGTCCAGCAAGTCCAGT 59.027 55.000 0.00 0.00 0.00 4.00
2239 2423 0.683973 AGAGTCCAGCAAGTCCAGTG 59.316 55.000 0.00 0.00 0.00 3.66
2240 2424 0.394565 GAGTCCAGCAAGTCCAGTGT 59.605 55.000 0.00 0.00 0.00 3.55
2241 2425 0.107456 AGTCCAGCAAGTCCAGTGTG 59.893 55.000 0.00 0.00 0.00 3.82
2242 2426 0.179045 GTCCAGCAAGTCCAGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
2243 2427 0.546122 TCCAGCAAGTCCAGTGTGTT 59.454 50.000 0.00 0.00 0.00 3.32
2244 2428 0.664761 CCAGCAAGTCCAGTGTGTTG 59.335 55.000 0.00 0.00 0.00 3.33
2245 2429 1.382522 CAGCAAGTCCAGTGTGTTGT 58.617 50.000 0.00 0.00 0.00 3.32
2246 2430 1.745087 CAGCAAGTCCAGTGTGTTGTT 59.255 47.619 0.00 0.00 0.00 2.83
2247 2431 2.942376 CAGCAAGTCCAGTGTGTTGTTA 59.058 45.455 0.00 0.00 0.00 2.41
2248 2432 3.565482 CAGCAAGTCCAGTGTGTTGTTAT 59.435 43.478 0.00 0.00 0.00 1.89
2249 2433 4.036734 CAGCAAGTCCAGTGTGTTGTTATT 59.963 41.667 0.00 0.00 0.00 1.40
2250 2434 4.036734 AGCAAGTCCAGTGTGTTGTTATTG 59.963 41.667 0.00 0.00 0.00 1.90
2251 2435 4.036262 GCAAGTCCAGTGTGTTGTTATTGA 59.964 41.667 0.00 0.00 0.00 2.57
2252 2436 5.278463 GCAAGTCCAGTGTGTTGTTATTGAT 60.278 40.000 0.00 0.00 0.00 2.57
2365 2583 6.483307 GCTTGTATTATGTGATCTGGTTGCTA 59.517 38.462 0.00 0.00 0.00 3.49
2371 2589 5.571784 ATGTGATCTGGTTGCTATTGTTG 57.428 39.130 0.00 0.00 0.00 3.33
2378 2596 7.611467 TGATCTGGTTGCTATTGTTGAAGTATT 59.389 33.333 0.00 0.00 0.00 1.89
2379 2597 9.109393 GATCTGGTTGCTATTGTTGAAGTATTA 57.891 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.322277 ACAGCATGCAGAGTTCCTGG 60.322 55.000 21.98 0.0 42.53 4.45
148 149 0.835941 AACATGCTGGGTGGCAAAAA 59.164 45.000 0.00 0.0 45.68 1.94
149 150 0.835941 AAACATGCTGGGTGGCAAAA 59.164 45.000 0.00 0.0 45.68 2.44
152 153 2.870119 GCAAACATGCTGGGTGGCA 61.870 57.895 0.00 0.0 46.63 4.92
213 214 2.932614 ACAAGTCTGCATACGATGAAGC 59.067 45.455 14.77 0.0 35.79 3.86
220 221 1.795768 ACACCACAAGTCTGCATACG 58.204 50.000 0.00 0.0 0.00 3.06
496 611 3.069586 TCATACTAATCTTGGGCGTGAGG 59.930 47.826 0.00 0.0 0.00 3.86
497 612 4.322080 TCATACTAATCTTGGGCGTGAG 57.678 45.455 0.00 0.0 0.00 3.51
521 636 0.553819 GGAGTGAGGAGGGAGAGCTA 59.446 60.000 0.00 0.0 0.00 3.32
600 715 3.207669 CAGCAAGATGAGCGGGGC 61.208 66.667 0.00 0.0 37.01 5.80
782 925 6.761714 GGGTGATGAATATACGAAACTGAACT 59.238 38.462 0.00 0.0 0.00 3.01
801 944 3.461085 AGCATGATAGAAGGTTGGGTGAT 59.539 43.478 0.00 0.0 0.00 3.06
857 1000 2.833943 GGGATGGCAGGAAGTGAAAATT 59.166 45.455 0.00 0.0 0.00 1.82
992 1135 1.277842 TGATGGTGTACATGCCGAAGT 59.722 47.619 0.00 0.0 40.72 3.01
1307 1450 5.637810 GCAGTAGTAAAACTCATGCAGTACA 59.362 40.000 10.06 0.0 38.74 2.90
1357 1500 5.404096 CATGCATGCAAAATCTCTGTGTTA 58.596 37.500 26.68 0.0 0.00 2.41
1373 1516 2.548480 CACTCATCAGGTAGCATGCATG 59.452 50.000 22.70 22.7 32.49 4.06
1400 1543 8.731605 TGCATACGAAGGTGAAATATTACAAAA 58.268 29.630 0.00 0.0 0.00 2.44
1482 1625 4.396166 AGTGACAGTGAAAACAAGTTGAGG 59.604 41.667 10.54 0.0 0.00 3.86
1590 1756 2.324330 CCGCTGTTGCATCCGTTCA 61.324 57.895 0.00 0.0 39.64 3.18
1742 1908 4.142708 CGCATACTAACATCACAAAGGCAA 60.143 41.667 0.00 0.0 0.00 4.52
1815 1981 8.885722 CGCCTAAAACAAAATACCATTCTACTA 58.114 33.333 0.00 0.0 0.00 1.82
1816 1982 7.627726 GCGCCTAAAACAAAATACCATTCTACT 60.628 37.037 0.00 0.0 0.00 2.57
2017 2190 8.458573 AACGGGAGCAAATATATTATGAACAA 57.541 30.769 0.00 0.0 0.00 2.83
2036 2209 4.997395 CAGAGAAGAATGAGAAAAACGGGA 59.003 41.667 0.00 0.0 0.00 5.14
2039 2212 7.800767 TGAATCAGAGAAGAATGAGAAAAACG 58.199 34.615 0.00 0.0 0.00 3.60
2079 2252 0.610232 ACAGCAACATGGCTTCCTCC 60.610 55.000 0.00 0.0 42.71 4.30
2230 2414 6.655003 CCTATCAATAACAACACACTGGACTT 59.345 38.462 0.00 0.0 0.00 3.01
2236 2420 6.054860 AGCTCCTATCAATAACAACACACT 57.945 37.500 0.00 0.0 0.00 3.55
2237 2421 6.149474 ACAAGCTCCTATCAATAACAACACAC 59.851 38.462 0.00 0.0 0.00 3.82
2238 2422 6.149308 CACAAGCTCCTATCAATAACAACACA 59.851 38.462 0.00 0.0 0.00 3.72
2239 2423 6.371548 TCACAAGCTCCTATCAATAACAACAC 59.628 38.462 0.00 0.0 0.00 3.32
2240 2424 6.472016 TCACAAGCTCCTATCAATAACAACA 58.528 36.000 0.00 0.0 0.00 3.33
2241 2425 6.985188 TCACAAGCTCCTATCAATAACAAC 57.015 37.500 0.00 0.0 0.00 3.32
2242 2426 7.168219 ACTTCACAAGCTCCTATCAATAACAA 58.832 34.615 0.00 0.0 0.00 2.83
2243 2427 6.711277 ACTTCACAAGCTCCTATCAATAACA 58.289 36.000 0.00 0.0 0.00 2.41
2244 2428 7.982354 ACTACTTCACAAGCTCCTATCAATAAC 59.018 37.037 0.00 0.0 0.00 1.89
2245 2429 8.079211 ACTACTTCACAAGCTCCTATCAATAA 57.921 34.615 0.00 0.0 0.00 1.40
2246 2430 7.661536 ACTACTTCACAAGCTCCTATCAATA 57.338 36.000 0.00 0.0 0.00 1.90
2247 2431 6.552445 ACTACTTCACAAGCTCCTATCAAT 57.448 37.500 0.00 0.0 0.00 2.57
2248 2432 6.663953 AGTACTACTTCACAAGCTCCTATCAA 59.336 38.462 0.00 0.0 0.00 2.57
2249 2433 6.188407 AGTACTACTTCACAAGCTCCTATCA 58.812 40.000 0.00 0.0 0.00 2.15
2250 2434 6.702716 AGTACTACTTCACAAGCTCCTATC 57.297 41.667 0.00 0.0 0.00 2.08
2252 2436 9.863650 AATATAGTACTACTTCACAAGCTCCTA 57.136 33.333 4.31 0.0 0.00 2.94
2378 2596 6.000840 TGGCAGAGATAAAAACACACACATA 58.999 36.000 0.00 0.0 0.00 2.29
2379 2597 4.826733 TGGCAGAGATAAAAACACACACAT 59.173 37.500 0.00 0.0 0.00 3.21


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

AutoCloner maintained by Alex Coulton.