Multiple sequence alignment - TraesCS6A01G265200

Loading Multiple Alignment...

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 TraesCS6A01G265200 chr6A 100.000 3431 0 0 1 3431 490228306 490224876 0.000000e+00 6336
1 TraesCS6A01G265200 chr1D 95.275 3471 120 15 1 3431 95412111 95408645 0.000000e+00 5461
2 TraesCS6A01G265200 chr1D 94.650 3458 151 15 1 3431 88013094 88009644 0.000000e+00 5330
3 TraesCS6A01G265200 chr1D 94.269 3455 161 15 1 3428 296768530 296771974 0.000000e+00 5249
4 TraesCS6A01G265200 chr1D 93.957 3475 160 16 1 3431 78754865 78751397 0.000000e+00 5208
5 TraesCS6A01G265200 chr3D 95.253 3455 128 12 1 3429 353281221 353284665 0.000000e+00 5439
6 TraesCS6A01G265200 chr3D 94.667 3469 136 18 1 3431 254423767 254420310 0.000000e+00 5336
7 TraesCS6A01G265200 chr7D 94.945 3462 140 17 1 3431 243734972 243731515 0.000000e+00 5391
8 TraesCS6A01G265200 chr5D 94.942 3460 140 15 1 3431 108670117 108666664 0.000000e+00 5387
9 TraesCS6A01G265200 chr2D 94.449 3459 157 15 1 3431 259247800 259244349 0.000000e+00 5291
10 TraesCS6A01G265200 chr4D 94.337 3461 160 17 1 3431 426270119 426266665 0.000000e+00 5273
11 TraesCS6A01G265200 chr4D 93.842 2501 134 8 948 3431 201249772 201252269 0.000000e+00 3747
12 TraesCS6A01G265200 chr4D 88.301 359 24 5 3087 3431 144580162 144579808 6.850000e-112 414
13 TraesCS6A01G265200 chr1A 92.695 3477 203 22 1 3431 303520070 303523541 0.000000e+00 4966
14 TraesCS6A01G265200 chr1A 93.571 3251 169 20 214 3431 277154040 277150797 0.000000e+00 4809
15 TraesCS6A01G265200 chr2A 92.411 3439 208 27 29 3431 160674576 160671155 0.000000e+00 4855
16 TraesCS6A01G265200 chr2A 93.030 3257 184 20 214 3431 367432668 367429416 0.000000e+00 4717
17 TraesCS6A01G265200 chr2A 94.844 1862 86 2 1 1852 377553021 377554882 0.000000e+00 2898
18 TraesCS6A01G265200 chr2A 95.500 1600 55 7 1847 3431 377567040 377568637 0.000000e+00 2540
19 TraesCS6A01G265200 chr5A 92.183 3441 225 17 29 3431 154818392 154814958 0.000000e+00 4824
20 TraesCS6A01G265200 chr5A 93.061 3257 182 23 214 3431 171373203 171369952 0.000000e+00 4723
21 TraesCS6A01G265200 chr6D 93.965 2502 123 11 1 2480 428022186 428019691 0.000000e+00 3759
22 TraesCS6A01G265200 chr3A 93.379 2024 109 12 1 2003 204358407 204356388 0.000000e+00 2972


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 TraesCS6A01G265200 chr6A 490224876 490228306 3430 True 6336 6336 100.000 1 3431 1 chr6A.!!$R1 3430
1 TraesCS6A01G265200 chr1D 95408645 95412111 3466 True 5461 5461 95.275 1 3431 1 chr1D.!!$R3 3430
2 TraesCS6A01G265200 chr1D 88009644 88013094 3450 True 5330 5330 94.650 1 3431 1 chr1D.!!$R2 3430
3 TraesCS6A01G265200 chr1D 296768530 296771974 3444 False 5249 5249 94.269 1 3428 1 chr1D.!!$F1 3427
4 TraesCS6A01G265200 chr1D 78751397 78754865 3468 True 5208 5208 93.957 1 3431 1 chr1D.!!$R1 3430
5 TraesCS6A01G265200 chr3D 353281221 353284665 3444 False 5439 5439 95.253 1 3429 1 chr3D.!!$F1 3428
6 TraesCS6A01G265200 chr3D 254420310 254423767 3457 True 5336 5336 94.667 1 3431 1 chr3D.!!$R1 3430
7 TraesCS6A01G265200 chr7D 243731515 243734972 3457 True 5391 5391 94.945 1 3431 1 chr7D.!!$R1 3430
8 TraesCS6A01G265200 chr5D 108666664 108670117 3453 True 5387 5387 94.942 1 3431 1 chr5D.!!$R1 3430
9 TraesCS6A01G265200 chr2D 259244349 259247800 3451 True 5291 5291 94.449 1 3431 1 chr2D.!!$R1 3430
10 TraesCS6A01G265200 chr4D 426266665 426270119 3454 True 5273 5273 94.337 1 3431 1 chr4D.!!$R2 3430
11 TraesCS6A01G265200 chr4D 201249772 201252269 2497 False 3747 3747 93.842 948 3431 1 chr4D.!!$F1 2483
12 TraesCS6A01G265200 chr1A 303520070 303523541 3471 False 4966 4966 92.695 1 3431 1 chr1A.!!$F1 3430
13 TraesCS6A01G265200 chr1A 277150797 277154040 3243 True 4809 4809 93.571 214 3431 1 chr1A.!!$R1 3217
14 TraesCS6A01G265200 chr2A 160671155 160674576 3421 True 4855 4855 92.411 29 3431 1 chr2A.!!$R1 3402
15 TraesCS6A01G265200 chr2A 367429416 367432668 3252 True 4717 4717 93.030 214 3431 1 chr2A.!!$R2 3217
16 TraesCS6A01G265200 chr2A 377553021 377554882 1861 False 2898 2898 94.844 1 1852 1 chr2A.!!$F1 1851
17 TraesCS6A01G265200 chr2A 377567040 377568637 1597 False 2540 2540 95.500 1847 3431 1 chr2A.!!$F2 1584
18 TraesCS6A01G265200 chr5A 154814958 154818392 3434 True 4824 4824 92.183 29 3431 1 chr5A.!!$R1 3402
19 TraesCS6A01G265200 chr5A 171369952 171373203 3251 True 4723 4723 93.061 214 3431 1 chr5A.!!$R2 3217
20 TraesCS6A01G265200 chr6D 428019691 428022186 2495 True 3759 3759 93.965 1 2480 1 chr6D.!!$R1 2479
21 TraesCS6A01G265200 chr3A 204356388 204358407 2019 True 2972 2972 93.379 1 2003 1 chr3A.!!$R1 2002

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
267 274 1.333619 CACCCGTGAACACCTCAAAAG 59.666 52.381 0.0 0.0 35.22 2.27 F
951 1028 1.678123 CCTTCCATCTCCACTGCACAG 60.678 57.143 0.0 0.0 0.00 3.66 F
1143 1220 1.292223 GCACGGCAAGGAGACACTA 59.708 57.895 0.0 0.0 0.00 2.74 F
1170 1247 1.597854 CTGCACCAGCGAACCAGAA 60.598 57.895 0.0 0.0 46.23 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1220 0.390866 CGCTGGTGCAGACAATCTCT 60.391 55.000 0.00 0.0 39.64 3.10 R
2241 2327 2.433868 TGTAGTCTTCCTGCGTGTTC 57.566 50.000 0.00 0.0 0.00 3.18 R
2305 2391 3.133003 GTGGTGTATGCATCTACTCCTGT 59.867 47.826 17.39 0.0 36.60 4.00 R
3144 3239 5.265191 TGAATCTAGTACTTGACTCCAGCT 58.735 41.667 12.15 0.0 39.81 4.24 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
161 166 3.244078 TGTCGACCAGTAACTCAGCAAAT 60.244 43.478 14.12 0.0 0.00 2.32
267 274 1.333619 CACCCGTGAACACCTCAAAAG 59.666 52.381 0.00 0.0 35.22 2.27
499 525 5.483937 ACACATAGTCTCACTGGTATTTGGA 59.516 40.000 0.00 0.0 0.00 3.53
529 555 2.169832 ACACTTCAATCACCAGTCCG 57.830 50.000 0.00 0.0 0.00 4.79
552 578 5.251764 GAGTACCACAGTAGAGGAGTACAA 58.748 45.833 0.00 0.0 34.03 2.41
699 728 6.069905 TGGGATTTAGCAGGTCATAAGTACAA 60.070 38.462 0.00 0.0 0.00 2.41
951 1028 1.678123 CCTTCCATCTCCACTGCACAG 60.678 57.143 0.00 0.0 0.00 3.66
1014 1091 2.514824 GCGATGGCAGAGGAACCC 60.515 66.667 0.00 0.0 39.62 4.11
1140 1217 2.280797 GTGCACGGCAAGGAGACA 60.281 61.111 0.00 0.0 41.47 3.41
1143 1220 1.292223 GCACGGCAAGGAGACACTA 59.708 57.895 0.00 0.0 0.00 2.74
1170 1247 1.597854 CTGCACCAGCGAACCAGAA 60.598 57.895 0.00 0.0 46.23 3.02
1191 1268 2.122167 GGCCGACGAGGTGATCTCT 61.122 63.158 0.00 0.0 43.70 3.10
1319 1396 2.811317 CGACGACCTCTGCTTGGC 60.811 66.667 0.00 0.0 0.00 4.52
1372 1449 2.856222 CCATCCTACTCATTTGCCCTC 58.144 52.381 0.00 0.0 0.00 4.30
2157 2243 2.995872 GCGCGAGTGGAGAGTTCCT 61.996 63.158 12.10 0.0 44.36 3.36
2241 2327 5.130292 ACAAAGGCATGAAGAAGAACATG 57.870 39.130 0.00 0.0 44.32 3.21
2305 2391 2.492088 CCAGACAACCTCATCGAGTACA 59.508 50.000 0.00 0.0 0.00 2.90
2382 2468 3.674753 CAGATGGTTCGGAAATTGCAAAC 59.325 43.478 1.71 0.0 0.00 2.93
2754 2846 6.752351 TGTTCTATGTCTAGTTTCGATTCAGC 59.248 38.462 0.00 0.0 0.00 4.26
3144 3239 7.222000 ACAAAAAGTTTCAGTCCAAGTTACA 57.778 32.000 0.00 0.0 0.00 2.41
3237 3338 5.512749 CCCTGATGCTGCTAGATACTTGAAT 60.513 44.000 0.00 0.0 0.00 2.57
3309 3434 0.170116 CAAGAGAGAGAGCGAGCGTT 59.830 55.000 0.00 0.0 0.00 4.84
3322 3447 4.968032 GCGTTGTGTATAAGCGCC 57.032 55.556 2.29 0.0 41.93 6.53
3403 3528 2.501610 CCCCCTCGACTAGCAAGC 59.498 66.667 0.00 0.0 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 3.553105 GGTCGACAGTAGTGTTTTTCGTT 59.447 43.478 18.91 0.00 36.88 3.85
499 525 8.006298 TGGTGATTGAAGTGTAATTGAACTTT 57.994 30.769 8.48 0.00 36.77 2.66
529 555 4.841422 TGTACTCCTCTACTGTGGTACTC 58.159 47.826 0.00 0.00 33.15 2.59
552 578 1.005924 GGGTTGGTGATGATGGAGGTT 59.994 52.381 0.00 0.00 0.00 3.50
699 728 3.384789 TGCACTGACTAGTCTTGTCAAGT 59.615 43.478 23.01 13.88 42.85 3.16
951 1028 4.876107 TGTGAGAGAGAAGTTTGTGGTTTC 59.124 41.667 0.00 0.00 0.00 2.78
1014 1091 1.081892 CTTGATGACGCTTGGTGGAG 58.918 55.000 0.00 0.00 0.00 3.86
1123 1200 2.280797 TGTCTCCTTGCCGTGCAC 60.281 61.111 6.82 6.82 38.71 4.57
1125 1202 0.737715 CTAGTGTCTCCTTGCCGTGC 60.738 60.000 0.00 0.00 0.00 5.34
1140 1217 2.093764 GCTGGTGCAGACAATCTCTAGT 60.094 50.000 0.00 0.00 39.41 2.57
1143 1220 0.390866 CGCTGGTGCAGACAATCTCT 60.391 55.000 0.00 0.00 39.64 3.10
1170 1247 1.218316 GATCACCTCGTCGGCCTTT 59.782 57.895 0.00 0.00 35.61 3.11
1191 1268 1.198713 CAAGCTTCCTCCAGAGCCTA 58.801 55.000 0.00 0.00 0.00 3.93
1319 1396 2.452813 GCCGCTGTGATGTGGTACG 61.453 63.158 0.00 0.00 39.62 3.67
2157 2243 3.569701 AGTCGTACTCTTTTCCGGTGTAA 59.430 43.478 0.00 0.00 0.00 2.41
2203 2289 4.796606 CCTTTGTAGAATGGGTGGATGAT 58.203 43.478 0.00 0.00 0.00 2.45
2241 2327 2.433868 TGTAGTCTTCCTGCGTGTTC 57.566 50.000 0.00 0.00 0.00 3.18
2305 2391 3.133003 GTGGTGTATGCATCTACTCCTGT 59.867 47.826 17.39 0.00 36.60 4.00
3144 3239 5.265191 TGAATCTAGTACTTGACTCCAGCT 58.735 41.667 12.15 0.00 39.81 4.24
3237 3338 1.540363 GGATTCGCTTATGGGCTCGAA 60.540 52.381 0.00 0.00 43.64 3.71
3276 3377 2.190488 CTCTTGACCTGTGGGCCCTC 62.190 65.000 25.70 21.33 35.63 4.30
3309 3434 1.487300 TACCTGGGCGCTTATACACA 58.513 50.000 7.64 0.00 0.00 3.72
3322 3447 5.450688 CGAACTCCTCTGAATACTTACCTGG 60.451 48.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.