Multiple sequence alignment - TraesCS3D01G430700

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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 TraesCS3D01G430700 chr3D 100.000 3665 0 0 1 3665 545033126 545036790 0.000000e+00 6769.0
1 TraesCS3D01G430700 chr3D 89.081 3352 263 37 1 3304 544823862 544827158 0.000000e+00 4067.0
2 TraesCS3D01G430700 chr3D 86.429 3338 335 41 29 3308 545060712 545063989 0.000000e+00 3546.0
3 TraesCS3D01G430700 chr3D 86.700 3188 305 45 27 3154 545155467 545158595 0.000000e+00 3428.0
4 TraesCS3D01G430700 chr3D 89.169 674 42 18 3002 3665 545064413 545065065 0.000000e+00 811.0
5 TraesCS3D01G430700 chr3D 85.792 366 29 10 3317 3665 544827289 544827648 2.080000e-97 366.0
6 TraesCS3D01G430700 chr3D 83.333 120 8 3 3197 3304 545158590 545158709 2.330000e-17 100.0
7 TraesCS3D01G430700 chr3B 92.577 3691 208 16 1 3665 720989504 720993154 0.000000e+00 5238.0
8 TraesCS3D01G430700 chr3B 90.393 3331 258 23 1 3308 721039115 721042406 0.000000e+00 4322.0
9 TraesCS3D01G430700 chr3B 87.257 3343 300 50 27 3303 721046280 721049562 0.000000e+00 3698.0
10 TraesCS3D01G430700 chr3A 95.364 3300 126 6 21 3304 681562061 681565349 0.000000e+00 5221.0
11 TraesCS3D01G430700 chr3A 90.426 3332 261 29 1 3308 681652852 681656149 0.000000e+00 4333.0
12 TraesCS3D01G430700 chr3A 91.158 3212 248 16 21 3207 681663069 681666269 0.000000e+00 4325.0
13 TraesCS3D01G430700 chr3A 90.439 3305 242 29 29 3308 681523489 681526744 0.000000e+00 4285.0
14 TraesCS3D01G430700 chr3A 88.822 2639 231 27 1 2606 681465858 681468465 0.000000e+00 3181.0
15 TraesCS3D01G430700 chr3A 92.456 1299 75 9 2372 3665 681640369 681641649 0.000000e+00 1834.0
16 TraesCS3D01G430700 chr3A 88.172 651 54 13 2591 3231 681468501 681469138 0.000000e+00 754.0
17 TraesCS3D01G430700 chr3A 85.366 738 71 24 2939 3665 681469476 681470187 0.000000e+00 730.0
18 TraesCS3D01G430700 chr3A 93.548 186 5 3 3317 3497 681469286 681469469 1.680000e-68 270.0
19 TraesCS3D01G430700 chr3A 89.831 59 6 0 3556 3614 681469215 681469273 3.920000e-10 76.8
20 TraesCS3D01G430700 chr1A 83.313 3344 408 66 20 3314 551635024 551631782 0.000000e+00 2946.0


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 TraesCS3D01G430700 chr3D 545033126 545036790 3664 False 6769.00 6769 100.0000 1 3665 1 chr3D.!!$F1 3664
1 TraesCS3D01G430700 chr3D 544823862 544827648 3786 False 2216.50 4067 87.4365 1 3665 2 chr3D.!!$F2 3664
2 TraesCS3D01G430700 chr3D 545060712 545065065 4353 False 2178.50 3546 87.7990 29 3665 2 chr3D.!!$F3 3636
3 TraesCS3D01G430700 chr3D 545155467 545158709 3242 False 1764.00 3428 85.0165 27 3304 2 chr3D.!!$F4 3277
4 TraesCS3D01G430700 chr3B 720989504 720993154 3650 False 5238.00 5238 92.5770 1 3665 1 chr3B.!!$F1 3664
5 TraesCS3D01G430700 chr3B 721039115 721049562 10447 False 4010.00 4322 88.8250 1 3308 2 chr3B.!!$F2 3307
6 TraesCS3D01G430700 chr3A 681562061 681565349 3288 False 5221.00 5221 95.3640 21 3304 1 chr3A.!!$F2 3283
7 TraesCS3D01G430700 chr3A 681652852 681656149 3297 False 4333.00 4333 90.4260 1 3308 1 chr3A.!!$F4 3307
8 TraesCS3D01G430700 chr3A 681663069 681666269 3200 False 4325.00 4325 91.1580 21 3207 1 chr3A.!!$F5 3186
9 TraesCS3D01G430700 chr3A 681523489 681526744 3255 False 4285.00 4285 90.4390 29 3308 1 chr3A.!!$F1 3279
10 TraesCS3D01G430700 chr3A 681640369 681641649 1280 False 1834.00 1834 92.4560 2372 3665 1 chr3A.!!$F3 1293
11 TraesCS3D01G430700 chr3A 681465858 681470187 4329 False 1002.36 3181 89.1478 1 3665 5 chr3A.!!$F6 3664
12 TraesCS3D01G430700 chr1A 551631782 551635024 3242 True 2946.00 2946 83.3130 20 3314 1 chr1A.!!$R1 3294

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
734 750 0.512952 GGAGTTACACAAGCTGCACG 59.487 55.000 1.02 0.00 0.00 5.34 F
1557 1593 0.035630 AGGCCAAGCAGAGTCATGAC 60.036 55.000 18.47 18.47 0.00 3.06 F
2351 2433 1.000938 CTTGTGGCTCAACCTTCTTGC 60.001 52.381 0.00 0.00 40.22 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2350 0.035458 AAAGACTTGTCCCGGAGCAG 59.965 55.000 0.73 0.0 0.00 4.24 R
2488 2570 1.663702 GGTCACCGACACCGTTGAG 60.664 63.158 0.00 0.0 37.88 3.02 R
3493 5211 2.045524 CCTCTGCACCCATGTAGATCT 58.954 52.381 0.00 0.0 45.27 2.75 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
18 19 1.228245 TGTTCCCCAAGAGCAGCAC 60.228 57.895 0.00 0.00 31.27 4.40
90 94 2.561478 ACAAAGACCACAACGGCTAT 57.439 45.000 0.00 0.00 39.03 2.97
147 151 3.994392 GACGCAAAGGAAGACATCTTACA 59.006 43.478 6.62 0.00 39.28 2.41
148 152 4.579869 ACGCAAAGGAAGACATCTTACAT 58.420 39.130 6.62 0.00 39.28 2.29
211 218 1.274703 AACCTGGTGCTCCGGATCAT 61.275 55.000 11.82 0.00 42.46 2.45
310 317 2.570752 AGAGCAGCTCAAGATCAAAGGA 59.429 45.455 24.64 0.00 32.06 3.36
353 360 5.556915 ACAACTTGAATTATCTTCCGGACA 58.443 37.500 1.83 0.00 0.00 4.02
383 399 3.686227 ATGAATGCCCCCTGTTTATCA 57.314 42.857 0.00 0.00 0.00 2.15
445 461 2.165998 ACCAGAAATGCTTTGAGCCTC 58.834 47.619 0.00 0.00 41.51 4.70
523 539 5.454755 GGCTAAAGAATACTGCTATCCACCA 60.455 44.000 0.00 0.00 0.00 4.17
553 569 6.377912 ACCTATAGACTATTCTCTTGCTGGT 58.622 40.000 0.00 0.00 32.75 4.00
734 750 0.512952 GGAGTTACACAAGCTGCACG 59.487 55.000 1.02 0.00 0.00 5.34
1557 1593 0.035630 AGGCCAAGCAGAGTCATGAC 60.036 55.000 18.47 18.47 0.00 3.06
2269 2350 4.811557 AGAAACCAAATATACGCTCTCTGC 59.188 41.667 0.00 0.00 38.57 4.26
2276 2357 2.069465 ATACGCTCTCTGCTGCTCCG 62.069 60.000 0.00 0.00 40.11 4.63
2351 2433 1.000938 CTTGTGGCTCAACCTTCTTGC 60.001 52.381 0.00 0.00 40.22 4.01
2488 2570 1.000955 TGAAGGAGCTCGAGTTCAACC 59.999 52.381 27.43 13.57 0.00 3.77
2521 2615 1.416401 GTGACCAAGTCCCTGTTGAGA 59.584 52.381 0.00 0.00 0.00 3.27
2740 2894 0.664761 TTGCACTCTGTTCTGCTTGC 59.335 50.000 0.00 0.00 34.29 4.01
2911 3067 4.813161 CCTCTGTATCGAACATCATTTGCT 59.187 41.667 0.00 0.00 37.50 3.91
2990 3150 9.406828 TCTTATTAATGTACAGCGTGATATCAC 57.593 33.333 23.47 23.47 43.15 3.06
3094 3288 0.670162 TTTCTGCAAACCAGCTGAGC 59.330 50.000 17.39 13.85 42.23 4.26
3158 3983 3.625649 TGTGCAGATTAGGCATGTGTA 57.374 42.857 0.00 0.00 44.11 2.90
3423 5140 0.172803 GATCCGTTAGGCTGTGACGT 59.827 55.000 15.32 0.00 37.47 4.34
3424 5141 1.402968 GATCCGTTAGGCTGTGACGTA 59.597 52.381 15.32 4.09 37.47 3.57
3425 5142 1.466856 TCCGTTAGGCTGTGACGTAT 58.533 50.000 15.32 0.00 37.47 3.06
3433 5150 6.523546 CGTTAGGCTGTGACGTATTATCTATG 59.476 42.308 0.00 0.00 32.52 2.23
3580 5316 5.801350 TCACTTCCTAATGCAAGAAATCG 57.199 39.130 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.179000 CAGGGGCTTGCTACTACTGG 59.821 60.000 0.00 0.00 0.00 4.00
90 94 5.512942 TTTGATTTGATCCTCACCCAGTA 57.487 39.130 0.00 0.00 0.00 2.74
147 151 1.183030 TTTGCCTTGCTGCAGCTCAT 61.183 50.000 36.61 0.00 43.21 2.90
148 152 1.183030 ATTTGCCTTGCTGCAGCTCA 61.183 50.000 36.61 24.93 43.21 4.26
310 317 6.317893 AGTTGTTTTTAATCTTGTCCACGAGT 59.682 34.615 0.00 0.00 0.00 4.18
353 360 3.925370 AGGGGGCATTCATACATATTCCT 59.075 43.478 0.00 0.00 0.00 3.36
445 461 0.447801 AATCGGCGCTGCAGTTTAAG 59.552 50.000 16.64 3.88 0.00 1.85
523 539 7.040961 GCAAGAGAATAGTCTATAGGTTCTCGT 60.041 40.741 20.02 17.23 45.74 4.18
553 569 4.536765 TGAGCACTGTATCATGGTAGAGA 58.463 43.478 16.60 0.00 0.00 3.10
734 750 0.965866 GGTAAAGCCTCCAAGGTGCC 60.966 60.000 0.00 0.00 37.80 5.01
743 759 5.048083 TGAATGATGTTGTTGGTAAAGCCTC 60.048 40.000 0.00 0.00 38.35 4.70
1557 1593 7.231317 TGCCATAGCCTTCCAATATCTTTTAAG 59.769 37.037 0.00 0.00 38.69 1.85
2269 2350 0.035458 AAAGACTTGTCCCGGAGCAG 59.965 55.000 0.73 0.00 0.00 4.24
2276 2357 2.249844 TCCACGAAAAGACTTGTCCC 57.750 50.000 0.00 0.00 0.00 4.46
2351 2433 1.364626 GATGGCCGAGCAGTCAACAG 61.365 60.000 0.00 0.00 0.00 3.16
2488 2570 1.663702 GGTCACCGACACCGTTGAG 60.664 63.158 0.00 0.00 37.88 3.02
2521 2615 3.245948 TGGTTTTTAATGGCCTCCCTCAT 60.246 43.478 3.32 0.00 0.00 2.90
2740 2894 4.022589 ACACAGCAGAATGAAATCAACAGG 60.023 41.667 0.00 0.00 39.69 4.00
2943 3099 4.158394 AGAAGTCAAATGTGTGCACAAACT 59.842 37.500 23.59 14.51 45.41 2.66
2990 3150 3.614870 GCAGAAACCCAACCAAAGCATAG 60.615 47.826 0.00 0.00 0.00 2.23
3149 3972 4.023450 CAGATTGTGGATCATACACATGCC 60.023 45.833 2.66 0.00 46.98 4.40
3158 3983 3.639672 TGCAGACAGATTGTGGATCAT 57.360 42.857 0.00 0.00 37.22 2.45
3424 5141 9.922477 TTCGGATAGATGACTACCATAGATAAT 57.078 33.333 0.00 0.00 35.17 1.28
3425 5142 9.749340 TTTCGGATAGATGACTACCATAGATAA 57.251 33.333 0.00 0.00 35.17 1.75
3433 5150 6.097915 TGGATTTTCGGATAGATGACTACC 57.902 41.667 0.00 0.00 0.00 3.18
3493 5211 2.045524 CCTCTGCACCCATGTAGATCT 58.954 52.381 0.00 0.00 45.27 2.75
3519 5237 5.007136 GTGTCTGAACTTTTCTGAAGGTCTG 59.993 44.000 5.53 5.17 38.98 3.51
3580 5316 3.198068 TGCAGGTCTTATGCTTCGATTC 58.802 45.455 0.00 0.00 44.17 2.52


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

AutoCloner maintained by Alex Coulton.