Multiple sequence alignment - TraesCS5D01G339600

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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 TraesCS5D01G339600 chr5D 100.000 4125 0 0 1 4125 428512523 428516647 0.000000e+00 7618
1 TraesCS5D01G339600 chr5D 87.991 3514 373 20 10 3494 428565834 428569327 0.000000e+00 4106
2 TraesCS5D01G339600 chr5D 86.958 3251 387 29 1 3230 428593294 428596528 0.000000e+00 3620
3 TraesCS5D01G339600 chr5D 84.921 3223 452 22 1 3206 428670957 428674162 0.000000e+00 3229
4 TraesCS5D01G339600 chr5B 86.746 3282 398 27 1 3261 517775222 517778487 0.000000e+00 3616
5 TraesCS5D01G339600 chr5B 86.216 3301 423 20 1 3276 517694683 517697976 0.000000e+00 3546
6 TraesCS5D01G339600 chr5B 84.823 3222 455 23 1 3205 517798021 517801225 0.000000e+00 3210
7 TraesCS5D01G339600 chr5B 91.018 1247 97 6 2263 3495 517706538 517707783 0.000000e+00 1668
8 TraesCS5D01G339600 chr5B 85.549 173 13 10 3323 3494 517697983 517698144 1.970000e-38 171
9 TraesCS5D01G339600 chr5A 85.043 3149 444 19 1 3136 544453220 544456354 0.000000e+00 3181
10 TraesCS5D01G339600 chr5A 94.763 2024 81 7 1492 3491 544163664 544165686 0.000000e+00 3127
11 TraesCS5D01G339600 chr5A 83.923 3166 447 48 17 3145 544502701 544505841 0.000000e+00 2970
12 TraesCS5D01G339600 chr5A 97.884 1512 27 2 2 1508 544158857 544160368 0.000000e+00 2610
13 TraesCS5D01G339600 chr5A 88.669 2074 218 12 1088 3152 544246354 544248419 0.000000e+00 2512
14 TraesCS5D01G339600 chr5A 92.026 627 48 2 3500 4125 632588870 632589495 0.000000e+00 880
15 TraesCS5D01G339600 chr2D 93.513 632 39 2 3496 4125 2518518 2517887 0.000000e+00 939
16 TraesCS5D01G339600 chr6B 92.722 632 42 4 3496 4125 426820619 426819990 0.000000e+00 909
17 TraesCS5D01G339600 chr1B 92.210 629 46 3 3499 4125 349512706 349513333 0.000000e+00 887
18 TraesCS5D01G339600 chr1B 91.561 628 47 5 3500 4125 373260556 373259933 0.000000e+00 861
19 TraesCS5D01G339600 chr7A 91.943 633 48 3 3496 4125 176273074 176273706 0.000000e+00 883
20 TraesCS5D01G339600 chr2B 91.918 631 50 1 3496 4125 763406279 763406909 0.000000e+00 881
21 TraesCS5D01G339600 chr2B 91.401 628 53 1 3499 4125 12164031 12163404 0.000000e+00 859
22 TraesCS5D01G339600 chr2A 92.071 618 45 4 3503 4119 27366936 27367550 0.000000e+00 867


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 TraesCS5D01G339600 chr5D 428512523 428516647 4124 False 7618.0 7618 100.0000 1 4125 1 chr5D.!!$F1 4124
1 TraesCS5D01G339600 chr5D 428565834 428569327 3493 False 4106.0 4106 87.9910 10 3494 1 chr5D.!!$F2 3484
2 TraesCS5D01G339600 chr5D 428593294 428596528 3234 False 3620.0 3620 86.9580 1 3230 1 chr5D.!!$F3 3229
3 TraesCS5D01G339600 chr5D 428670957 428674162 3205 False 3229.0 3229 84.9210 1 3206 1 chr5D.!!$F4 3205
4 TraesCS5D01G339600 chr5B 517775222 517778487 3265 False 3616.0 3616 86.7460 1 3261 1 chr5B.!!$F2 3260
5 TraesCS5D01G339600 chr5B 517798021 517801225 3204 False 3210.0 3210 84.8230 1 3205 1 chr5B.!!$F3 3204
6 TraesCS5D01G339600 chr5B 517694683 517698144 3461 False 1858.5 3546 85.8825 1 3494 2 chr5B.!!$F4 3493
7 TraesCS5D01G339600 chr5B 517706538 517707783 1245 False 1668.0 1668 91.0180 2263 3495 1 chr5B.!!$F1 1232
8 TraesCS5D01G339600 chr5A 544453220 544456354 3134 False 3181.0 3181 85.0430 1 3136 1 chr5A.!!$F2 3135
9 TraesCS5D01G339600 chr5A 544502701 544505841 3140 False 2970.0 2970 83.9230 17 3145 1 chr5A.!!$F3 3128
10 TraesCS5D01G339600 chr5A 544158857 544165686 6829 False 2868.5 3127 96.3235 2 3491 2 chr5A.!!$F5 3489
11 TraesCS5D01G339600 chr5A 544246354 544248419 2065 False 2512.0 2512 88.6690 1088 3152 1 chr5A.!!$F1 2064
12 TraesCS5D01G339600 chr5A 632588870 632589495 625 False 880.0 880 92.0260 3500 4125 1 chr5A.!!$F4 625
13 TraesCS5D01G339600 chr2D 2517887 2518518 631 True 939.0 939 93.5130 3496 4125 1 chr2D.!!$R1 629
14 TraesCS5D01G339600 chr6B 426819990 426820619 629 True 909.0 909 92.7220 3496 4125 1 chr6B.!!$R1 629
15 TraesCS5D01G339600 chr1B 349512706 349513333 627 False 887.0 887 92.2100 3499 4125 1 chr1B.!!$F1 626
16 TraesCS5D01G339600 chr1B 373259933 373260556 623 True 861.0 861 91.5610 3500 4125 1 chr1B.!!$R1 625
17 TraesCS5D01G339600 chr7A 176273074 176273706 632 False 883.0 883 91.9430 3496 4125 1 chr7A.!!$F1 629
18 TraesCS5D01G339600 chr2B 763406279 763406909 630 False 881.0 881 91.9180 3496 4125 1 chr2B.!!$F1 629
19 TraesCS5D01G339600 chr2B 12163404 12164031 627 True 859.0 859 91.4010 3499 4125 1 chr2B.!!$R1 626
20 TraesCS5D01G339600 chr2A 27366936 27367550 614 False 867.0 867 92.0710 3503 4119 1 chr2A.!!$F1 616

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
970 972 0.955905 ACGAAAACCAATTGTCCGGG 59.044 50.0 0.00 0.0 0.00 5.73 F
2199 5529 2.573941 GCAGAATGGCATTTGAGGAC 57.426 50.0 14.93 0.0 35.86 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2513 5844 1.071542 GAGCTATCCTCCTTTCCCAGC 59.928 57.143 0.0 0.0 34.35 4.85 R
3745 7141 0.324460 ACTAAGGAGACGGGGGACAG 60.324 60.000 0.0 0.0 0.00 3.51 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
71 72 2.093658 GTCGCTCCCTTACCTCATCAAA 60.094 50.000 0.00 0.00 0.00 2.69
142 143 1.815003 CGGCTCTCTTTCCATGCTTTT 59.185 47.619 0.00 0.00 0.00 2.27
242 243 2.354259 GACCTCTCCAGCAACAATCTG 58.646 52.381 0.00 0.00 0.00 2.90
844 846 1.641577 GACCAGTGCCGTCAAGTATC 58.358 55.000 0.00 0.00 0.00 2.24
970 972 0.955905 ACGAAAACCAATTGTCCGGG 59.044 50.000 0.00 0.00 0.00 5.73
2059 5386 3.788672 CCAGTGGGTCTTCCTATGC 57.211 57.895 0.00 0.00 36.20 3.14
2199 5529 2.573941 GCAGAATGGCATTTGAGGAC 57.426 50.000 14.93 0.00 35.86 3.85
2513 5844 1.941325 GAACTAGCATCCCAGTTCCG 58.059 55.000 3.61 0.00 43.12 4.30
2993 6333 6.554334 TTCTACTGGAAGAAATTTTGGACG 57.446 37.500 0.00 0.00 37.43 4.79
3163 6524 6.132056 GCTTGCAGATGTATTATTTCAGTCG 58.868 40.000 0.00 0.00 0.00 4.18
3233 6596 9.646522 ATCTATCTGCAAACCAAATAAATAGGT 57.353 29.630 0.00 0.00 37.20 3.08
3281 6659 3.266636 TGGGTCACAATATTACGCTGTG 58.733 45.455 5.74 2.66 41.47 3.66
3282 6660 2.031683 GGGTCACAATATTACGCTGTGC 59.968 50.000 0.43 0.00 40.22 4.57
3302 6680 2.799412 GCTATTGCTCTTCCAGTGATCG 59.201 50.000 0.00 0.00 36.03 3.69
3428 6819 5.677319 TCCTTCATCTTTACCACTACCAG 57.323 43.478 0.00 0.00 0.00 4.00
3465 6856 9.677567 TCTTTAAAAATTGAGTCGGAAATTCTG 57.322 29.630 0.00 0.00 0.00 3.02
3476 6867 4.154918 GTCGGAAATTCTGAGATGCACTTT 59.845 41.667 4.50 0.00 31.37 2.66
3556 6947 2.046700 CGAAAACCCTAGCCGCCA 60.047 61.111 0.00 0.00 0.00 5.69
3762 7158 1.684734 GCTGTCCCCCGTCTCCTTA 60.685 63.158 0.00 0.00 0.00 2.69
3933 7329 1.539372 ATCCGTGGTTGGTGGGGTA 60.539 57.895 0.00 0.00 0.00 3.69
3968 7364 1.144057 CTGGACCGGGAGAAATCCG 59.856 63.158 6.32 0.00 46.43 4.18
4021 7417 4.118584 GCAGGTGCCATTTCCCTT 57.881 55.556 0.00 0.00 34.31 3.95
4072 7468 1.692042 CCTCCTGCTCCATGACCCT 60.692 63.158 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.682885 CTGCAATGCCGGCACCAA 61.683 61.111 35.50 16.99 36.11 3.67
27 28 2.040412 GGAATCTCAGGGTGTCCAGTTT 59.960 50.000 0.00 0.00 34.83 2.66
71 72 0.171455 GATTGTCGCTGAGGTCGAGT 59.829 55.000 0.00 0.00 36.56 4.18
142 143 1.694150 CACCAGAGAAGTTGAGGGTGA 59.306 52.381 2.56 0.00 46.67 4.02
242 243 2.442830 GGAGGGATTTGGCCAGCC 60.443 66.667 5.11 9.28 0.00 4.85
844 846 3.927142 GTCTAAGTGAAGACATGTTCCCG 59.073 47.826 0.00 0.00 44.41 5.14
970 972 5.527214 CCAATTTTCCAAAACTTTGAGGGAC 59.473 40.000 3.72 0.00 40.55 4.46
2513 5844 1.071542 GAGCTATCCTCCTTTCCCAGC 59.928 57.143 0.00 0.00 34.35 4.85
2993 6333 0.249573 TCGGGTTGTGGAAGTCGTTC 60.250 55.000 0.00 0.00 0.00 3.95
3153 6514 3.979948 TGAACCGAACACGACTGAAATA 58.020 40.909 0.00 0.00 0.00 1.40
3158 6519 1.521423 GTTCTGAACCGAACACGACTG 59.479 52.381 9.38 0.00 42.15 3.51
3233 6596 7.953005 TTCTATGATGCCCAACAGAAATAAA 57.047 32.000 0.00 0.00 0.00 1.40
3281 6659 2.799412 CGATCACTGGAAGAGCAATAGC 59.201 50.000 0.00 0.00 38.25 2.97
3282 6660 4.052159 ACGATCACTGGAAGAGCAATAG 57.948 45.455 0.00 0.00 37.43 1.73
3302 6680 4.314740 AAGCTTGATCGAGGATCTGTAC 57.685 45.455 12.06 0.00 39.56 2.90
3391 6777 1.210722 GAAGGAAGGTCAGGGGCTAAG 59.789 57.143 0.00 0.00 0.00 2.18
3428 6819 8.088365 ACTCAATTTTTAAAGAACCCACATAGC 58.912 33.333 0.00 0.00 0.00 2.97
3465 6856 9.495754 GATTTTCTTACATACAAAGTGCATCTC 57.504 33.333 0.00 0.00 0.00 2.75
3476 6867 6.818644 GCCAGAGACTGATTTTCTTACATACA 59.181 38.462 0.00 0.00 32.44 2.29
3639 7034 2.308968 GAAGCAGCCAGATCCTCGCT 62.309 60.000 0.00 0.00 0.00 4.93
3745 7141 0.324460 ACTAAGGAGACGGGGGACAG 60.324 60.000 0.00 0.00 0.00 3.51
3817 7213 4.070552 GACGCGAACAGGGAGGCT 62.071 66.667 15.93 0.00 36.53 4.58
4013 7409 1.210722 GAAGCCTCCGAGAAGGGAAAT 59.789 52.381 0.00 0.00 41.52 2.17
4017 7413 2.286127 GACGAAGCCTCCGAGAAGGG 62.286 65.000 0.00 0.00 41.52 3.95
4021 7417 2.046604 TCGACGAAGCCTCCGAGA 60.047 61.111 0.00 0.00 0.00 4.04
4072 7468 4.090090 TGAAAAGACAAGGGTTTTCACCA 58.910 39.130 6.22 0.00 46.43 4.17


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

AutoCloner maintained by Alex Coulton.