Multiple sequence alignment - TraesCS5A01G421300

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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 TraesCS5A01G421300 chr5A 100.000 3101 0 0 1 3101 607272650 607275750 0.000000e+00 5727
1 TraesCS5A01G421300 chr3D 97.454 3103 71 7 1 3101 589281290 589278194 0.000000e+00 5286
2 TraesCS5A01G421300 chr5D 97.358 3104 76 6 1 3101 6187191 6190291 0.000000e+00 5273
3 TraesCS5A01G421300 chr5D 97.293 3103 79 5 1 3101 503279974 503276875 0.000000e+00 5260
4 TraesCS5A01G421300 chr5D 96.295 3104 107 8 1 3101 432405244 432402146 0.000000e+00 5088
5 TraesCS5A01G421300 chr5D 97.716 2802 60 4 302 3101 503216770 503219569 0.000000e+00 4817
6 TraesCS5A01G421300 chr1D 97.165 3104 82 6 1 3101 254399859 254396759 0.000000e+00 5240
7 TraesCS5A01G421300 chr2A 96.037 3104 98 8 1 3101 335836899 335839980 0.000000e+00 5027
8 TraesCS5A01G421300 chr4A 95.498 3110 129 8 1 3101 309513374 309516481 0.000000e+00 4957
9 TraesCS5A01G421300 chr4B 95.397 3107 120 11 1 3101 308694733 308697822 0.000000e+00 4924
10 TraesCS5A01G421300 chr6D 97.645 2803 61 5 302 3101 168253477 168256277 0.000000e+00 4806
11 TraesCS5A01G421300 chr3B 97.574 2803 62 6 302 3101 201525576 201528375 0.000000e+00 4795
12 TraesCS5A01G421300 chr6B 97.638 254 6 0 1 254 450081065 450080812 1.320000e-118 436
13 TraesCS5A01G421300 chr7D 95.205 146 7 0 222 367 204018550 204018405 6.690000e-57 231
14 TraesCS5A01G421300 chr2D 96.899 129 3 1 233 360 235487354 235487226 6.740000e-52 215


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 TraesCS5A01G421300 chr5A 607272650 607275750 3100 False 5727 5727 100.000 1 3101 1 chr5A.!!$F1 3100
1 TraesCS5A01G421300 chr3D 589278194 589281290 3096 True 5286 5286 97.454 1 3101 1 chr3D.!!$R1 3100
2 TraesCS5A01G421300 chr5D 6187191 6190291 3100 False 5273 5273 97.358 1 3101 1 chr5D.!!$F1 3100
3 TraesCS5A01G421300 chr5D 503276875 503279974 3099 True 5260 5260 97.293 1 3101 1 chr5D.!!$R2 3100
4 TraesCS5A01G421300 chr5D 432402146 432405244 3098 True 5088 5088 96.295 1 3101 1 chr5D.!!$R1 3100
5 TraesCS5A01G421300 chr5D 503216770 503219569 2799 False 4817 4817 97.716 302 3101 1 chr5D.!!$F2 2799
6 TraesCS5A01G421300 chr1D 254396759 254399859 3100 True 5240 5240 97.165 1 3101 1 chr1D.!!$R1 3100
7 TraesCS5A01G421300 chr2A 335836899 335839980 3081 False 5027 5027 96.037 1 3101 1 chr2A.!!$F1 3100
8 TraesCS5A01G421300 chr4A 309513374 309516481 3107 False 4957 4957 95.498 1 3101 1 chr4A.!!$F1 3100
9 TraesCS5A01G421300 chr4B 308694733 308697822 3089 False 4924 4924 95.397 1 3101 1 chr4B.!!$F1 3100
10 TraesCS5A01G421300 chr6D 168253477 168256277 2800 False 4806 4806 97.645 302 3101 1 chr6D.!!$F1 2799
11 TraesCS5A01G421300 chr3B 201525576 201528375 2799 False 4795 4795 97.574 302 3101 1 chr3B.!!$F1 2799

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
972 1010 0.326595 TTCCAAGCGCAGGATAACCA 59.673 50.0 20.31 4.53 38.94 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2379 1.066858 ACACCTATCTTGAGCACACGG 60.067 52.381 0.0 0.0 0.0 4.94 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
206 213 7.828717 TGCTGTTGAAGTTCCATCTATTAATGA 59.171 33.333 0.00 0.00 0.00 2.57
461 469 9.297037 ACCATAGGATTTGTTATGTAAATAGGC 57.703 33.333 0.00 0.00 0.00 3.93
529 537 1.699634 GGGTAGAATGCTAGATGCCCA 59.300 52.381 0.00 0.00 42.00 5.36
676 712 8.380099 TCCTTTTTAAAGAGTGGCTTCTATGTA 58.620 33.333 5.15 0.00 38.28 2.29
685 721 8.256356 AGAGTGGCTTCTATGTACAATATCTT 57.744 34.615 0.00 0.00 0.00 2.40
703 739 3.087031 TCTTGATCGAAGTACGGAGGTT 58.913 45.455 0.00 0.00 42.82 3.50
972 1010 0.326595 TTCCAAGCGCAGGATAACCA 59.673 50.000 20.31 4.53 38.94 3.67
1237 1278 3.960102 ACCCTCTTTTGCAATGAGTTTCA 59.040 39.130 21.02 0.00 32.43 2.69
1247 1288 5.491070 TGCAATGAGTTTCACTATAGCACT 58.509 37.500 0.00 0.00 0.00 4.40
1540 1582 3.953542 TCTACATCCTAGGTCTCTGCA 57.046 47.619 9.08 0.00 0.00 4.41
1550 1592 1.556911 AGGTCTCTGCATTCCGTCATT 59.443 47.619 0.00 0.00 0.00 2.57
1690 1732 5.535753 ACCACTGCTTAGCTTTCAATTTT 57.464 34.783 5.60 0.00 0.00 1.82
2182 2224 6.659242 ACCAGATATGTCTTTTTGATTCCGTT 59.341 34.615 0.00 0.00 30.42 4.44
2233 2275 0.949582 ACCTCCCCCTCTATGCCTTA 59.050 55.000 0.00 0.00 0.00 2.69
2337 2379 0.108281 GCCTGTCTACGGTTCCCTTC 60.108 60.000 0.00 0.00 0.00 3.46
2347 2389 1.070786 GTTCCCTTCCGTGTGCTCA 59.929 57.895 0.00 0.00 0.00 4.26
2348 2390 0.534203 GTTCCCTTCCGTGTGCTCAA 60.534 55.000 0.00 0.00 0.00 3.02
2530 2574 4.473196 TCCAGGTAGTCAATGGCTATTCAA 59.527 41.667 0.00 0.00 33.92 2.69
2577 2621 4.396166 AGAGTTCGACCCAATGCTTTATTG 59.604 41.667 0.00 0.00 44.67 1.90
2719 2766 3.701542 TGCTCTGAGTTCCAGTATCGATT 59.298 43.478 1.71 0.00 43.38 3.34
3087 3134 5.128499 TGAAAGAGAGATTGAGAGGGATCAC 59.872 44.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
461 469 7.752239 GCGATTCATAATGGAAAGGAACATATG 59.248 37.037 0.00 0.00 0.00 1.78
529 537 5.479124 AGAAACAATAGTAACGTGGTCCT 57.521 39.130 0.00 0.00 0.00 3.85
623 657 4.017126 AGGAGTAATCAGATGTGACACGA 58.983 43.478 0.00 0.00 34.75 4.35
676 712 6.387041 TCCGTACTTCGATCAAGATATTGT 57.613 37.500 10.61 0.00 42.86 2.71
685 721 3.877559 TCTAACCTCCGTACTTCGATCA 58.122 45.455 0.00 0.00 42.86 2.92
932 970 7.351166 TGGAAGAAGAACTAGGAAAAGGAAAA 58.649 34.615 0.00 0.00 0.00 2.29
972 1010 1.959710 AAAAACCCACAACCCCTTGT 58.040 45.000 0.00 0.00 41.61 3.16
1005 1046 2.282180 GGCGGTGAAGGGAAAGCA 60.282 61.111 0.00 0.00 0.00 3.91
1124 1165 1.544246 GACAAGTGGGTAATGTTGGGC 59.456 52.381 0.00 0.00 0.00 5.36
1412 1454 5.630121 AGATCCATCTGTCTAGAGATCGTT 58.370 41.667 10.21 0.00 38.60 3.85
1540 1582 4.949856 AGAACATAAGCCAAATGACGGAAT 59.050 37.500 0.00 0.00 0.00 3.01
1550 1592 5.252547 TGCTACATGAAGAACATAAGCCAA 58.747 37.500 0.00 0.00 41.98 4.52
1690 1732 7.174413 TCACATTTAATTTGATGGTCAGAGGA 58.826 34.615 5.92 0.00 0.00 3.71
1721 1763 4.982241 TGTTTCAAAGAGAGGAGGACAT 57.018 40.909 0.00 0.00 0.00 3.06
1722 1764 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.00 0.00 4.02
1888 1930 5.655090 TGATCCAATTTGACTACCTCTACGA 59.345 40.000 0.00 0.00 0.00 3.43
1984 2026 3.561313 GGAAATGCCCTACCTTTGAGTGA 60.561 47.826 0.00 0.00 0.00 3.41
2058 2100 7.856415 AGAGATATATTTTACATCCCAGAGGC 58.144 38.462 0.00 0.00 0.00 4.70
2182 2224 8.770828 GCGCCTATACTGTAAAATAGATTTTCA 58.229 33.333 0.00 2.75 40.24 2.69
2337 2379 1.066858 ACACCTATCTTGAGCACACGG 60.067 52.381 0.00 0.00 0.00 4.94
2405 2447 8.927675 TTCTATTCCACTTCTAGATAGAGGAC 57.072 38.462 15.45 0.00 34.00 3.85
2434 2477 2.574369 TGATCATTACCCTTCAACCGGT 59.426 45.455 0.00 0.00 36.08 5.28
2518 2562 3.954258 GGTGGTAGCTTTGAATAGCCATT 59.046 43.478 0.00 0.00 42.20 3.16
2530 2574 3.868619 TTGGTGTTAAGGTGGTAGCTT 57.131 42.857 0.00 0.00 39.52 3.74
2577 2621 2.961526 TCGGGATTCACTAAGACAGC 57.038 50.000 0.00 0.00 0.00 4.40
2764 2811 9.739276 ATCATCCATACATAACGAATTGGTATT 57.261 29.630 0.00 0.00 0.00 1.89
2844 2891 3.654201 GCTGGATGCACACGAACA 58.346 55.556 0.00 0.00 42.31 3.18
2990 3037 7.534239 GCCATCTCGGAATATTTTCGATTTAAC 59.466 37.037 12.88 3.62 36.56 2.01
2992 3039 6.708502 TGCCATCTCGGAATATTTTCGATTTA 59.291 34.615 12.88 5.46 36.56 1.40


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

AutoCloner maintained by Alex Coulton.