Multiple sequence alignment - TraesCS3A01G361600

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 TraesCS3A01G361600 chr3A 100.000 2691 0 0 434 3124 609945333 609942643 0.000000e+00 4970.0
1 TraesCS3A01G361600 chr3A 94.397 2695 134 14 444 3124 734661899 734659208 0.000000e+00 4124.0
2 TraesCS3A01G361600 chr3A 95.939 2487 94 7 636 3117 26628173 26625689 0.000000e+00 4026.0
3 TraesCS3A01G361600 chr3A 100.000 163 0 0 1 163 609945766 609945604 5.060000e-78 302.0
4 TraesCS3A01G361600 chr3A 95.652 161 7 0 3 163 734662644 734662484 3.090000e-65 259.0
5 TraesCS3A01G361600 chr7A 94.947 2533 116 11 598 3124 714969610 714972136 0.000000e+00 3958.0
6 TraesCS3A01G361600 chr7A 94.716 2555 119 13 580 3124 111947271 111949819 0.000000e+00 3956.0
7 TraesCS3A01G361600 chr2D 94.193 2566 134 14 569 3124 635127526 635124966 0.000000e+00 3899.0
8 TraesCS3A01G361600 chr5D 94.127 2503 135 10 630 3124 208495123 208497621 0.000000e+00 3797.0
9 TraesCS3A01G361600 chr6A 93.276 2543 153 11 597 3124 18058580 18061119 0.000000e+00 3733.0
10 TraesCS3A01G361600 chr4A 92.715 2567 161 18 576 3124 177774125 177771567 0.000000e+00 3681.0
11 TraesCS3A01G361600 chr4A 85.366 82 5 2 503 577 651987876 651987957 9.290000e-11 78.7
12 TraesCS3A01G361600 chr5B 90.815 2711 216 30 435 3124 495480709 495478011 0.000000e+00 3596.0
13 TraesCS3A01G361600 chr5B 85.185 81 9 2 503 580 467066295 467066215 2.580000e-11 80.5
14 TraesCS3A01G361600 chr2B 92.857 70 4 1 511 579 96032493 96032562 1.980000e-17 100.0
15 TraesCS3A01G361600 chr2B 84.884 86 4 4 503 579 741990801 741990886 9.290000e-11 78.7
16 TraesCS3A01G361600 chr1D 87.059 85 4 2 502 579 339309348 339309432 4.290000e-14 89.8
17 TraesCS3A01G361600 chr1D 85.882 85 5 2 502 579 462971643 462971727 2.000000e-12 84.2
18 TraesCS3A01G361600 chr1A 100.000 35 0 0 503 537 386417069 386417035 7.230000e-07 65.8


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 TraesCS3A01G361600 chr3A 609942643 609945766 3123 True 2636.0 4970 100.0000 1 3124 2 chr3A.!!$R2 3123
1 TraesCS3A01G361600 chr3A 26625689 26628173 2484 True 4026.0 4026 95.9390 636 3117 1 chr3A.!!$R1 2481
2 TraesCS3A01G361600 chr3A 734659208 734662644 3436 True 2191.5 4124 95.0245 3 3124 2 chr3A.!!$R3 3121
3 TraesCS3A01G361600 chr7A 714969610 714972136 2526 False 3958.0 3958 94.9470 598 3124 1 chr7A.!!$F2 2526
4 TraesCS3A01G361600 chr7A 111947271 111949819 2548 False 3956.0 3956 94.7160 580 3124 1 chr7A.!!$F1 2544
5 TraesCS3A01G361600 chr2D 635124966 635127526 2560 True 3899.0 3899 94.1930 569 3124 1 chr2D.!!$R1 2555
6 TraesCS3A01G361600 chr5D 208495123 208497621 2498 False 3797.0 3797 94.1270 630 3124 1 chr5D.!!$F1 2494
7 TraesCS3A01G361600 chr6A 18058580 18061119 2539 False 3733.0 3733 93.2760 597 3124 1 chr6A.!!$F1 2527
8 TraesCS3A01G361600 chr4A 177771567 177774125 2558 True 3681.0 3681 92.7150 576 3124 1 chr4A.!!$R1 2548
9 TraesCS3A01G361600 chr5B 495478011 495480709 2698 True 3596.0 3596 90.8150 435 3124 1 chr5B.!!$R2 2689

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
573 908 1.071471 CAACGGGCTTCTGTGGACT 59.929 57.895 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 2845 0.036164 AGCCAACTATGTGCGAACCA 59.964 50.0 0.0 0.0 0.0 3.67 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
59 60 2.202743 GTCGCTGGCATCGCACTA 60.203 61.111 5.76 0.00 0.00 2.74
63 64 1.524621 GCTGGCATCGCACTATGGT 60.525 57.895 0.00 0.00 0.00 3.55
65 66 1.217585 CTGGCATCGCACTATGGTCG 61.218 60.000 0.00 0.00 0.00 4.79
480 811 4.657824 CTTGGTCGCCGTCCACGT 62.658 66.667 1.67 0.00 37.74 4.49
481 812 4.953868 TTGGTCGCCGTCCACGTG 62.954 66.667 9.08 9.08 37.74 4.49
573 908 1.071471 CAACGGGCTTCTGTGGACT 59.929 57.895 0.00 0.00 0.00 3.85
704 1044 3.470645 AATATTTCGCGTAGAAGCCCT 57.529 42.857 5.77 0.00 40.40 5.19
709 1049 1.519455 CGCGTAGAAGCCCTTGGAG 60.519 63.158 0.00 0.00 0.00 3.86
1173 1520 3.254166 AGTTTGAAACTGAGAATGCGCAT 59.746 39.130 19.28 19.28 41.01 4.73
1235 1582 6.888105 TGAAAGATGAGTATATGGCTGAACA 58.112 36.000 0.00 0.00 0.00 3.18
1325 1672 1.007118 TGTAGAGGCAGAGTGGATCCA 59.993 52.381 11.44 11.44 0.00 3.41
1367 1714 2.374170 AGACGGTTGGGGAGTACAATTT 59.626 45.455 0.00 0.00 0.00 1.82
1428 1775 4.157289 GGTACTCAGATTACCGACACTCAA 59.843 45.833 1.33 0.00 29.93 3.02
1544 1891 4.087892 CGTCCTCCAGGTGGCAGG 62.088 72.222 2.19 7.75 36.34 4.85
1682 2029 1.746991 GCAAGAAGAAGGGCCCTCG 60.747 63.158 28.84 8.88 0.00 4.63
1889 2240 2.440796 CCCATGGCGGCACTCATT 60.441 61.111 16.34 0.00 0.00 2.57
1909 2260 0.188587 ATGATCTCTACGCCCCCTGA 59.811 55.000 0.00 0.00 0.00 3.86
1932 2283 3.788145 CCATCGCGGTAACCCCCA 61.788 66.667 6.13 0.00 0.00 4.96
1957 2308 3.118454 CATCGCGGCGACTTTGGT 61.118 61.111 28.88 7.78 39.18 3.67
1989 2340 1.971167 GCCAACGTTGCCATGGAGA 60.971 57.895 22.93 0.00 36.27 3.71
2385 2745 1.729284 GCCCGAATGGAAGAAACGTA 58.271 50.000 0.00 0.00 37.49 3.57
2485 2845 0.107897 TTATGACAATCGCCGGCTGT 60.108 50.000 26.68 22.41 0.00 4.40
2558 2918 9.473007 TGGGAACAACTTTGATCATTAATGATA 57.527 29.630 26.97 12.88 42.22 2.15
3117 3478 1.401761 TGTTTGCCTGCTGTCAACAT 58.598 45.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
464 795 4.953868 CACGTGGACGGCGACCAA 62.954 66.667 30.89 13.77 44.95 3.67
557 892 2.743718 CAGTCCACAGAAGCCCGT 59.256 61.111 0.00 0.00 0.00 5.28
704 1044 2.354510 CAGCGAAAACAGACAACTCCAA 59.645 45.455 0.00 0.00 0.00 3.53
709 1049 5.059710 GCATATTTCAGCGAAAACAGACAAC 59.940 40.000 7.59 0.00 35.11 3.32
997 1344 1.134220 GTGGACAATTCCGGCCATCTA 60.134 52.381 2.24 0.00 46.37 1.98
1149 1496 4.274705 TGCGCATTCTCAGTTTCAAACTTA 59.725 37.500 5.66 0.00 40.46 2.24
1173 1520 1.270785 TGACGGAGAAAATGCAGAGCA 60.271 47.619 0.00 0.00 44.86 4.26
1235 1582 0.251077 CCAAAGGCCAGAAGCACTCT 60.251 55.000 5.01 0.00 46.50 3.24
1325 1672 1.347707 TGAAGTCCGCAAACCTCAGAT 59.652 47.619 0.00 0.00 0.00 2.90
1367 1714 0.981183 ACAAATCCGGTGTAGAGCCA 59.019 50.000 0.00 0.00 0.00 4.75
1428 1775 6.794534 AGTGGATAGGGTTTTCTCAATCTTT 58.205 36.000 0.00 0.00 0.00 2.52
1885 2236 2.832129 GGGGGCGTAGAGATCATAATGA 59.168 50.000 0.00 0.00 0.00 2.57
1889 2240 1.427753 TCAGGGGGCGTAGAGATCATA 59.572 52.381 0.00 0.00 0.00 2.15
1937 2288 4.388499 AAAGTCGCCGCGATGGGT 62.388 61.111 20.03 2.04 38.42 4.51
1950 2301 3.799232 GCGTCACTAGAGACAACCAAAGT 60.799 47.826 18.62 0.00 38.43 2.66
1957 2308 1.335597 CGTTGGCGTCACTAGAGACAA 60.336 52.381 18.62 8.39 38.43 3.18
2225 2580 4.024133 TGAATAAATGTCATCCAATCGCCG 60.024 41.667 0.00 0.00 0.00 6.46
2385 2745 2.267642 TTGCGCTATCGGCAAGGT 59.732 55.556 9.73 0.00 44.79 3.50
2485 2845 0.036164 AGCCAACTATGTGCGAACCA 59.964 50.000 0.00 0.00 0.00 3.67
2558 2918 1.337447 CGACTCCGGGTACAACAATGT 60.337 52.381 0.00 0.00 43.74 2.71
2560 2920 1.067354 GTCGACTCCGGGTACAACAAT 60.067 52.381 8.70 0.00 36.24 2.71
2608 2968 0.109365 CATGAAAACCATTGGCGCGA 60.109 50.000 12.10 0.00 31.94 5.87
2832 3193 7.782897 ATATTTCTCATCATCCTAAGTCCGA 57.217 36.000 0.00 0.00 0.00 4.55
3011 3372 2.430367 GGACCGCATATGTCCCCC 59.570 66.667 4.29 0.00 45.38 5.40


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

AutoCloner maintained by Alex Coulton.