Multiple sequence alignment - TraesCS5A01G279800

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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 TraesCS5A01G279800 chr5A 100.000 3723 0 0 1 3723 489013862 489010140 0.000000e+00 6876.0
1 TraesCS5A01G279800 chr4A 97.803 3733 68 7 1 3723 245406562 245402834 0.000000e+00 6427.0
2 TraesCS5A01G279800 chr3D 89.411 3088 268 36 630 3682 220634961 220638024 0.000000e+00 3836.0
3 TraesCS5A01G279800 chr3D 90.859 1641 119 19 551 2168 204073336 204074968 0.000000e+00 2170.0
4 TraesCS5A01G279800 chr3D 89.050 1516 146 17 2172 3682 204088041 204089541 0.000000e+00 1862.0
5 TraesCS5A01G279800 chr3D 89.982 569 50 5 1 564 204072512 204073078 0.000000e+00 728.0
6 TraesCS5A01G279800 chr3D 89.104 569 54 6 1 564 220634079 220634644 0.000000e+00 701.0
7 TraesCS5A01G279800 chr3D 94.231 52 3 0 551 602 220634913 220634964 3.080000e-11 80.5
8 TraesCS5A01G279800 chr3D 100.000 41 0 0 3683 3723 204089637 204089677 3.990000e-10 76.8
9 TraesCS5A01G279800 chr3D 100.000 41 0 0 3683 3723 220638118 220638158 3.990000e-10 76.8
10 TraesCS5A01G279800 chr6A 92.759 2334 135 16 551 2851 180857153 180859485 0.000000e+00 3343.0
11 TraesCS5A01G279800 chr6A 90.170 824 64 6 2904 3723 180859495 180860305 0.000000e+00 1057.0
12 TraesCS5A01G279800 chr6A 91.260 492 39 3 1 488 180856432 180856923 0.000000e+00 667.0
13 TraesCS5A01G279800 chr6A 89.346 413 39 4 3312 3723 180860342 180860750 7.130000e-142 514.0
14 TraesCS5A01G279800 chr3B 92.609 2327 133 20 562 2851 496830430 496832754 0.000000e+00 3308.0
15 TraesCS5A01G279800 chr3B 89.808 834 65 12 2899 3723 496836599 496837421 0.000000e+00 1051.0
16 TraesCS5A01G279800 chr3B 91.586 309 19 6 2549 2851 496836288 496836595 1.600000e-113 420.0
17 TraesCS5A01G279800 chr4B 91.542 2341 154 24 551 2851 224358096 224355760 0.000000e+00 3186.0
18 TraesCS5A01G279800 chr4B 91.076 381 25 6 1 372 224358784 224358404 1.190000e-139 507.0
19 TraesCS5A01G279800 chr4B 93.548 124 8 0 3600 3723 224354322 224354199 6.350000e-43 185.0
20 TraesCS5A01G279800 chr4B 97.778 45 1 0 2807 2851 224354031 224353987 1.110000e-10 78.7
21 TraesCS5A01G279800 chr2B 93.368 1523 84 14 1346 2851 77373277 77371755 0.000000e+00 2237.0
22 TraesCS5A01G279800 chr2B 89.545 813 71 8 551 1350 77386606 77385795 0.000000e+00 1018.0
23 TraesCS5A01G279800 chr2B 88.849 834 69 12 2899 3723 77371751 77370933 0.000000e+00 1003.0
24 TraesCS5A01G279800 chr2B 89.760 459 35 9 1 450 77395974 77395519 8.970000e-161 577.0
25 TraesCS5A01G279800 chr2B 88.596 342 28 9 3312 3645 77370896 77370558 4.480000e-109 405.0
26 TraesCS5A01G279800 chr2D 87.849 1111 101 20 551 1634 257213949 257215052 0.000000e+00 1273.0
27 TraesCS5A01G279800 chr2D 88.764 801 79 9 1683 2475 257215055 257215852 0.000000e+00 970.0
28 TraesCS5A01G279800 chr2D 87.238 572 58 10 1 564 257202864 257203428 4.060000e-179 638.0
29 TraesCS5A01G279800 chr2D 87.712 236 24 5 2518 2749 257215850 257216084 1.700000e-68 270.0
30 TraesCS5A01G279800 chr1B 86.691 1112 113 23 551 1634 386621333 386620229 0.000000e+00 1201.0
31 TraesCS5A01G279800 chr1B 88.764 801 81 7 1683 2475 86703928 86703129 0.000000e+00 972.0
32 TraesCS5A01G279800 chr1B 85.915 568 60 16 8 564 386622156 386621598 4.140000e-164 588.0
33 TraesCS5A01G279800 chr1B 85.563 568 61 15 8 564 86705871 86705314 3.220000e-160 575.0


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 TraesCS5A01G279800 chr5A 489010140 489013862 3722 True 6876.000000 6876 100.000000 1 3723 1 chr5A.!!$R1 3722
1 TraesCS5A01G279800 chr4A 245402834 245406562 3728 True 6427.000000 6427 97.803000 1 3723 1 chr4A.!!$R1 3722
2 TraesCS5A01G279800 chr3D 204072512 204074968 2456 False 1449.000000 2170 90.420500 1 2168 2 chr3D.!!$F1 2167
3 TraesCS5A01G279800 chr3D 220634079 220638158 4079 False 1173.575000 3836 93.186500 1 3723 4 chr3D.!!$F3 3722
4 TraesCS5A01G279800 chr3D 204088041 204089677 1636 False 969.400000 1862 94.525000 2172 3723 2 chr3D.!!$F2 1551
5 TraesCS5A01G279800 chr6A 180856432 180860750 4318 False 1395.250000 3343 90.883750 1 3723 4 chr6A.!!$F1 3722
6 TraesCS5A01G279800 chr3B 496830430 496837421 6991 False 1593.000000 3308 91.334333 562 3723 3 chr3B.!!$F1 3161
7 TraesCS5A01G279800 chr4B 224353987 224358784 4797 True 989.175000 3186 93.486000 1 3723 4 chr4B.!!$R1 3722
8 TraesCS5A01G279800 chr2B 77370558 77373277 2719 True 1215.000000 2237 90.271000 1346 3723 3 chr2B.!!$R3 2377
9 TraesCS5A01G279800 chr2B 77385795 77386606 811 True 1018.000000 1018 89.545000 551 1350 1 chr2B.!!$R1 799
10 TraesCS5A01G279800 chr2D 257213949 257216084 2135 False 837.666667 1273 88.108333 551 2749 3 chr2D.!!$F2 2198
11 TraesCS5A01G279800 chr2D 257202864 257203428 564 False 638.000000 638 87.238000 1 564 1 chr2D.!!$F1 563
12 TraesCS5A01G279800 chr1B 386620229 386622156 1927 True 894.500000 1201 86.303000 8 1634 2 chr1B.!!$R2 1626
13 TraesCS5A01G279800 chr1B 86703129 86705871 2742 True 773.500000 972 87.163500 8 2475 2 chr1B.!!$R1 2467

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
859 1204 2.143122 TGTGAGACGCCAGAAATTCAC 58.857 47.619 0.00 0.0 36.4 3.18 F
1471 1833 1.699634 TCTGGTTAGCTGCTTTGGTCT 59.300 47.619 7.79 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2449 1.196127 GTTCCTTGAAAGGTTACGCCG 59.804 52.381 8.91 0.0 46.54 6.46 R
3321 7837 2.434336 TCGTTAGCTTCCTATGTGGCAT 59.566 45.455 0.00 0.0 35.26 4.40 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
32 33 4.152580 TGCGTTAAACATTAAGCATCGTCA 59.847 37.500 0.00 0.00 0.00 4.35
377 391 7.836842 ACCAAAATTAAACCTAACTGCCATAG 58.163 34.615 0.00 0.00 0.00 2.23
859 1204 2.143122 TGTGAGACGCCAGAAATTCAC 58.857 47.619 0.00 0.00 36.40 3.18
1240 1592 4.825085 TCTAGCCGTTCAAGTTTCCATTTT 59.175 37.500 0.00 0.00 0.00 1.82
1279 1639 4.844884 ACCTAATACTTGGCAAGGAGTTC 58.155 43.478 29.26 0.00 0.00 3.01
1471 1833 1.699634 TCTGGTTAGCTGCTTTGGTCT 59.300 47.619 7.79 0.00 0.00 3.85
2075 2449 3.243234 CCATGACTCGTGGAGATACACTC 60.243 52.174 11.49 0.00 42.73 3.51
2196 2575 7.801315 CGCTGTTCTTTAAAGTATTTGCAAGTA 59.199 33.333 14.74 0.00 39.63 2.24
2259 2638 2.195727 TGATGAAGGAGGTGTATGGCA 58.804 47.619 0.00 0.00 0.00 4.92
2262 2641 3.737559 TGAAGGAGGTGTATGGCAAAT 57.262 42.857 0.00 0.00 0.00 2.32
3449 7966 7.014711 TCTCTGTCTCAAGATGTTAACTTCACT 59.985 37.037 20.10 7.13 0.00 3.41
3452 7969 7.445121 TGTCTCAAGATGTTAACTTCACTCAT 58.555 34.615 20.10 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.255149 CCAAGAGTCAAGCAGCTCAAAAT 59.745 43.478 0.00 0.00 34.39 1.82
473 489 7.898309 CGCAGGATATAATGATAAAAGCGTTAC 59.102 37.037 0.00 0.00 36.06 2.50
477 493 6.243551 CACGCAGGATATAATGATAAAAGCG 58.756 40.000 0.00 0.00 44.98 4.68
787 1131 0.036732 TAGCCCAAGACCTGCAACAG 59.963 55.000 0.00 0.00 0.00 3.16
796 1140 4.816990 GCTCGTCTAGCCCAAGAC 57.183 61.111 2.20 2.20 46.25 3.01
814 1158 6.928979 TGGTCTCGAACAAACTAAATTCAA 57.071 33.333 0.00 0.00 0.00 2.69
859 1204 8.911247 TCAATATGTCTTCATCCGATATTACG 57.089 34.615 0.00 0.00 35.70 3.18
1019 1365 2.564721 GCTCTGGGCCACAAACACC 61.565 63.158 0.00 0.00 34.27 4.16
1279 1639 5.375417 TTCACTGTGCATATTTGTCAAGG 57.625 39.130 2.12 0.00 0.00 3.61
1459 1821 2.684843 CCAGCGAGACCAAAGCAGC 61.685 63.158 0.00 0.00 0.00 5.25
2075 2449 1.196127 GTTCCTTGAAAGGTTACGCCG 59.804 52.381 8.91 0.00 46.54 6.46
2259 2638 7.168219 TGCCTTGAAGAGTTGTATGTAGATTT 58.832 34.615 0.00 0.00 0.00 2.17
2262 2641 5.724328 CTGCCTTGAAGAGTTGTATGTAGA 58.276 41.667 0.00 0.00 0.00 2.59
3147 7638 6.039159 TGTCTCATAAACAATTGCACTTGACA 59.961 34.615 22.12 10.80 0.00 3.58
3321 7837 2.434336 TCGTTAGCTTCCTATGTGGCAT 59.566 45.455 0.00 0.00 35.26 4.40
3672 8898 2.357075 TCACTGTACAAACGTTTGGCA 58.643 42.857 36.52 31.18 42.34 4.92


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

AutoCloner maintained by Alex Coulton.