Multiple sequence alignment - TraesCS5A01G095700

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 TraesCS5A01G095700 chr5A 100.000 2767 0 0 1 2767 133817750 133820516 0.000000e+00 5110
1 TraesCS5A01G095700 chr5A 95.810 2124 59 3 1 2121 345672839 345670743 0.000000e+00 3402
2 TraesCS5A01G095700 chr5A 94.772 1970 85 15 753 2712 501869175 501871136 0.000000e+00 3051
3 TraesCS5A01G095700 chr5A 94.913 1376 61 8 753 2121 5809481 5808108 0.000000e+00 2145
4 TraesCS5A01G095700 chr4A 96.123 2734 81 5 1 2712 490340961 490343691 0.000000e+00 4438
5 TraesCS5A01G095700 chr4A 95.154 1651 67 9 1 1650 429488137 429489775 0.000000e+00 2593
6 TraesCS5A01G095700 chr3A 95.764 2715 103 8 1 2712 513294964 513297669 0.000000e+00 4366
7 TraesCS5A01G095700 chr3A 93.698 1571 74 8 1 1569 733887401 733885854 0.000000e+00 2329
8 TraesCS5A01G095700 chr6A 95.541 2736 94 10 1 2712 401364444 401367175 0.000000e+00 4351
9 TraesCS5A01G095700 chr1A 95.553 2586 91 4 150 2712 575419163 575421747 0.000000e+00 4117
10 TraesCS5A01G095700 chr1A 96.003 2327 85 6 392 2712 580783461 580785785 0.000000e+00 3775
11 TraesCS5A01G095700 chr1A 100.000 59 0 0 2709 2767 7950798 7950856 2.910000e-20 110
12 TraesCS5A01G095700 chr1A 100.000 59 0 0 2709 2767 50645840 50645782 2.910000e-20 110
13 TraesCS5A01G095700 chr1A 100.000 59 0 0 2709 2767 471028030 471028088 2.910000e-20 110
14 TraesCS5A01G095700 chr1A 100.000 59 0 0 2709 2767 471028692 471028750 2.910000e-20 110
15 TraesCS5A01G095700 chr1A 100.000 59 0 0 2709 2767 575422266 575422324 2.910000e-20 110
16 TraesCS5A01G095700 chr7B 96.236 1913 69 3 802 2712 471054623 471056534 0.000000e+00 3131
17 TraesCS5A01G095700 chr2B 95.431 1926 85 3 789 2712 131501159 131499235 0.000000e+00 3066
18 TraesCS5A01G095700 chr3B 95.607 1912 66 4 802 2712 317287062 317288956 0.000000e+00 3049
19 TraesCS5A01G095700 chr7A 95.379 1623 62 8 1 1617 644066760 644065145 0.000000e+00 2569
20 TraesCS5A01G095700 chr7A 95.305 1576 62 9 1 1569 633712557 633710987 0.000000e+00 2490
21 TraesCS5A01G095700 chrUn 100.000 59 0 0 2709 2767 38467101 38467159 2.910000e-20 110
22 TraesCS5A01G095700 chrUn 100.000 59 0 0 2709 2767 38467762 38467820 2.910000e-20 110
23 TraesCS5A01G095700 chrUn 100.000 59 0 0 2709 2767 39690513 39690571 2.910000e-20 110
24 TraesCS5A01G095700 chrUn 100.000 59 0 0 2709 2767 409319997 409320055 2.910000e-20 110


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 TraesCS5A01G095700 chr5A 133817750 133820516 2766 False 5110.0 5110 100.0000 1 2767 1 chr5A.!!$F1 2766
1 TraesCS5A01G095700 chr5A 345670743 345672839 2096 True 3402.0 3402 95.8100 1 2121 1 chr5A.!!$R2 2120
2 TraesCS5A01G095700 chr5A 501869175 501871136 1961 False 3051.0 3051 94.7720 753 2712 1 chr5A.!!$F2 1959
3 TraesCS5A01G095700 chr5A 5808108 5809481 1373 True 2145.0 2145 94.9130 753 2121 1 chr5A.!!$R1 1368
4 TraesCS5A01G095700 chr4A 490340961 490343691 2730 False 4438.0 4438 96.1230 1 2712 1 chr4A.!!$F2 2711
5 TraesCS5A01G095700 chr4A 429488137 429489775 1638 False 2593.0 2593 95.1540 1 1650 1 chr4A.!!$F1 1649
6 TraesCS5A01G095700 chr3A 513294964 513297669 2705 False 4366.0 4366 95.7640 1 2712 1 chr3A.!!$F1 2711
7 TraesCS5A01G095700 chr3A 733885854 733887401 1547 True 2329.0 2329 93.6980 1 1569 1 chr3A.!!$R1 1568
8 TraesCS5A01G095700 chr6A 401364444 401367175 2731 False 4351.0 4351 95.5410 1 2712 1 chr6A.!!$F1 2711
9 TraesCS5A01G095700 chr1A 580783461 580785785 2324 False 3775.0 3775 96.0030 392 2712 1 chr1A.!!$F2 2320
10 TraesCS5A01G095700 chr1A 575419163 575422324 3161 False 2113.5 4117 97.7765 150 2767 2 chr1A.!!$F4 2617
11 TraesCS5A01G095700 chr7B 471054623 471056534 1911 False 3131.0 3131 96.2360 802 2712 1 chr7B.!!$F1 1910
12 TraesCS5A01G095700 chr2B 131499235 131501159 1924 True 3066.0 3066 95.4310 789 2712 1 chr2B.!!$R1 1923
13 TraesCS5A01G095700 chr3B 317287062 317288956 1894 False 3049.0 3049 95.6070 802 2712 1 chr3B.!!$F1 1910
14 TraesCS5A01G095700 chr7A 644065145 644066760 1615 True 2569.0 2569 95.3790 1 1617 1 chr7A.!!$R2 1616
15 TraesCS5A01G095700 chr7A 633710987 633712557 1570 True 2490.0 2490 95.3050 1 1569 1 chr7A.!!$R1 1568

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
944 965 1.061711 GCTGTCTAGTGCTTGATTGCG 59.938 52.381 0.0 0.0 35.36 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 2404 0.106819 GGGAGTAGCTACGAGGGTCA 60.107 60.0 17.99 0.0 0.0 4.02 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
39 40 4.141711 CCTTGCTAGGTATGCTAGTTTCCA 60.142 45.833 5.98 0.00 36.74 3.53
944 965 1.061711 GCTGTCTAGTGCTTGATTGCG 59.938 52.381 0.00 0.00 35.36 4.85
1062 1083 2.282040 GGCAGCAGGCTTCACAGT 60.282 61.111 0.00 0.00 44.01 3.55
1331 1352 2.210116 GACGACAACACCATGTTCACT 58.790 47.619 0.00 0.00 38.77 3.41
1345 1366 6.183360 ACCATGTTCACTCTTTGTTGCATTTA 60.183 34.615 0.00 0.00 0.00 1.40
1422 1461 2.685017 AGCAGAGCGGGGATGACA 60.685 61.111 0.00 0.00 0.00 3.58
1427 1490 1.377202 GAGCGGGGATGACAAGCAA 60.377 57.895 0.00 0.00 0.00 3.91
1667 1805 2.413142 GCCTGCAATCCCACAGCTC 61.413 63.158 0.00 0.00 32.37 4.09
1692 1830 1.203038 ACAGGACCATGCCAATTGTGA 60.203 47.619 4.43 0.00 0.00 3.58
1790 1928 4.999950 AGATGTTAAGAAGGTGTTCAGCAG 59.000 41.667 4.86 0.00 34.82 4.24
1829 1967 9.973246 CTTGTTAGTGTAATATGAACATGTCAC 57.027 33.333 0.00 0.00 39.72 3.67
2263 2404 2.070783 CGCCAAAAAGCATGCATTTCT 58.929 42.857 20.12 8.84 0.00 2.52
2305 2446 1.838073 AATTCGGACCACCTTCGGCT 61.838 55.000 0.00 0.00 0.00 5.52
2337 2478 2.871096 ACCGGCTGGAATTTGAACTA 57.129 45.000 21.41 0.00 39.21 2.24
2363 2504 1.583054 CTCCATAGCTTGCCCGTTAC 58.417 55.000 0.00 0.00 0.00 2.50
2455 2596 2.212110 AAACCCTAGCCACGGACGT 61.212 57.895 0.00 0.00 0.00 4.34
2456 2597 2.163601 AAACCCTAGCCACGGACGTC 62.164 60.000 7.13 7.13 0.00 4.34
2666 2807 4.144297 TGGCTTTCAAGTCAAACTAGCAT 58.856 39.130 0.00 0.00 37.77 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.733337 GTCACTGTGAAGAGAACCACAT 58.267 45.455 12.81 0.00 41.75 3.21
186 188 5.163513 CCGCTGCATCTTTTTAGACAAATT 58.836 37.500 0.00 0.00 0.00 1.82
329 331 6.474427 ACACCGATATAGTCATGTACAAAACG 59.526 38.462 0.00 0.00 0.00 3.60
680 684 7.984422 TGCACTTGTGGATATTTATGATAGG 57.016 36.000 2.81 0.00 0.00 2.57
944 965 3.057526 GGGTCAAGCAGTGGTTAATTGTC 60.058 47.826 7.35 0.00 0.00 3.18
1062 1083 1.777878 ACCACCAACACTTCCCACATA 59.222 47.619 0.00 0.00 0.00 2.29
1331 1352 3.230134 ACCTGGCTAAATGCAACAAAGA 58.770 40.909 0.00 0.00 45.15 2.52
1345 1366 1.918253 CTGCTCCCATTACCTGGCT 59.082 57.895 0.00 0.00 44.46 4.75
1422 1461 2.040544 CGTCATCCCCGCTTTGCTT 61.041 57.895 0.00 0.00 0.00 3.91
1427 1490 2.363795 TCCTCGTCATCCCCGCTT 60.364 61.111 0.00 0.00 0.00 4.68
1692 1830 2.273538 ACGCGGATGTACTCCTCTAT 57.726 50.000 12.47 0.00 42.47 1.98
1790 1928 6.872628 ACACTAACAAGCTTAAACCTAACC 57.127 37.500 0.00 0.00 0.00 2.85
1842 1980 5.609423 TGAGCATGCACAAAATTAAACCTT 58.391 33.333 21.98 0.00 0.00 3.50
2263 2404 0.106819 GGGAGTAGCTACGAGGGTCA 60.107 60.000 17.99 0.00 0.00 4.02
2305 2446 1.377202 GCCGGTTCCAGCTGAATCA 60.377 57.895 17.39 0.00 33.37 2.57
2455 2596 0.180171 ACCGATTTCATCATGGCGGA 59.820 50.000 13.56 0.00 41.11 5.54
2456 2597 0.588252 GACCGATTTCATCATGGCGG 59.412 55.000 0.00 0.00 43.95 6.13
2461 2602 4.457603 TCAAAAACCGACCGATTTCATCAT 59.542 37.500 0.00 0.00 0.00 2.45
2635 2776 6.409524 TTGACTTGAAAGCCATGAATCTTT 57.590 33.333 0.00 0.62 35.44 2.52
2666 2807 0.179032 AACGGATGCGGCCATATCAA 60.179 50.000 12.44 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.