Multiple sequence alignment - TraesCS2A01G574100

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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 TraesCS2A01G574100 chr2A 100.000 2501 0 0 1 2501 769227810 769230310 0.000000e+00 4619.0
1 TraesCS2A01G574100 chr2A 97.561 2501 57 2 1 2501 115130187 115132683 0.000000e+00 4277.0
2 TraesCS2A01G574100 chr5A 97.804 2505 47 3 1 2501 650150702 650153202 0.000000e+00 4314.0
3 TraesCS2A01G574100 chr5A 94.847 621 23 2 1784 2396 647553084 647553703 0.000000e+00 961.0
4 TraesCS2A01G574100 chr5A 89.873 79 2 1 2429 2501 647553699 647553777 2.050000e-16 97.1
5 TraesCS2A01G574100 chr4A 97.521 2501 58 2 1 2501 604389228 604386732 0.000000e+00 4272.0
6 TraesCS2A01G574100 chr4A 91.816 2456 123 24 1 2396 521945401 521947838 0.000000e+00 3350.0
7 TraesCS2A01G574100 chr4A 89.873 79 2 1 2429 2501 521947834 521947912 2.050000e-16 97.1
8 TraesCS2A01G574100 chr6A 97.367 2507 53 4 1 2501 162654563 162657062 0.000000e+00 4252.0
9 TraesCS2A01G574100 chr3A 97.973 2269 41 3 1 2269 636533320 636531057 0.000000e+00 3930.0
10 TraesCS2A01G574100 chr4B 93.108 2394 93 24 56 2399 657805212 657802841 0.000000e+00 3441.0
11 TraesCS2A01G574100 chr4B 98.148 54 1 0 2429 2482 657802848 657802795 7.360000e-16 95.3
12 TraesCS2A01G574100 chr7D 93.363 2275 107 19 52 2301 92234276 92232021 0.000000e+00 3325.0
13 TraesCS2A01G574100 chr7D 93.278 2276 103 20 52 2301 631818323 631816072 0.000000e+00 3310.0
14 TraesCS2A01G574100 chr3D 93.372 2263 107 17 65 2301 45062954 45060709 0.000000e+00 3308.0
15 TraesCS2A01G574100 chr5B 92.395 1578 70 20 883 2429 69032176 69033734 0.000000e+00 2204.0
16 TraesCS2A01G574100 chr2B 97.243 798 21 1 1 797 69352211 69353008 0.000000e+00 1351.0
17 TraesCS2A01G574100 chr1B 97.243 798 21 1 1 797 460163864 460163067 0.000000e+00 1351.0
18 TraesCS2A01G574100 chr1B 96.996 799 21 3 1 797 448519302 448520099 0.000000e+00 1339.0
19 TraesCS2A01G574100 chr1B 93.269 104 6 1 2306 2409 460161660 460161558 4.310000e-33 152.0
20 TraesCS2A01G574100 chr1B 93.269 104 6 1 2306 2409 544795871 544795769 4.310000e-33 152.0
21 TraesCS2A01G574100 chr6B 96.621 799 25 2 1 797 661539116 661539914 0.000000e+00 1325.0
22 TraesCS2A01G574100 chrUn 98.113 53 1 0 2429 2481 356222620 356222672 2.650000e-15 93.5
23 TraesCS2A01G574100 chr6D 98.113 53 1 0 2429 2481 61155983 61155931 2.650000e-15 93.5


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 TraesCS2A01G574100 chr2A 769227810 769230310 2500 False 4619.00 4619 100.0000 1 2501 1 chr2A.!!$F2 2500
1 TraesCS2A01G574100 chr2A 115130187 115132683 2496 False 4277.00 4277 97.5610 1 2501 1 chr2A.!!$F1 2500
2 TraesCS2A01G574100 chr5A 650150702 650153202 2500 False 4314.00 4314 97.8040 1 2501 1 chr5A.!!$F1 2500
3 TraesCS2A01G574100 chr5A 647553084 647553777 693 False 529.05 961 92.3600 1784 2501 2 chr5A.!!$F2 717
4 TraesCS2A01G574100 chr4A 604386732 604389228 2496 True 4272.00 4272 97.5210 1 2501 1 chr4A.!!$R1 2500
5 TraesCS2A01G574100 chr4A 521945401 521947912 2511 False 1723.55 3350 90.8445 1 2501 2 chr4A.!!$F1 2500
6 TraesCS2A01G574100 chr6A 162654563 162657062 2499 False 4252.00 4252 97.3670 1 2501 1 chr6A.!!$F1 2500
7 TraesCS2A01G574100 chr3A 636531057 636533320 2263 True 3930.00 3930 97.9730 1 2269 1 chr3A.!!$R1 2268
8 TraesCS2A01G574100 chr4B 657802795 657805212 2417 True 1768.15 3441 95.6280 56 2482 2 chr4B.!!$R1 2426
9 TraesCS2A01G574100 chr7D 92232021 92234276 2255 True 3325.00 3325 93.3630 52 2301 1 chr7D.!!$R1 2249
10 TraesCS2A01G574100 chr7D 631816072 631818323 2251 True 3310.00 3310 93.2780 52 2301 1 chr7D.!!$R2 2249
11 TraesCS2A01G574100 chr3D 45060709 45062954 2245 True 3308.00 3308 93.3720 65 2301 1 chr3D.!!$R1 2236
12 TraesCS2A01G574100 chr5B 69032176 69033734 1558 False 2204.00 2204 92.3950 883 2429 1 chr5B.!!$F1 1546
13 TraesCS2A01G574100 chr2B 69352211 69353008 797 False 1351.00 1351 97.2430 1 797 1 chr2B.!!$F1 796
14 TraesCS2A01G574100 chr1B 448519302 448520099 797 False 1339.00 1339 96.9960 1 797 1 chr1B.!!$F1 796
15 TraesCS2A01G574100 chr1B 460161558 460163864 2306 True 751.50 1351 95.2560 1 2409 2 chr1B.!!$R2 2408
16 TraesCS2A01G574100 chr6B 661539116 661539914 798 False 1325.00 1325 96.6210 1 797 1 chr6B.!!$F1 796

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
662 692 1.065126 GTTTCTATGGCTGCCCAGTCT 60.065 52.381 17.53 0.0 46.24 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1644 2.302733 ACTTCACATTCCCCCAAAATGC 59.697 45.455 0.0 0.0 37.58 3.56 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
323 326 5.670485 CCATGGATGTTGCTTAGTGTAGTA 58.330 41.667 5.56 0.00 0.00 1.82
435 447 4.458989 GTGTTAGGGTTCATGCTGATTTGA 59.541 41.667 0.00 0.00 0.00 2.69
662 692 1.065126 GTTTCTATGGCTGCCCAGTCT 60.065 52.381 17.53 0.00 46.24 3.24
1103 1145 0.777446 AGGGAGTTGGCCAAGCTTAA 59.223 50.000 21.21 0.00 0.00 1.85
1173 1215 7.943079 TGATGTATCCAAGATGTTTGATTGT 57.057 32.000 0.00 0.00 0.00 2.71
1232 1286 2.977808 AGTGGAGGAGGAAGAACTTGA 58.022 47.619 0.00 0.00 0.00 3.02
1233 1287 2.903135 AGTGGAGGAGGAAGAACTTGAG 59.097 50.000 0.00 0.00 0.00 3.02
1234 1288 2.900546 GTGGAGGAGGAAGAACTTGAGA 59.099 50.000 0.00 0.00 0.00 3.27
1441 1495 1.285023 GTTGTTGCTGAGCTGCTGG 59.715 57.895 7.01 0.26 0.00 4.85
1529 1583 5.447818 GCTGTGATATGTTGGTGAAGTAAGC 60.448 44.000 0.00 0.00 0.00 3.09
1590 1644 5.003160 TGACTTCAAGTGATTATGGGTGTG 58.997 41.667 0.00 0.00 0.00 3.82
1719 1775 7.607991 CCTATGCTATTAAGTAGTGGAAATGGG 59.392 40.741 0.00 0.00 32.72 4.00
1867 1933 3.213206 ACTCTCTGACCAAATGCAACA 57.787 42.857 0.00 0.00 0.00 3.33
1965 2032 2.912025 CAGCCGCCACCCAAAAGT 60.912 61.111 0.00 0.00 0.00 2.66
2029 2096 3.403558 GGGGAGGCTGTGGAGGTC 61.404 72.222 0.00 0.00 0.00 3.85
2156 2229 4.286032 ACAAGGTACTGGAGAAGTGCAATA 59.714 41.667 0.00 0.00 42.87 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.697761 CGTGTGATCCCGACCGACT 61.698 63.158 0.00 0.00 0.00 4.18
323 326 5.356751 ACAGTATCACACACACAACAACAAT 59.643 36.000 0.00 0.00 0.00 2.71
435 447 6.265196 TCAACTTGCACTGTTCATTAAATCCT 59.735 34.615 1.70 0.00 0.00 3.24
662 692 8.956426 CAGAAAACTTAATTGGCATCTAACCTA 58.044 33.333 0.00 0.00 0.00 3.08
913 955 5.860941 ACACCACAATTCACACCATTTTA 57.139 34.783 0.00 0.00 0.00 1.52
1103 1145 4.098349 TGCAAAGCTTGTCATTTTCAGTCT 59.902 37.500 0.00 0.00 0.00 3.24
1173 1215 0.415830 TGTCCACCCTACCATCCTGA 59.584 55.000 0.00 0.00 0.00 3.86
1232 1286 6.252995 TCTAGCTCCTTCTTCTTCTTCTTCT 58.747 40.000 0.00 0.00 0.00 2.85
1233 1287 6.405842 CCTCTAGCTCCTTCTTCTTCTTCTTC 60.406 46.154 0.00 0.00 0.00 2.87
1234 1288 5.422012 CCTCTAGCTCCTTCTTCTTCTTCTT 59.578 44.000 0.00 0.00 0.00 2.52
1441 1495 2.019984 CTTGCTGCCATACCCTTCTTC 58.980 52.381 0.00 0.00 0.00 2.87
1529 1583 7.004086 TCCTTATATAAAGGCCTTTGGATGTG 58.996 38.462 35.99 22.67 37.34 3.21
1590 1644 2.302733 ACTTCACATTCCCCCAAAATGC 59.697 45.455 0.00 0.00 37.58 3.56
1677 1733 5.945310 AGCATAGGTGATCCATTACAACAT 58.055 37.500 0.00 0.00 35.89 2.71
1719 1775 6.864342 TCCACAACTTAGTAGCATAAGAGAC 58.136 40.000 9.53 0.00 36.46 3.36
1867 1933 2.842496 GGTTGGGTTTAGTAGGCCTAGT 59.158 50.000 23.57 23.57 0.00 2.57
1896 1963 5.313506 GGGGAGGGGTTTATATTGAGAGATT 59.686 44.000 0.00 0.00 0.00 2.40
1965 2032 4.223953 GTCAGGATCCATCTGTAGGGTTA 58.776 47.826 15.82 0.00 34.15 2.85
2156 2229 6.205658 GTGAAAACCAGCTCTAGTTCTTCATT 59.794 38.462 14.35 1.10 0.00 2.57


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

AutoCloner maintained by Alex Coulton.