Multiple sequence alignment - TraesCS5A01G474100

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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 TraesCS5A01G474100 chr5A 100.000 2498 0 0 1 2498 650150702 650153199 0.000000e+00 4614.0
1 TraesCS5A01G474100 chr5A 89.660 706 28 15 1785 2482 647553084 647553752 0.000000e+00 857.0
2 TraesCS5A01G474100 chr2A 97.802 2502 47 3 1 2498 769227810 769230307 0.000000e+00 4309.0
3 TraesCS5A01G474100 chr2A 97.359 2499 60 3 1 2498 115130187 115132680 0.000000e+00 4244.0
4 TraesCS5A01G474100 chr4A 97.399 2499 59 3 1 2498 604389228 604386735 0.000000e+00 4250.0
5 TraesCS5A01G474100 chr4A 91.684 2453 132 24 1 2396 521945401 521947838 0.000000e+00 3334.0
6 TraesCS5A01G474100 chr4A 98.148 54 1 0 2429 2482 521947834 521947887 7.360000e-16 95.3
7 TraesCS5A01G474100 chr6A 97.204 2504 57 3 1 2498 162654563 162657059 0.000000e+00 4224.0
8 TraesCS5A01G474100 chr3A 98.063 2271 35 6 1 2269 636533320 636531057 0.000000e+00 3941.0
9 TraesCS5A01G474100 chr4B 93.096 2390 101 22 56 2399 657805212 657802841 0.000000e+00 3441.0
10 TraesCS5A01G474100 chr4B 98.148 54 1 0 2429 2482 657802848 657802795 7.360000e-16 95.3
11 TraesCS5A01G474100 chr7D 93.307 2271 116 17 52 2301 92234276 92232021 0.000000e+00 3319.0
12 TraesCS5A01G474100 chr5D 93.269 2273 110 22 52 2301 408555069 408552817 0.000000e+00 3310.0
13 TraesCS5A01G474100 chr3D 93.390 2254 115 14 69 2301 45062949 45060709 0.000000e+00 3306.0
14 TraesCS5A01G474100 chr2B 96.883 802 24 1 1 801 69352211 69353012 0.000000e+00 1341.0
15 TraesCS5A01G474100 chr1B 96.770 805 25 1 1 804 460163864 460163060 0.000000e+00 1341.0
16 TraesCS5A01G474100 chr1B 96.875 800 20 4 1 797 448519302 448520099 0.000000e+00 1334.0
17 TraesCS5A01G474100 chrUn 96.519 316 11 0 1986 2301 356222196 356222511 7.920000e-145 523.0
18 TraesCS5A01G474100 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 TraesCS5A01G474100 chr5A 650150702 650153199 2497 False 4614.00 4614 100.000 1 2498 1 chr5A.!!$F2 2497
1 TraesCS5A01G474100 chr5A 647553084 647553752 668 False 857.00 857 89.660 1785 2482 1 chr5A.!!$F1 697
2 TraesCS5A01G474100 chr2A 769227810 769230307 2497 False 4309.00 4309 97.802 1 2498 1 chr2A.!!$F2 2497
3 TraesCS5A01G474100 chr2A 115130187 115132680 2493 False 4244.00 4244 97.359 1 2498 1 chr2A.!!$F1 2497
4 TraesCS5A01G474100 chr4A 604386735 604389228 2493 True 4250.00 4250 97.399 1 2498 1 chr4A.!!$R1 2497
5 TraesCS5A01G474100 chr4A 521945401 521947887 2486 False 1714.65 3334 94.916 1 2482 2 chr4A.!!$F1 2481
6 TraesCS5A01G474100 chr6A 162654563 162657059 2496 False 4224.00 4224 97.204 1 2498 1 chr6A.!!$F1 2497
7 TraesCS5A01G474100 chr3A 636531057 636533320 2263 True 3941.00 3941 98.063 1 2269 1 chr3A.!!$R1 2268
8 TraesCS5A01G474100 chr4B 657802795 657805212 2417 True 1768.15 3441 95.622 56 2482 2 chr4B.!!$R1 2426
9 TraesCS5A01G474100 chr7D 92232021 92234276 2255 True 3319.00 3319 93.307 52 2301 1 chr7D.!!$R1 2249
10 TraesCS5A01G474100 chr5D 408552817 408555069 2252 True 3310.00 3310 93.269 52 2301 1 chr5D.!!$R1 2249
11 TraesCS5A01G474100 chr3D 45060709 45062949 2240 True 3306.00 3306 93.390 69 2301 1 chr3D.!!$R1 2232
12 TraesCS5A01G474100 chr2B 69352211 69353012 801 False 1341.00 1341 96.883 1 801 1 chr2B.!!$F1 800
13 TraesCS5A01G474100 chr1B 460163060 460163864 804 True 1341.00 1341 96.770 1 804 1 chr1B.!!$R1 803
14 TraesCS5A01G474100 chr1B 448519302 448520099 797 False 1334.00 1334 96.875 1 797 1 chr1B.!!$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
525 571 0.690762 TGGTTGTAGGAGGAACCAGC 59.309 55.0 0.0 0.0 45.37 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2113 0.614415 CTCCTCCTCCTCTGTGCAGT 60.614 60.0 0.0 0.0 0.0 4.4 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
67 68 1.672682 ACGCTCGCTCACTCTCTCA 60.673 57.895 0.00 0.00 0.00 3.27
229 232 1.160137 GAGGTTGTCAGCATGGACAC 58.840 55.000 4.49 1.74 46.76 3.67
230 233 0.767375 AGGTTGTCAGCATGGACACT 59.233 50.000 4.49 0.00 46.76 3.55
403 415 5.104067 GGATTGAGGTAACCTAGGGTTCATT 60.104 44.000 14.81 3.91 43.05 2.57
525 571 0.690762 TGGTTGTAGGAGGAACCAGC 59.309 55.000 0.00 0.00 45.37 4.85
1161 1219 6.350361 CCAAGCTTGTTGATGATGTATCCAAA 60.350 38.462 24.35 0.00 34.77 3.28
1227 1285 3.326297 AGAAACAAGTGGAGGAGGAAGAG 59.674 47.826 0.00 0.00 0.00 2.85
1287 1348 2.827921 GTTGGAGGTGCAGATGGAAAAT 59.172 45.455 0.00 0.00 0.00 1.82
1459 1520 1.289160 AGAAGGGTATGGCAGCAAGA 58.711 50.000 0.00 0.00 0.00 3.02
1558 1619 4.603610 AGGCCTTTATATAAGGATGTGGCT 59.396 41.667 0.00 4.45 39.81 4.75
1733 1794 8.884323 TGGAAATGGATCTCTTATGCTACTAAT 58.116 33.333 0.00 0.00 0.00 1.73
1734 1795 9.732130 GGAAATGGATCTCTTATGCTACTAATT 57.268 33.333 0.00 0.00 0.00 1.40
1998 2069 1.271271 GGATCCTGACATGGGAGATGC 60.271 57.143 3.84 0.00 36.21 3.91
2042 2113 3.585289 TGTGGAGGTTAGGACAATAGCAA 59.415 43.478 0.00 0.00 0.00 3.91
2312 2417 6.511121 GCGCTATGACTGATCTAGCTATCTAC 60.511 46.154 0.00 0.00 36.55 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.364842 AGGGGAGTGAGCGAGCAT 60.365 61.111 0.00 0.00 0.00 3.79
152 155 2.751436 GGCATTGCGGCAAGGAGA 60.751 61.111 29.08 2.26 40.76 3.71
229 232 5.123979 GGCAAAGAACTTACCATAAGTCCAG 59.876 44.000 1.85 0.00 0.00 3.86
230 233 5.007682 GGCAAAGAACTTACCATAAGTCCA 58.992 41.667 1.85 0.00 0.00 4.02
403 415 5.547465 CATGAACCCTAACACTGTACAGAA 58.453 41.667 29.30 10.28 0.00 3.02
910 968 5.010516 CACCACAATTCACACCATTTTCCTA 59.989 40.000 0.00 0.00 0.00 2.94
1161 1219 3.175594 ACCATCCTGCCAATCAAACATT 58.824 40.909 0.00 0.00 0.00 2.71
1227 1285 3.684305 GCTCCTTCTTCTTCTTCTCAAGC 59.316 47.826 0.00 0.00 0.00 4.01
1287 1348 3.947196 TCTGCTCTTTTGCAAGTTTGAGA 59.053 39.130 17.90 9.77 42.83 3.27
1459 1520 4.460731 GGCCTTGATTTGCTCTAACTTCTT 59.539 41.667 0.00 0.00 0.00 2.52
1558 1619 5.125900 CCATAATCACTTGAAGTCATGCCAA 59.874 40.000 0.00 0.00 0.00 4.52
1703 1764 7.141758 AGCATAAGAGATCCATTTCCACTAA 57.858 36.000 0.00 0.00 0.00 2.24
1736 1797 9.686683 ACTTAATAGCATAAAAGATCCACAACT 57.313 29.630 0.00 0.00 0.00 3.16
1844 1911 2.906389 TGCATTTGGTCAGAGAGTAGGT 59.094 45.455 0.00 0.00 0.00 3.08
1845 1912 3.616956 TGCATTTGGTCAGAGAGTAGG 57.383 47.619 0.00 0.00 0.00 3.18
1998 2069 0.980231 CTCCCCCTCTTCCTCTGTGG 60.980 65.000 0.00 0.00 37.10 4.17
2042 2113 0.614415 CTCCTCCTCCTCTGTGCAGT 60.614 60.000 0.00 0.00 0.00 4.40
2335 2440 7.610305 TCACAAAAACTACCAAAACTCTCTCTT 59.390 33.333 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.