Multiple sequence alignment - TraesCS4D01G156200

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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 TraesCS4D01G156200 chr4D 100.000 2246 0 0 1 2246 210026550 210024305 0.000000e+00 4148.0
1 TraesCS4D01G156200 chr3A 94.311 2250 123 5 1 2246 575149679 575151927 0.000000e+00 3441.0
2 TraesCS4D01G156200 chr3A 95.706 1304 52 4 1 1302 433764538 433765839 0.000000e+00 2095.0
3 TraesCS4D01G156200 chr7B 95.624 1691 71 3 4 1693 365876205 365874517 0.000000e+00 2710.0
4 TraesCS4D01G156200 chr7B 92.650 517 28 4 1730 2246 365874524 365874018 0.000000e+00 736.0
5 TraesCS4D01G156200 chr7B 89.032 155 16 1 1590 1744 58733216 58733369 8.190000e-45 191.0
6 TraesCS4D01G156200 chr7B 98.182 55 1 0 1818 1872 456310160 456310106 1.840000e-16 97.1
7 TraesCS4D01G156200 chr5A 94.110 1528 77 9 1 1523 173529034 173527515 0.000000e+00 2311.0
8 TraesCS4D01G156200 chr5A 93.754 1457 82 5 791 2246 683752375 683750927 0.000000e+00 2178.0
9 TraesCS4D01G156200 chr5A 93.621 1458 87 4 791 2246 681747178 681748631 0.000000e+00 2172.0
10 TraesCS4D01G156200 chr1B 95.058 1295 61 3 1 1293 40282524 40283817 0.000000e+00 2034.0
11 TraesCS4D01G156200 chr4B 93.897 1229 63 4 1 1227 239620487 239621705 0.000000e+00 1844.0
12 TraesCS4D01G156200 chr4B 89.610 77 4 3 1894 1969 225960677 225960604 6.600000e-16 95.3
13 TraesCS4D01G156200 chr5B 96.163 808 30 1 4 810 415416733 415415926 0.000000e+00 1319.0
14 TraesCS4D01G156200 chr5B 94.335 406 23 0 1642 2047 415395028 415394623 6.810000e-175 623.0
15 TraesCS4D01G156200 chr5B 92.742 124 9 0 1523 1646 415415926 415415803 1.770000e-41 180.0
16 TraesCS4D01G156200 chr5D 93.096 898 50 8 1 889 68971085 68971979 0.000000e+00 1304.0
17 TraesCS4D01G156200 chr1A 92.857 896 48 12 1 889 558759028 558758142 0.000000e+00 1286.0
18 TraesCS4D01G156200 chr4A 91.825 893 60 10 1 889 292710035 292709152 0.000000e+00 1232.0
19 TraesCS4D01G156200 chr4A 92.647 68 5 0 1805 1872 469883643 469883710 5.100000e-17 99.0
20 TraesCS4D01G156200 chr7A 96.995 732 20 2 659 1389 617960339 617959609 0.000000e+00 1229.0
21 TraesCS4D01G156200 chr7A 85.816 141 14 4 1397 1536 105315099 105315234 6.460000e-31 145.0
22 TraesCS4D01G156200 chr3D 94.286 105 6 0 1905 2009 116560736 116560632 6.420000e-36 161.0
23 TraesCS4D01G156200 chr7D 93.000 100 7 0 1905 2004 574406570 574406471 1.800000e-31 147.0
24 TraesCS4D01G156200 chr7D 88.750 80 6 2 1891 1969 240513340 240513417 6.600000e-16 95.3
25 TraesCS4D01G156200 chr2A 95.062 81 4 0 1222 1302 769585500 769585580 6.510000e-26 128.0
26 TraesCS4D01G156200 chr2B 96.552 58 2 0 1815 1872 317548932 317548989 1.840000e-16 97.1


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 TraesCS4D01G156200 chr4D 210024305 210026550 2245 True 4148.0 4148 100.0000 1 2246 1 chr4D.!!$R1 2245
1 TraesCS4D01G156200 chr3A 575149679 575151927 2248 False 3441.0 3441 94.3110 1 2246 1 chr3A.!!$F2 2245
2 TraesCS4D01G156200 chr3A 433764538 433765839 1301 False 2095.0 2095 95.7060 1 1302 1 chr3A.!!$F1 1301
3 TraesCS4D01G156200 chr7B 365874018 365876205 2187 True 1723.0 2710 94.1370 4 2246 2 chr7B.!!$R2 2242
4 TraesCS4D01G156200 chr5A 173527515 173529034 1519 True 2311.0 2311 94.1100 1 1523 1 chr5A.!!$R1 1522
5 TraesCS4D01G156200 chr5A 683750927 683752375 1448 True 2178.0 2178 93.7540 791 2246 1 chr5A.!!$R2 1455
6 TraesCS4D01G156200 chr5A 681747178 681748631 1453 False 2172.0 2172 93.6210 791 2246 1 chr5A.!!$F1 1455
7 TraesCS4D01G156200 chr1B 40282524 40283817 1293 False 2034.0 2034 95.0580 1 1293 1 chr1B.!!$F1 1292
8 TraesCS4D01G156200 chr4B 239620487 239621705 1218 False 1844.0 1844 93.8970 1 1227 1 chr4B.!!$F1 1226
9 TraesCS4D01G156200 chr5B 415415803 415416733 930 True 749.5 1319 94.4525 4 1646 2 chr5B.!!$R2 1642
10 TraesCS4D01G156200 chr5D 68971085 68971979 894 False 1304.0 1304 93.0960 1 889 1 chr5D.!!$F1 888
11 TraesCS4D01G156200 chr1A 558758142 558759028 886 True 1286.0 1286 92.8570 1 889 1 chr1A.!!$R1 888
12 TraesCS4D01G156200 chr4A 292709152 292710035 883 True 1232.0 1232 91.8250 1 889 1 chr4A.!!$R1 888
13 TraesCS4D01G156200 chr7A 617959609 617960339 730 True 1229.0 1229 96.9950 659 1389 1 chr7A.!!$R1 730

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
68 69 5.010516 AGGCAGTTTGTGTGCATAAATACAA 59.989 36.0 0.0 0.0 43.12 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1811 0.392863 ACAATACTGGATGCAGCGCA 60.393 50.0 14.95 5.73 44.86 6.09 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
26 27 5.727434 AGGAGCAAAATAAAGGCAAATCTG 58.273 37.500 0.00 0.0 0.00 2.90
28 29 5.809051 GGAGCAAAATAAAGGCAAATCTGAG 59.191 40.000 0.00 0.0 0.00 3.35
66 67 5.059404 AGGCAGTTTGTGTGCATAAATAC 57.941 39.130 0.00 0.0 43.12 1.89
68 69 5.010516 AGGCAGTTTGTGTGCATAAATACAA 59.989 36.000 0.00 0.0 43.12 2.41
98 101 5.899299 AGCAAAATGAGGCATAGAAATCAC 58.101 37.500 0.00 0.0 0.00 3.06
432 443 6.940739 ACATGATTCAGCTAAGTAGACAAGT 58.059 36.000 0.00 0.0 0.00 3.16
482 495 9.489084 GCACATGATTTGTATACATAACTCCTA 57.511 33.333 6.36 0.0 36.57 2.94
832 849 9.113876 GATTGGTTTCTGTACGAAAATAAACTG 57.886 33.333 12.33 0.0 42.87 3.16
1491 1516 8.961092 TGCGAATAAATACTACTAACGTGAATC 58.039 33.333 0.00 0.0 0.00 2.52
1542 1567 6.511416 ACTATAATAACAGCAGCTCAGTCAG 58.489 40.000 0.00 0.0 0.00 3.51
1562 1587 3.558674 GCCCACTGCAATCTACACT 57.441 52.632 0.00 0.0 40.77 3.55
1681 1708 0.877071 CAGGAACACGCATGAAAGCT 59.123 50.000 0.00 0.0 0.00 3.74
1784 1811 5.584551 ATCTAGAACAAAACAGAACCCCT 57.415 39.130 0.00 0.0 0.00 4.79
1808 1835 1.331756 CTGCATCCAGTATTGTTCGGC 59.668 52.381 0.00 0.0 34.31 5.54
1890 1923 8.621532 TGCAGAACAATAATTTGTCTAAGACT 57.378 30.769 0.00 0.0 45.30 3.24
1923 1956 6.743575 AACTCCAACATAAGCATAGTCAAC 57.256 37.500 0.00 0.0 0.00 3.18
1987 2020 1.481871 GATAAGAGGGGTCCGTGACA 58.518 55.000 6.41 0.0 33.68 3.58
2087 2120 2.579201 CCTTGGCAGATCCGTCGT 59.421 61.111 0.00 0.0 37.80 4.34
2193 2226 3.548587 CAACTTCATGAACAGAGCAACG 58.451 45.455 3.38 0.0 0.00 4.10
2218 2251 2.591144 TGCTGTCATGTGCGTGCA 60.591 55.556 0.00 0.0 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.253685 TGCCTACAAGTTAATGTGCTCTC 58.746 43.478 0.00 0.00 34.75 3.20
28 29 4.003648 ACTGCCTACAAGTTAATGTGCTC 58.996 43.478 0.00 0.00 34.75 4.26
66 67 6.730960 ATGCCTCATTTTGCTTGTTTATTG 57.269 33.333 0.00 0.00 0.00 1.90
68 69 7.408756 TCTATGCCTCATTTTGCTTGTTTAT 57.591 32.000 0.00 0.00 0.00 1.40
98 101 9.737427 CTGTTGATAGTAACTACTTGTATCCAG 57.263 37.037 0.00 0.00 37.73 3.86
121 124 7.549488 GTGATTGGAGTAGTATTTACTTGCTGT 59.451 37.037 0.00 0.00 37.73 4.40
482 495 8.169977 TGCTTTCTAATCAAGTTCTTGAACAT 57.830 30.769 17.28 10.35 34.24 2.71
832 849 2.366533 GGTTACCCTTCCTTTAGCTGC 58.633 52.381 0.00 0.00 0.00 5.25
953 972 5.697178 CGAGAGGTCTCTAGTTAATGATCGA 59.303 44.000 5.48 0.00 40.61 3.59
983 1002 0.174162 CATGGCTGTTAGGGCTTTGC 59.826 55.000 0.00 0.00 0.00 3.68
1272 1291 3.390135 TGCTACTGTTACACTGTCTTGC 58.610 45.455 0.00 0.00 32.45 4.01
1355 1376 6.562608 ACCCAAGCAATTATTATAGAGGGAGA 59.437 38.462 0.00 0.00 36.44 3.71
1491 1516 6.543430 TCCATTTTGTTGAGAATAATGGGG 57.457 37.500 11.10 0.00 0.00 4.96
1784 1811 0.392863 ACAATACTGGATGCAGCGCA 60.393 50.000 14.95 5.73 44.86 6.09
1808 1835 9.530129 GACAGATTATTGTTTGAGTTAAGTTCG 57.470 33.333 0.00 0.00 0.00 3.95
1890 1923 8.357290 TGCTTATGTTGGAGTTACTAAGTCTA 57.643 34.615 4.05 0.00 0.00 2.59
1970 2003 1.203087 TCTTGTCACGGACCCCTCTTA 60.203 52.381 2.23 0.00 0.00 2.10
1987 2020 0.682855 CTGTCGGGAGAGGAGCTCTT 60.683 60.000 14.64 5.66 41.35 2.85
2118 2151 3.168528 AACTCCACGTGCAGGGGT 61.169 61.111 11.96 0.00 46.04 4.95
2193 2226 1.436600 CACATGACAGCACTGGACTC 58.563 55.000 0.00 0.00 34.19 3.36
2218 2251 7.147846 CCATTTGGCCTAATGTAGTTTTCTCAT 60.148 37.037 29.89 0.00 34.42 2.90


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

AutoCloner maintained by Alex Coulton.