Multiple sequence alignment - TraesCS4B01G147200

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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 TraesCS4B01G147200 chr4B 100.000 2439 0 0 1 2439 209301266 209298828 0.000000e+00 4505.0
1 TraesCS4B01G147200 chr4B 88.340 506 37 9 965 1468 334716543 334716058 2.700000e-164 588.0
2 TraesCS4B01G147200 chr4B 98.947 95 1 0 2084 2178 70584323 70584417 1.160000e-38 171.0
3 TraesCS4B01G147200 chr4B 94.898 98 5 0 220 317 585650247 585650150 1.170000e-33 154.0
4 TraesCS4B01G147200 chr4B 89.623 106 9 2 1887 1992 546077720 546077617 1.520000e-27 134.0
5 TraesCS4B01G147200 chr5A 98.119 2446 39 4 1 2439 19247241 19249686 0.000000e+00 4255.0
6 TraesCS4B01G147200 chr7D 97.953 2443 43 6 1 2439 203501601 203499162 0.000000e+00 4228.0
7 TraesCS4B01G147200 chr7D 97.912 2443 45 4 1 2439 381925603 381923163 0.000000e+00 4224.0
8 TraesCS4B01G147200 chr1A 97.871 2442 45 6 1 2439 498689625 498692062 0.000000e+00 4215.0
9 TraesCS4B01G147200 chr7B 97.831 2443 46 5 1 2439 716877179 716879618 0.000000e+00 4211.0
10 TraesCS4B01G147200 chr7B 97.709 2444 50 5 1 2439 742991047 742988605 0.000000e+00 4198.0
11 TraesCS4B01G147200 chr6B 96.643 2443 75 5 1 2439 297474673 297472234 0.000000e+00 4050.0
12 TraesCS4B01G147200 chr6B 97.207 179 5 0 694 872 507458934 507458756 1.100000e-78 303.0
13 TraesCS4B01G147200 chr6B 97.030 101 3 0 862 962 200292495 200292395 1.160000e-38 171.0
14 TraesCS4B01G147200 chr6B 100.000 35 0 0 312 346 439856696 439856662 5.630000e-07 65.8
15 TraesCS4B01G147200 chr2A 96.425 2322 75 6 1 2321 444323448 444325762 0.000000e+00 3821.0
16 TraesCS4B01G147200 chr2A 93.447 412 22 2 1360 1767 673088321 673087911 7.460000e-170 606.0
17 TraesCS4B01G147200 chr2A 96.392 194 7 0 491 684 736548075 736547882 1.090000e-83 320.0
18 TraesCS4B01G147200 chr2A 100.000 64 0 0 98 161 3789386 3789323 4.260000e-23 119.0
19 TraesCS4B01G147200 chr2A 100.000 46 0 0 1819 1864 588462198 588462153 4.320000e-13 86.1
20 TraesCS4B01G147200 chr5B 96.129 155 5 1 2270 2423 316721508 316721354 4.030000e-63 252.0


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 TraesCS4B01G147200 chr4B 209298828 209301266 2438 True 4505 4505 100.000 1 2439 1 chr4B.!!$R1 2438
1 TraesCS4B01G147200 chr5A 19247241 19249686 2445 False 4255 4255 98.119 1 2439 1 chr5A.!!$F1 2438
2 TraesCS4B01G147200 chr7D 203499162 203501601 2439 True 4228 4228 97.953 1 2439 1 chr7D.!!$R1 2438
3 TraesCS4B01G147200 chr7D 381923163 381925603 2440 True 4224 4224 97.912 1 2439 1 chr7D.!!$R2 2438
4 TraesCS4B01G147200 chr1A 498689625 498692062 2437 False 4215 4215 97.871 1 2439 1 chr1A.!!$F1 2438
5 TraesCS4B01G147200 chr7B 716877179 716879618 2439 False 4211 4211 97.831 1 2439 1 chr7B.!!$F1 2438
6 TraesCS4B01G147200 chr7B 742988605 742991047 2442 True 4198 4198 97.709 1 2439 1 chr7B.!!$R1 2438
7 TraesCS4B01G147200 chr6B 297472234 297474673 2439 True 4050 4050 96.643 1 2439 1 chr6B.!!$R2 2438
8 TraesCS4B01G147200 chr2A 444323448 444325762 2314 False 3821 3821 96.425 1 2321 1 chr2A.!!$F1 2320

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
967 968 1.072159 GAACCTGCTGCTCAGTGGT 59.928 57.895 0.0 9.63 41.25 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2239 1.337167 GGCCATTTCGAGCAAGCTTTT 60.337 47.619 0.0 0.0 0.0 2.27 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
203 204 4.574421 TGCGTATGAGAACATTGTAATGGG 59.426 41.667 9.22 0.00 40.70 4.00
206 207 5.997746 CGTATGAGAACATTGTAATGGGGAT 59.002 40.000 9.22 0.00 40.70 3.85
228 229 5.304686 TGGTCATAGCCGAAATAGGATTT 57.695 39.130 0.00 0.00 0.00 2.17
230 231 4.083271 GGTCATAGCCGAAATAGGATTTGC 60.083 45.833 0.00 0.00 30.49 3.68
507 508 5.750067 GCTGCAGAAAAAGAAGATTTGTTGA 59.250 36.000 20.43 0.00 0.00 3.18
509 510 7.042254 GCTGCAGAAAAAGAAGATTTGTTGAAT 60.042 33.333 20.43 0.00 0.00 2.57
641 642 9.849752 ATAGATATCAGGTGCCCACATATATAT 57.150 33.333 5.32 0.00 0.00 0.86
666 667 5.186797 AGTCAAAAGAGAGATTGAGTCCGAT 59.813 40.000 0.00 0.00 34.90 4.18
700 701 1.573108 TCTTGGGGCTCGAGAGATTT 58.427 50.000 18.75 0.00 40.84 2.17
873 874 7.836183 GCTTGGATTATATATCCATTTGGTCCT 59.164 37.037 13.86 0.00 46.51 3.85
967 968 1.072159 GAACCTGCTGCTCAGTGGT 59.928 57.895 0.00 9.63 41.25 4.16
1063 1064 0.036765 TAGAACGTCGGCAGGCAAAT 60.037 50.000 0.00 0.00 0.00 2.32
1065 1066 1.573829 GAACGTCGGCAGGCAAATCA 61.574 55.000 0.00 0.00 0.00 2.57
1354 1359 4.081476 GGAAGCTGCAGGGATTACAAAAAT 60.081 41.667 17.12 0.00 0.00 1.82
1474 1479 2.578021 AGAGGGGAAGATTAGCAAAGCA 59.422 45.455 0.00 0.00 0.00 3.91
1576 1581 0.109132 GCCTTCATTTCGTTGGCAGG 60.109 55.000 0.00 0.00 42.79 4.85
1607 1612 0.334676 TCCAATCCATTCGGGGCTTT 59.665 50.000 0.00 0.00 37.22 3.51
2110 2128 0.538057 TCTGGAGGGCAAGCTGTTTG 60.538 55.000 0.00 0.00 39.88 2.93
2221 2239 0.958822 GAAAGCCGGGAGAAAAAGCA 59.041 50.000 2.18 0.00 0.00 3.91
2295 2313 5.449177 AAAGCGTCACTTTTCTCAAAAGGAG 60.449 40.000 12.24 5.70 46.73 3.69
2376 2395 4.069312 TCATCAAGTGGGTAAGGTAGGA 57.931 45.455 0.00 0.00 0.00 2.94
2431 2450 4.826556 ACAAAGCTAAGAAGTAGGCTGAG 58.173 43.478 0.00 0.00 35.08 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.447443 CAGTGGGAGTAGTGACTAGCA 58.553 52.381 0.00 0.0 35.45 3.49
161 162 0.326808 AGGAATACCCCCGTTAGCCA 60.327 55.000 0.00 0.0 36.73 4.75
203 204 3.260884 TCCTATTTCGGCTATGACCATCC 59.739 47.826 0.00 0.0 0.00 3.51
206 207 4.974645 AATCCTATTTCGGCTATGACCA 57.025 40.909 0.00 0.0 0.00 4.02
507 508 2.856231 TGCTTCCTATGGGGGTACAATT 59.144 45.455 0.00 0.0 35.33 2.32
509 510 1.974028 TGCTTCCTATGGGGGTACAA 58.026 50.000 0.00 0.0 35.33 2.41
641 642 5.710567 TCGGACTCAATCTCTCTTTTGACTA 59.289 40.000 0.00 0.0 0.00 2.59
700 701 3.949430 ACTTGTGGGGCCCTATCTATTA 58.051 45.455 25.93 0.0 0.00 0.98
794 795 4.768130 TGGAAAACAACTTTCACGTTCA 57.232 36.364 0.00 0.0 44.61 3.18
873 874 1.596934 GTGTGGAATGGCCGAGAGA 59.403 57.895 0.00 0.0 40.66 3.10
1063 1064 1.137086 GATAGCAGCCTTCCTTCGTGA 59.863 52.381 0.00 0.0 0.00 4.35
1065 1066 0.466124 GGATAGCAGCCTTCCTTCGT 59.534 55.000 4.28 0.0 0.00 3.85
1175 1177 2.881111 ACCACTAAAGGAAAGGCTCC 57.119 50.000 0.00 0.0 45.81 4.70
1255 1257 2.107378 TGTTTGAGCCTATGTTCACCCA 59.893 45.455 0.00 0.0 30.81 4.51
1328 1333 0.998928 TAATCCCTGCAGCTTCCCAA 59.001 50.000 8.66 0.0 0.00 4.12
1354 1359 1.817740 GCAACACAGGAAAGCACCCTA 60.818 52.381 0.00 0.0 31.64 3.53
1399 1404 4.084276 GGAAGAAAGAAAGTCGAAGAGCAC 60.084 45.833 0.00 0.0 36.95 4.40
1400 1405 4.058817 GGAAGAAAGAAAGTCGAAGAGCA 58.941 43.478 0.00 0.0 36.95 4.26
1474 1479 1.988846 CCCCTCCCTCTGTCTTTTTCT 59.011 52.381 0.00 0.0 0.00 2.52
1576 1581 2.632377 TGGATTGGATCGTTTCTGCTC 58.368 47.619 0.00 0.0 0.00 4.26
2110 2128 7.201929 CCCTACCCTAAGAAAGAAGTCACTATC 60.202 44.444 0.00 0.0 0.00 2.08
2221 2239 1.337167 GGCCATTTCGAGCAAGCTTTT 60.337 47.619 0.00 0.0 0.00 2.27
2237 2255 1.481802 CGAGGGTTAGGGTATAGGCCA 60.482 57.143 5.01 0.0 0.00 5.36
2285 2303 5.009110 GTCAGAAAAACTCCCTCCTTTTGAG 59.991 44.000 0.00 0.0 41.07 3.02
2295 2313 4.398319 TGGATTCAGTCAGAAAAACTCCC 58.602 43.478 0.00 0.0 40.22 4.30
2376 2395 4.753516 AAGGCAAAGCTTAAGTGGTTTT 57.246 36.364 0.00 0.0 35.77 2.43


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

AutoCloner maintained by Alex Coulton.