Multiple sequence alignment - TraesCS3B01G369500

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 TraesCS3B01G369500 chr3B 100.000 2318 0 0 1 2318 581640947 581638630 0.000000e+00 4281.0
1 TraesCS3B01G369500 chr3B 97.297 37 1 0 1668 1704 581639242 581639206 1.920000e-06 63.9
2 TraesCS3B01G369500 chr3B 97.297 37 1 0 1706 1742 581639280 581639244 1.920000e-06 63.9
3 TraesCS3B01G369500 chr3B 100.000 30 0 0 2266 2295 505993096 505993067 3.220000e-04 56.5
4 TraesCS3B01G369500 chr2A 97.844 1345 29 0 1 1345 770135505 770136849 0.000000e+00 2324.0
5 TraesCS3B01G369500 chr2B 97.976 1235 23 1 1 1233 22558252 22557018 0.000000e+00 2141.0
6 TraesCS3B01G369500 chr3A 94.862 1343 69 0 1 1343 703710700 703709358 0.000000e+00 2098.0
7 TraesCS3B01G369500 chr3A 91.667 240 17 3 1348 1586 584749079 584748842 1.720000e-86 329.0
8 TraesCS3B01G369500 chr3A 96.104 154 5 1 1788 1941 584748511 584748359 1.380000e-62 250.0
9 TraesCS3B01G369500 chr7A 93.299 1343 89 1 1 1343 110824165 110822824 0.000000e+00 1980.0
10 TraesCS3B01G369500 chr5B 90.089 1352 132 2 1 1350 543291291 543292642 0.000000e+00 1753.0
11 TraesCS3B01G369500 chr7B 89.673 1346 133 2 1 1346 504462858 504461519 0.000000e+00 1711.0
12 TraesCS3B01G369500 chr7B 97.143 35 1 0 2269 2303 373066104 373066138 2.490000e-05 60.2
13 TraesCS3B01G369500 chr7D 88.914 1344 148 1 2 1345 22720731 22719389 0.000000e+00 1655.0
14 TraesCS3B01G369500 chr7D 89.191 1286 138 1 59 1344 423401199 423399915 0.000000e+00 1604.0
15 TraesCS3B01G369500 chr7D 87.658 1345 165 1 2 1346 561612815 561611472 0.000000e+00 1563.0
16 TraesCS3B01G369500 chr7D 97.143 35 1 0 2262 2296 510874219 510874253 2.490000e-05 60.2
17 TraesCS3B01G369500 chr7D 96.875 32 0 1 2265 2296 517572217 517572247 4.000000e-03 52.8
18 TraesCS3B01G369500 chr3D 95.147 989 29 7 1348 2318 443590768 443589781 0.000000e+00 1543.0
19 TraesCS3B01G369500 chr3D 97.297 37 1 0 1706 1742 443590446 443590410 1.920000e-06 63.9
20 TraesCS3B01G369500 chr3D 97.222 36 1 0 1669 1704 443590407 443590372 6.920000e-06 62.1
21 TraesCS3B01G369500 chr6B 100.000 30 0 0 2266 2295 713473814 713473785 3.220000e-04 56.5
22 TraesCS3B01G369500 chr1A 100.000 30 0 0 2267 2296 178340297 178340268 3.220000e-04 56.5
23 TraesCS3B01G369500 chr1B 94.286 35 0 2 2262 2296 556267141 556267173 4.000000e-03 52.8
24 TraesCS3B01G369500 chr1B 94.286 35 0 2 2262 2296 556306688 556306720 4.000000e-03 52.8


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 TraesCS3B01G369500 chr3B 581638630 581640947 2317 True 1469.600000 4281 98.198000 1 2318 3 chr3B.!!$R2 2317
1 TraesCS3B01G369500 chr2A 770135505 770136849 1344 False 2324.000000 2324 97.844000 1 1345 1 chr2A.!!$F1 1344
2 TraesCS3B01G369500 chr2B 22557018 22558252 1234 True 2141.000000 2141 97.976000 1 1233 1 chr2B.!!$R1 1232
3 TraesCS3B01G369500 chr3A 703709358 703710700 1342 True 2098.000000 2098 94.862000 1 1343 1 chr3A.!!$R1 1342
4 TraesCS3B01G369500 chr3A 584748359 584749079 720 True 289.500000 329 93.885500 1348 1941 2 chr3A.!!$R2 593
5 TraesCS3B01G369500 chr7A 110822824 110824165 1341 True 1980.000000 1980 93.299000 1 1343 1 chr7A.!!$R1 1342
6 TraesCS3B01G369500 chr5B 543291291 543292642 1351 False 1753.000000 1753 90.089000 1 1350 1 chr5B.!!$F1 1349
7 TraesCS3B01G369500 chr7B 504461519 504462858 1339 True 1711.000000 1711 89.673000 1 1346 1 chr7B.!!$R1 1345
8 TraesCS3B01G369500 chr7D 22719389 22720731 1342 True 1655.000000 1655 88.914000 2 1345 1 chr7D.!!$R1 1343
9 TraesCS3B01G369500 chr7D 423399915 423401199 1284 True 1604.000000 1604 89.191000 59 1344 1 chr7D.!!$R2 1285
10 TraesCS3B01G369500 chr7D 561611472 561612815 1343 True 1563.000000 1563 87.658000 2 1346 1 chr7D.!!$R3 1344
11 TraesCS3B01G369500 chr3D 443589781 443590768 987 True 556.333333 1543 96.555333 1348 2318 3 chr3D.!!$R1 970

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
355 358 2.936202 TGAGAATTATGGCCTGGAAGC 58.064 47.619 3.32 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1494 0.179 ATCCTCATGTTCCCGCAGAC 59.821 55.0 0.0 0.0 0.0 3.51 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
355 358 2.936202 TGAGAATTATGGCCTGGAAGC 58.064 47.619 3.32 0.00 0.00 3.86
770 773 7.015001 GGATGATATTCTCAAAGGGAAAATGCT 59.985 37.037 0.00 0.00 37.44 3.79
831 834 4.069232 CCTCTTCACTGGCCGCGA 62.069 66.667 8.23 0.00 0.00 5.87
1128 1131 5.185056 GTCTGTTTATGGGCATTTGGTACTT 59.815 40.000 0.00 0.00 0.00 2.24
1154 1157 2.497273 TCAAGCGTCATCTTCAGGATCA 59.503 45.455 0.00 0.00 31.27 2.92
1181 1184 8.203485 AGAGTTTGTTCCATCAAAAATAAAGCA 58.797 29.630 0.00 0.00 38.71 3.91
1388 1391 5.289595 TGTACTTGTGTACTTCTGCTTGAG 58.710 41.667 7.67 0.00 46.70 3.02
1446 1449 3.754965 TGCAGAAGGAATATATGGCACC 58.245 45.455 0.00 0.00 0.00 5.01
1450 1453 5.547465 CAGAAGGAATATATGGCACCGTAA 58.453 41.667 0.00 0.00 0.00 3.18
1460 1463 2.432444 TGGCACCGTAAAATTCTGAGG 58.568 47.619 0.00 0.00 0.00 3.86
1491 1494 1.636988 CGGTTAAGTTGCCGGAGTAG 58.363 55.000 5.05 0.00 43.85 2.57
1606 1628 1.202348 GTATGACAGGGTTTTGGCAGC 59.798 52.381 0.00 0.00 39.98 5.25
1610 1632 2.192861 CAGGGTTTTGGCAGCACGA 61.193 57.895 0.00 0.00 0.00 4.35
1633 1655 5.557891 AAACAACTGCATTCTGAGATAGC 57.442 39.130 0.00 0.36 0.00 2.97
1659 1809 7.222611 CGGCCATTAAAAGAATGTAAAAGGATG 59.777 37.037 2.24 0.00 0.00 3.51
1749 1899 7.861630 TCTAAAGCACATCTTACAGTTTGTTC 58.138 34.615 0.00 0.00 33.88 3.18
1905 2080 0.837691 TCCAGCCTGAGACACCATGT 60.838 55.000 0.00 0.00 0.00 3.21
2035 2210 2.486918 CCTGGCAGGCAAAAAGAAAAG 58.513 47.619 22.68 0.00 0.00 2.27
2056 2234 5.419239 AGAAGAGAGAAGCAAATACAGCT 57.581 39.130 0.00 0.00 45.97 4.24
2068 2246 7.277174 AGCAAATACAGCTTTACAAGTCTTT 57.723 32.000 0.00 0.00 39.87 2.52
2274 2464 8.894731 CACGTATATATCCATGTAAGCTACTCT 58.105 37.037 0.00 0.00 0.00 3.24
2306 2496 7.620094 TCCCATAATATAAGAGGGAGTAGCTTC 59.380 40.741 0.00 0.00 43.39 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
355 358 1.079503 GCTAAAGCACCGGAGACAAG 58.920 55.000 9.46 0.00 41.59 3.16
1128 1131 3.429960 CCTGAAGATGACGCTTGATCTCA 60.430 47.826 0.00 0.00 0.00 3.27
1181 1184 4.235079 TGTGCTACCCTATTTTGCTCAT 57.765 40.909 0.00 0.00 0.00 2.90
1388 1391 2.098117 CCTCTTCACGCCAAATTGATCC 59.902 50.000 0.00 0.00 0.00 3.36
1446 1449 4.261322 CCATGGATGCCTCAGAATTTTACG 60.261 45.833 5.56 0.00 0.00 3.18
1450 1453 2.037144 GCCATGGATGCCTCAGAATTT 58.963 47.619 18.40 0.00 0.00 1.82
1460 1463 0.947244 CTTAACCGAGCCATGGATGC 59.053 55.000 18.40 0.00 0.00 3.91
1473 1476 2.233186 AGACTACTCCGGCAACTTAACC 59.767 50.000 0.00 0.00 0.00 2.85
1475 1478 2.353406 GCAGACTACTCCGGCAACTTAA 60.353 50.000 0.00 0.00 0.00 1.85
1491 1494 0.179000 ATCCTCATGTTCCCGCAGAC 59.821 55.000 0.00 0.00 0.00 3.51
1502 1505 1.335810 CAACATTGCCGGATCCTCATG 59.664 52.381 5.05 8.71 0.00 3.07
1606 1628 3.951306 TCAGAATGCAGTTGTTTTCGTG 58.049 40.909 0.00 0.00 34.76 4.35
1610 1632 5.391310 CGCTATCTCAGAATGCAGTTGTTTT 60.391 40.000 0.00 0.00 34.76 2.43
1633 1655 6.626302 TCCTTTTACATTCTTTTAATGGCCG 58.374 36.000 0.00 0.00 32.14 6.13
1659 1809 1.137513 GTTGCTACCTCACACACGAC 58.862 55.000 0.00 0.00 0.00 4.34
1749 1899 9.233232 GACTACTAATTGTTCCTTTTGTTTGTG 57.767 33.333 0.00 0.00 0.00 3.33
1905 2080 6.306199 TGATCTTTTGAATCTGGTTTCAGGA 58.694 36.000 0.00 0.00 41.23 3.86
1952 2127 6.608002 CCCAGTAGTCTCTTAAGTACTCCATT 59.392 42.308 13.97 0.00 33.97 3.16
2028 2203 8.682936 TGTATTTGCTTCTCTCTTCTTTTCTT 57.317 30.769 0.00 0.00 0.00 2.52
2030 2205 7.020602 GCTGTATTTGCTTCTCTCTTCTTTTC 58.979 38.462 0.00 0.00 0.00 2.29
2033 2208 5.803552 AGCTGTATTTGCTTCTCTCTTCTT 58.196 37.500 0.00 0.00 37.52 2.52
2056 2234 5.061179 GCTGGTGTAGGAAAGACTTGTAAA 58.939 41.667 0.00 0.00 0.00 2.01
2068 2246 6.780522 TCTGTATACATATTGCTGGTGTAGGA 59.219 38.462 5.91 0.00 32.45 2.94
2140 2328 2.929531 AGCTCTGACTGTGTGTATCG 57.070 50.000 0.00 0.00 0.00 2.92
2274 2464 5.015924 TCCCTCTTATATTATGGGACGGAGA 59.984 44.000 0.00 0.00 41.57 3.71


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

AutoCloner maintained by Alex Coulton.