Multiple sequence alignment - TraesCS4B01G172300

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 TraesCS4B01G172300 chr4B 100.000 2237 0 0 1 2237 376426935 376424699 0.000000e+00 4132
1 TraesCS4B01G172300 chr4B 87.204 211 11 2 67 277 369782515 369782321 2.240000e-55 226
2 TraesCS4B01G172300 chr4D 93.487 1305 48 7 514 1787 301954829 301953531 0.000000e+00 1905
3 TraesCS4B01G172300 chr4D 93.992 516 17 4 1 515 301955460 301954958 0.000000e+00 769
4 TraesCS4B01G172300 chr4D 96.266 241 8 1 1997 2237 301953099 301952860 5.790000e-106 394
5 TraesCS4B01G172300 chr4D 89.773 176 8 2 1826 2001 301953318 301953153 1.350000e-52 217
6 TraesCS4B01G172300 chr4A 91.975 1109 58 11 514 1608 178372657 178373748 0.000000e+00 1526
7 TraesCS4B01G172300 chr4A 88.760 516 30 9 1 515 178372041 178372529 6.830000e-170 606
8 TraesCS4B01G172300 chr4A 95.851 241 9 1 1997 2237 178374413 178374652 2.690000e-104 388
9 TraesCS4B01G172300 chr4A 86.301 219 14 5 59 277 527578572 527578370 8.040000e-55 224
10 TraesCS4B01G172300 chr4A 89.385 179 8 3 1826 2004 178374194 178374361 4.840000e-52 215
11 TraesCS4B01G172300 chr6A 82.629 426 51 16 961 1375 67646529 67646942 2.730000e-94 355
12 TraesCS4B01G172300 chr6B 89.100 211 7 2 67 277 578014838 578015032 4.770000e-62 248
13 TraesCS4B01G172300 chr6B 88.626 211 8 5 67 277 101245376 101245182 2.220000e-60 243
14 TraesCS4B01G172300 chr3B 88.152 211 9 2 67 277 52857635 52857441 1.030000e-58 237
15 TraesCS4B01G172300 chr1B 87.215 219 12 2 59 277 188443722 188443924 3.710000e-58 235
16 TraesCS4B01G172300 chr1B 86.893 206 11 11 71 276 83210759 83210570 1.350000e-52 217
17 TraesCS4B01G172300 chr2B 87.678 211 10 2 67 277 198532241 198532047 4.800000e-57 231
18 TraesCS4B01G172300 chr3D 87.037 216 11 3 57 272 75769133 75768935 6.210000e-56 228
19 TraesCS4B01G172300 chr1A 87.264 212 11 8 66 277 330764288 330764093 6.210000e-56 228
20 TraesCS4B01G172300 chr2D 85.520 221 15 5 57 277 348078309 348078106 4.840000e-52 215
21 TraesCS4B01G172300 chr7A 86.058 208 9 7 70 277 219382255 219382068 2.910000e-49 206
22 TraesCS4B01G172300 chr3A 84.475 219 15 7 59 277 323383775 323383974 4.870000e-47 198


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 TraesCS4B01G172300 chr4B 376424699 376426935 2236 True 4132.00 4132 100.00000 1 2237 1 chr4B.!!$R2 2236
1 TraesCS4B01G172300 chr4D 301952860 301955460 2600 True 821.25 1905 93.37950 1 2237 4 chr4D.!!$R1 2236
2 TraesCS4B01G172300 chr4A 178372041 178374652 2611 False 683.75 1526 91.49275 1 2237 4 chr4A.!!$F1 2236

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
740 873 0.976073 TTCCTGTGACGGAGGGATCC 60.976 60.0 1.92 1.92 33.89 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2247 0.038526 AGTGAATGCAGCTTGCTTGC 60.039 50.0 9.12 9.09 45.31 4.01 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
204 206 1.547675 GGATGACAAAGGCAAGACCCA 60.548 52.381 0.00 0.00 40.58 4.51
210 212 3.421844 ACAAAGGCAAGACCCAAGATAC 58.578 45.455 0.00 0.00 40.58 2.24
211 213 3.074538 ACAAAGGCAAGACCCAAGATACT 59.925 43.478 0.00 0.00 40.58 2.12
218 220 5.012561 GGCAAGACCCAAGATACTGAGATAT 59.987 44.000 0.00 0.00 0.00 1.63
377 380 7.145323 TCCATAAGCCGAAAAGAAAAGAAAAG 58.855 34.615 0.00 0.00 0.00 2.27
385 388 8.012809 GCCGAAAAGAAAAGAAAAGAAAAACAA 58.987 29.630 0.00 0.00 0.00 2.83
508 511 6.179756 TCCATCTGATTTCGATTCCTTTTGA 58.820 36.000 0.00 0.00 0.00 2.69
604 737 3.420893 CTGGTTTGCAGTCCTTGGATTA 58.579 45.455 9.94 0.00 0.00 1.75
647 780 8.023706 GTGATTTTCAGAAATTCCCTAGTTGTC 58.976 37.037 13.02 0.00 35.65 3.18
740 873 0.976073 TTCCTGTGACGGAGGGATCC 60.976 60.000 1.92 1.92 33.89 3.36
840 973 5.410439 GGTGGAAGTCATAACGTATGTGTTT 59.590 40.000 0.00 0.00 37.45 2.83
959 1103 2.102070 TTGGTGGCACATAAGTACCG 57.898 50.000 20.82 0.00 44.52 4.02
1080 1224 1.168714 ATGAAGACCGCTTTCTTGGC 58.831 50.000 1.65 0.00 35.90 4.52
1146 1290 0.693049 AGTCGTTGAAGGGGCAGATT 59.307 50.000 0.00 0.00 0.00 2.40
1249 1393 2.394563 GGCTGAGGCTCTTTGTCGC 61.395 63.158 16.72 8.23 38.73 5.19
1255 1399 1.372997 GGCTCTTTGTCGCGTCTCA 60.373 57.895 5.77 1.28 0.00 3.27
1346 1490 2.744202 GGATGTTCACGCTGACTTGAAT 59.256 45.455 0.00 0.00 36.56 2.57
1347 1491 3.425359 GGATGTTCACGCTGACTTGAATG 60.425 47.826 0.00 0.00 36.56 2.67
1348 1492 2.560504 TGTTCACGCTGACTTGAATGT 58.439 42.857 0.00 0.00 36.56 2.71
1380 1527 3.507622 GCTTTGTTGCTGTAAATCCCTCT 59.492 43.478 0.00 0.00 0.00 3.69
1423 1570 4.339530 TCCTCCTGTATGACTTCTGAATCG 59.660 45.833 0.00 0.00 0.00 3.34
1470 1617 0.742990 GGGTATGCACTTGCGCTACA 60.743 55.000 9.73 0.00 45.83 2.74
1473 1620 2.869801 GGTATGCACTTGCGCTACATTA 59.130 45.455 9.73 0.00 45.83 1.90
1520 1667 8.554011 TCTAATTTAAACCTGGGTACTGCTTAT 58.446 33.333 0.00 0.00 0.00 1.73
1561 1708 0.920664 GCAGAACCAACGTTTTGTGC 59.079 50.000 16.12 16.12 36.65 4.57
1636 1813 1.923864 CGGTTGTTTTTGTGAAGGTGC 59.076 47.619 0.00 0.00 0.00 5.01
1640 1817 4.092821 GGTTGTTTTTGTGAAGGTGCTTTC 59.907 41.667 0.00 0.00 0.00 2.62
1651 1835 5.701290 GTGAAGGTGCTTTCTGTTGTAGTAT 59.299 40.000 0.00 0.00 0.00 2.12
1653 1837 6.770785 TGAAGGTGCTTTCTGTTGTAGTATTT 59.229 34.615 0.00 0.00 0.00 1.40
1658 1846 8.726988 GGTGCTTTCTGTTGTAGTATTTCATTA 58.273 33.333 0.00 0.00 0.00 1.90
1662 1850 9.722056 CTTTCTGTTGTAGTATTTCATTATGCC 57.278 33.333 0.00 0.00 0.00 4.40
1673 1861 0.457035 CATTATGCCGGCACTGCTTT 59.543 50.000 35.50 18.23 39.97 3.51
1674 1862 1.135024 CATTATGCCGGCACTGCTTTT 60.135 47.619 35.50 17.37 39.97 2.27
1675 1863 1.827681 TTATGCCGGCACTGCTTTTA 58.172 45.000 35.50 16.13 39.97 1.52
1709 1897 2.026822 TCATCCTGGGCTTCTCAACTTC 60.027 50.000 0.00 0.00 0.00 3.01
1727 1915 6.760298 TCAACTTCAGATGATGATCAAGCTAC 59.240 38.462 0.00 0.00 37.89 3.58
1746 1934 2.472029 ACGGGAGAAGGATGATTGACT 58.528 47.619 0.00 0.00 0.00 3.41
1752 1940 4.749099 GGAGAAGGATGATTGACTCATTCG 59.251 45.833 0.00 0.00 44.83 3.34
1753 1941 5.350504 AGAAGGATGATTGACTCATTCGT 57.649 39.130 0.00 0.00 44.83 3.85
1754 1942 5.114780 AGAAGGATGATTGACTCATTCGTG 58.885 41.667 1.20 0.00 44.83 4.35
1755 1943 4.478206 AGGATGATTGACTCATTCGTGT 57.522 40.909 1.20 0.00 44.83 4.49
1819 2172 7.202016 TGTCAGACAAAAGTATTTAAGCTGG 57.798 36.000 0.00 0.00 37.28 4.85
1860 2246 5.968261 CGTGTGTATCTGTACATTCTCTCAG 59.032 44.000 0.00 0.00 42.43 3.35
1861 2247 6.269315 GTGTGTATCTGTACATTCTCTCAGG 58.731 44.000 0.00 0.00 42.43 3.86
1862 2248 5.163509 TGTGTATCTGTACATTCTCTCAGGC 60.164 44.000 0.00 0.00 42.43 4.85
1863 2249 4.956075 TGTATCTGTACATTCTCTCAGGCA 59.044 41.667 0.00 0.00 35.94 4.75
1891 2277 6.674694 AGCTGCATTCACTGATTAAACTAG 57.325 37.500 1.02 0.00 0.00 2.57
1899 2285 9.234384 CATTCACTGATTAAACTAGGTACGTAG 57.766 37.037 18.68 18.68 0.00 3.51
1903 2289 8.341173 CACTGATTAAACTAGGTACGTAGGTAG 58.659 40.741 22.83 14.22 0.00 3.18
1910 2296 8.992835 AAACTAGGTACGTAGGTAGAAATTTG 57.007 34.615 22.83 0.00 0.00 2.32
1944 2330 5.547465 CCAGGACGGATGCTAACATTATTA 58.453 41.667 0.00 0.00 36.35 0.98
1945 2331 6.173339 CCAGGACGGATGCTAACATTATTAT 58.827 40.000 0.00 0.00 36.35 1.28
1946 2332 6.655003 CCAGGACGGATGCTAACATTATTATT 59.345 38.462 0.00 0.00 36.35 1.40
1947 2333 7.822334 CCAGGACGGATGCTAACATTATTATTA 59.178 37.037 0.00 0.00 36.35 0.98
1948 2334 9.383519 CAGGACGGATGCTAACATTATTATTAT 57.616 33.333 0.00 0.00 36.35 1.28
1949 2335 9.959721 AGGACGGATGCTAACATTATTATTATT 57.040 29.630 0.00 0.00 36.35 1.40
1990 2376 8.260099 TGCCTCTCTTAGTATGTAGTAGTAGA 57.740 38.462 0.00 0.00 0.00 2.59
2029 2473 1.284408 GTGATAGAGCGGCGAGAGG 59.716 63.158 12.98 0.00 0.00 3.69
2141 2585 2.162681 CCAAAGGGCAAGTAAGAGTGG 58.837 52.381 0.00 0.00 0.00 4.00
2158 2602 4.803426 GAGCTGGGGTCGAGCGTG 62.803 72.222 8.77 2.29 41.61 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 173 9.812347 TGCCTTTGTCATCCATCTATATAAAAT 57.188 29.630 0.00 0.00 0.00 1.82
172 174 9.639563 TTGCCTTTGTCATCCATCTATATAAAA 57.360 29.630 0.00 0.00 0.00 1.52
193 195 2.503356 CTCAGTATCTTGGGTCTTGCCT 59.497 50.000 0.00 0.00 37.43 4.75
204 206 7.178097 TGCACTATCAGCATATCTCAGTATCTT 59.822 37.037 0.00 0.00 37.02 2.40
210 212 4.389382 GCTTGCACTATCAGCATATCTCAG 59.611 45.833 2.44 0.00 42.33 3.35
211 213 4.040095 AGCTTGCACTATCAGCATATCTCA 59.960 41.667 9.84 0.00 42.33 3.27
218 220 2.474561 GCAGCTTGCACTATCAGCA 58.525 52.632 9.84 0.00 44.26 4.41
377 380 2.139917 GCCCCCGACAAATTGTTTTTC 58.860 47.619 0.00 0.00 0.00 2.29
385 388 2.677228 CCTGAGCCCCCGACAAAT 59.323 61.111 0.00 0.00 0.00 2.32
392 395 3.803162 GAGAAGCCCTGAGCCCCC 61.803 72.222 0.00 0.00 45.47 5.40
508 511 9.968870 TTTTCAAAAATAAACTGCTATTACCGT 57.031 25.926 0.00 0.00 0.00 4.83
536 669 2.589540 CGAAGCACAGGGCCCATA 59.410 61.111 27.56 0.00 46.50 2.74
620 753 7.505585 ACAACTAGGGAATTTCTGAAAATCACA 59.494 33.333 19.50 7.50 33.93 3.58
647 780 7.967908 AGAAATTCACACTAGGGAGTATATGG 58.032 38.462 0.00 0.00 33.32 2.74
695 828 3.949754 CCATGTGAGCAAACCATCACTAT 59.050 43.478 6.85 0.00 44.90 2.12
740 873 5.535753 AAATTTCAAGGTTCACTGGGAAG 57.464 39.130 0.00 0.00 35.82 3.46
840 973 6.061441 ACATGACTGGACAAGAAAATACACA 58.939 36.000 0.00 0.00 0.00 3.72
986 1130 5.468072 CACAAGCCCATCTCTGTATATGAAC 59.532 44.000 0.00 0.00 0.00 3.18
1116 1260 0.378962 TCAACGACTTTGTTTGCCCG 59.621 50.000 0.00 0.00 36.49 6.13
1146 1290 2.900273 GCGTAGATGAGCCCCACA 59.100 61.111 0.00 0.00 0.00 4.17
1249 1393 0.249868 TCAACCCAACAGCTGAGACG 60.250 55.000 23.35 7.39 0.00 4.18
1255 1399 2.664402 ATCAGTTCAACCCAACAGCT 57.336 45.000 0.00 0.00 0.00 4.24
1380 1527 4.289672 AGGAAAGATTACCCTCAGAGCAAA 59.710 41.667 0.00 0.00 0.00 3.68
1470 1617 9.466497 AGAGTGAACATTTACATGGTGATTAAT 57.534 29.630 0.00 0.00 34.27 1.40
1473 1620 8.862325 TTAGAGTGAACATTTACATGGTGATT 57.138 30.769 0.00 0.00 34.27 2.57
1493 1640 6.415573 AGCAGTACCCAGGTTTAAATTAGAG 58.584 40.000 0.00 0.00 0.00 2.43
1506 1653 5.527582 GTCATTAACCATAAGCAGTACCCAG 59.472 44.000 0.00 0.00 0.00 4.45
1508 1655 5.433526 TGTCATTAACCATAAGCAGTACCC 58.566 41.667 0.00 0.00 0.00 3.69
1520 1667 4.887071 GCCACCAGATAATGTCATTAACCA 59.113 41.667 9.31 0.00 0.00 3.67
1558 1705 2.480037 GGCAAATAAGGCAAAACTGCAC 59.520 45.455 0.00 0.00 36.33 4.57
1561 1708 2.986479 GACGGCAAATAAGGCAAAACTG 59.014 45.455 0.00 0.00 0.00 3.16
1608 1758 5.122512 TCACAAAAACAACCGAAAACAGA 57.877 34.783 0.00 0.00 0.00 3.41
1636 1813 9.722056 GGCATAATGAAATACTACAACAGAAAG 57.278 33.333 0.00 0.00 0.00 2.62
1640 1817 6.658831 CCGGCATAATGAAATACTACAACAG 58.341 40.000 0.00 0.00 0.00 3.16
1651 1835 0.455410 GCAGTGCCGGCATAATGAAA 59.545 50.000 35.23 2.76 0.00 2.69
1653 1837 0.394216 AAGCAGTGCCGGCATAATGA 60.394 50.000 35.23 4.69 0.00 2.57
1658 1846 1.185315 AATAAAAGCAGTGCCGGCAT 58.815 45.000 35.23 17.70 0.00 4.40
1662 1850 9.730420 AGTTTAAATATAATAAAAGCAGTGCCG 57.270 29.630 12.58 0.00 0.00 5.69
1675 1863 9.301897 GAAGCCCAGGATGAGTTTAAATATAAT 57.698 33.333 0.00 0.00 39.69 1.28
1690 1878 1.988107 TGAAGTTGAGAAGCCCAGGAT 59.012 47.619 0.00 0.00 0.00 3.24
1696 1884 4.511527 TCATCATCTGAAGTTGAGAAGCC 58.488 43.478 0.00 0.00 0.00 4.35
1709 1897 3.006217 TCCCGTAGCTTGATCATCATCTG 59.994 47.826 0.00 0.00 0.00 2.90
1727 1915 2.432146 TGAGTCAATCATCCTTCTCCCG 59.568 50.000 0.00 0.00 31.12 5.14
1746 1934 5.175090 TGCAACACAAAATACACGAATGA 57.825 34.783 0.00 0.00 0.00 2.57
1752 1940 5.005299 GTCCAACTTGCAACACAAAATACAC 59.995 40.000 0.00 0.00 37.96 2.90
1753 1941 5.105752 GTCCAACTTGCAACACAAAATACA 58.894 37.500 0.00 0.00 37.96 2.29
1754 1942 5.105752 TGTCCAACTTGCAACACAAAATAC 58.894 37.500 0.00 0.00 37.96 1.89
1755 1943 5.126222 TCTGTCCAACTTGCAACACAAAATA 59.874 36.000 0.00 0.00 37.96 1.40
1819 2172 4.025480 ACACACGTTCGAATTTGTAAGGTC 60.025 41.667 12.67 0.00 0.00 3.85
1860 2246 1.012486 GTGAATGCAGCTTGCTTGCC 61.012 55.000 9.12 1.74 45.31 4.52
1861 2247 0.038526 AGTGAATGCAGCTTGCTTGC 60.039 50.000 9.12 9.09 45.31 4.01
1862 2248 1.268625 TCAGTGAATGCAGCTTGCTTG 59.731 47.619 9.12 0.00 45.31 4.01
1863 2249 1.612676 TCAGTGAATGCAGCTTGCTT 58.387 45.000 9.12 1.25 45.31 3.91
1879 2265 8.668510 TCTACCTACGTACCTAGTTTAATCAG 57.331 38.462 0.00 0.00 0.00 2.90
1891 2277 6.073112 TGCAAACAAATTTCTACCTACGTACC 60.073 38.462 0.00 0.00 0.00 3.34
1899 2285 4.627035 GGCTCATGCAAACAAATTTCTACC 59.373 41.667 0.00 0.00 41.91 3.18
1903 2289 3.434299 CCTGGCTCATGCAAACAAATTTC 59.566 43.478 0.00 0.00 41.91 2.17
1910 2296 1.503542 CGTCCTGGCTCATGCAAAC 59.496 57.895 0.00 0.00 41.91 2.93
1944 2330 6.780457 GCAATGTGGCCTGGATATAATAAT 57.220 37.500 3.32 0.00 0.00 1.28
1990 2376 0.407139 ATTCCCCAGCACTGCTTCTT 59.593 50.000 0.00 0.00 36.40 2.52
2029 2473 1.333619 TCTCCAAAGTTTGCGCTCAAC 59.666 47.619 9.73 11.98 30.75 3.18
2042 2486 7.852550 ACTCATATCTCTCATCATCTCCAAA 57.147 36.000 0.00 0.00 0.00 3.28
2126 2570 0.615850 AGCTCCACTCTTACTTGCCC 59.384 55.000 0.00 0.00 0.00 5.36
2141 2585 4.803426 CACGCTCGACCCCAGCTC 62.803 72.222 0.00 0.00 34.45 4.09
2213 2657 1.446907 CTGTCTCCACAATGCACCTC 58.553 55.000 0.00 0.00 29.82 3.85


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

AutoCloner maintained by Alex Coulton.