Multiple sequence alignment - TraesCS4D01G153600

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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 TraesCS4D01G153600 chr4D 100.000 2578 0 0 1 2578 195032608 195030031 0.000000e+00 4761.0
1 TraesCS4D01G153600 chr4D 88.399 1724 172 16 139 1835 52079016 52080738 0.000000e+00 2050.0
2 TraesCS4D01G153600 chr1D 89.542 1989 159 28 1 1955 165150102 165152075 0.000000e+00 2475.0
3 TraesCS4D01G153600 chr1D 87.654 81 6 3 2501 2578 165152059 165152138 9.820000e-15 91.6
4 TraesCS4D01G153600 chr7A 89.397 1858 162 13 1 1835 133735937 133737782 0.000000e+00 2307.0
5 TraesCS4D01G153600 chr7A 96.745 553 16 2 1949 2500 319592009 319591458 0.000000e+00 920.0
6 TraesCS4D01G153600 chr3D 88.811 1859 183 14 1 1835 373976007 373977864 0.000000e+00 2257.0
7 TraesCS4D01G153600 chr3D 87.627 1867 196 21 1 1835 262962002 262960139 0.000000e+00 2135.0
8 TraesCS4D01G153600 chr3D 91.332 946 76 4 1 942 543638873 543637930 0.000000e+00 1288.0
9 TraesCS4D01G153600 chr3D 96.869 543 16 1 1959 2500 365531887 365531345 0.000000e+00 907.0
10 TraesCS4D01G153600 chr2D 87.830 1972 173 31 7 1955 422741514 422739587 0.000000e+00 2250.0
11 TraesCS4D01G153600 chr2D 85.112 1874 233 31 1 1833 6325365 6323497 0.000000e+00 1873.0
12 TraesCS4D01G153600 chr7B 87.924 1946 185 28 2 1909 686793060 686791127 0.000000e+00 2246.0
13 TraesCS4D01G153600 chr7B 88.020 1369 120 24 618 1955 337174734 337176089 0.000000e+00 1580.0
14 TraesCS4D01G153600 chr7B 88.889 81 5 3 2501 2578 337176073 337176152 2.110000e-16 97.1
15 TraesCS4D01G153600 chr5A 88.530 1857 169 26 2 1835 148245147 148243312 0.000000e+00 2209.0
16 TraesCS4D01G153600 chr5A 96.703 546 16 2 1957 2500 47457305 47456760 0.000000e+00 907.0
17 TraesCS4D01G153600 chr5A 95.139 576 24 4 1929 2500 8513450 8512875 0.000000e+00 905.0
18 TraesCS4D01G153600 chr6D 88.049 1866 186 21 2 1835 370681389 370679529 0.000000e+00 2176.0
19 TraesCS4D01G153600 chr2A 87.507 1873 190 23 4 1835 298392990 298391121 0.000000e+00 2122.0
20 TraesCS4D01G153600 chr2A 96.886 546 16 1 1956 2500 90419683 90420228 0.000000e+00 913.0
21 TraesCS4D01G153600 chr2B 86.205 1979 205 32 3 1955 293939400 293941336 0.000000e+00 2080.0
22 TraesCS4D01G153600 chr2B 89.058 1380 128 15 240 1607 350425113 350423745 0.000000e+00 1690.0
23 TraesCS4D01G153600 chr2B 81.543 1387 197 35 458 1817 260986122 260984768 0.000000e+00 1088.0
24 TraesCS4D01G153600 chr3B 96.886 546 16 1 1956 2500 398842376 398842921 0.000000e+00 913.0
25 TraesCS4D01G153600 chr3B 87.928 613 50 9 1233 1835 146636602 146637200 0.000000e+00 701.0
26 TraesCS4D01G153600 chr6A 96.703 546 17 1 1956 2500 410901504 410902049 0.000000e+00 907.0
27 TraesCS4D01G153600 chr4B 96.703 546 17 1 1956 2500 199715570 199715025 0.000000e+00 907.0
28 TraesCS4D01G153600 chr3A 96.703 546 17 1 1956 2500 369399092 369399637 0.000000e+00 907.0
29 TraesCS4D01G153600 chr5B 97.778 45 1 0 2532 2576 457866278 457866234 7.650000e-11 78.7
30 TraesCS4D01G153600 chr5B 97.778 45 1 0 2532 2576 457946611 457946567 7.650000e-11 78.7


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 TraesCS4D01G153600 chr4D 195030031 195032608 2577 True 4761.00 4761 100.0000 1 2578 1 chr4D.!!$R1 2577
1 TraesCS4D01G153600 chr4D 52079016 52080738 1722 False 2050.00 2050 88.3990 139 1835 1 chr4D.!!$F1 1696
2 TraesCS4D01G153600 chr1D 165150102 165152138 2036 False 1283.30 2475 88.5980 1 2578 2 chr1D.!!$F1 2577
3 TraesCS4D01G153600 chr7A 133735937 133737782 1845 False 2307.00 2307 89.3970 1 1835 1 chr7A.!!$F1 1834
4 TraesCS4D01G153600 chr7A 319591458 319592009 551 True 920.00 920 96.7450 1949 2500 1 chr7A.!!$R1 551
5 TraesCS4D01G153600 chr3D 373976007 373977864 1857 False 2257.00 2257 88.8110 1 1835 1 chr3D.!!$F1 1834
6 TraesCS4D01G153600 chr3D 262960139 262962002 1863 True 2135.00 2135 87.6270 1 1835 1 chr3D.!!$R1 1834
7 TraesCS4D01G153600 chr3D 543637930 543638873 943 True 1288.00 1288 91.3320 1 942 1 chr3D.!!$R3 941
8 TraesCS4D01G153600 chr3D 365531345 365531887 542 True 907.00 907 96.8690 1959 2500 1 chr3D.!!$R2 541
9 TraesCS4D01G153600 chr2D 422739587 422741514 1927 True 2250.00 2250 87.8300 7 1955 1 chr2D.!!$R2 1948
10 TraesCS4D01G153600 chr2D 6323497 6325365 1868 True 1873.00 1873 85.1120 1 1833 1 chr2D.!!$R1 1832
11 TraesCS4D01G153600 chr7B 686791127 686793060 1933 True 2246.00 2246 87.9240 2 1909 1 chr7B.!!$R1 1907
12 TraesCS4D01G153600 chr7B 337174734 337176152 1418 False 838.55 1580 88.4545 618 2578 2 chr7B.!!$F1 1960
13 TraesCS4D01G153600 chr5A 148243312 148245147 1835 True 2209.00 2209 88.5300 2 1835 1 chr5A.!!$R3 1833
14 TraesCS4D01G153600 chr5A 47456760 47457305 545 True 907.00 907 96.7030 1957 2500 1 chr5A.!!$R2 543
15 TraesCS4D01G153600 chr5A 8512875 8513450 575 True 905.00 905 95.1390 1929 2500 1 chr5A.!!$R1 571
16 TraesCS4D01G153600 chr6D 370679529 370681389 1860 True 2176.00 2176 88.0490 2 1835 1 chr6D.!!$R1 1833
17 TraesCS4D01G153600 chr2A 298391121 298392990 1869 True 2122.00 2122 87.5070 4 1835 1 chr2A.!!$R1 1831
18 TraesCS4D01G153600 chr2A 90419683 90420228 545 False 913.00 913 96.8860 1956 2500 1 chr2A.!!$F1 544
19 TraesCS4D01G153600 chr2B 293939400 293941336 1936 False 2080.00 2080 86.2050 3 1955 1 chr2B.!!$F1 1952
20 TraesCS4D01G153600 chr2B 350423745 350425113 1368 True 1690.00 1690 89.0580 240 1607 1 chr2B.!!$R2 1367
21 TraesCS4D01G153600 chr2B 260984768 260986122 1354 True 1088.00 1088 81.5430 458 1817 1 chr2B.!!$R1 1359
22 TraesCS4D01G153600 chr3B 398842376 398842921 545 False 913.00 913 96.8860 1956 2500 1 chr3B.!!$F2 544
23 TraesCS4D01G153600 chr3B 146636602 146637200 598 False 701.00 701 87.9280 1233 1835 1 chr3B.!!$F1 602
24 TraesCS4D01G153600 chr6A 410901504 410902049 545 False 907.00 907 96.7030 1956 2500 1 chr6A.!!$F1 544
25 TraesCS4D01G153600 chr4B 199715025 199715570 545 True 907.00 907 96.7030 1956 2500 1 chr4B.!!$R1 544
26 TraesCS4D01G153600 chr3A 369399092 369399637 545 False 907.00 907 96.7030 1956 2500 1 chr3A.!!$F1 544


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
575 599 0.107703 GACTTCCACCATCGCATCCA 60.108 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2467 0.179 GCCACACGAGGAAGGATCAT 59.821 55.0 0.0 0.0 0.0 2.45 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
41 42 3.211865 CGTGCCTACTGAGGTAGTATCA 58.788 50.000 0.00 0.00 45.78 2.15
218 223 3.076621 CAGCAAACACATGAAGGAGCTA 58.923 45.455 0.00 0.00 0.00 3.32
575 599 0.107703 GACTTCCACCATCGCATCCA 60.108 55.000 0.00 0.00 0.00 3.41
585 609 1.667724 CATCGCATCCAGAGGAAACAC 59.332 52.381 0.00 0.00 34.34 3.32
623 649 5.456822 GTGATTTCAAGCTCACACTGAAAAC 59.543 40.000 13.06 11.32 41.13 2.43
751 789 2.660189 GCAACAGCTGCCATGTTAAT 57.340 45.000 15.27 0.00 46.13 1.40
768 807 9.180678 CCATGTTAATGAAGTGTGAACTTTTAC 57.819 33.333 0.00 0.00 35.67 2.01
815 857 8.495148 CACTTAAAATATTGGGCAACTTTGTTC 58.505 33.333 0.00 0.00 0.00 3.18
902 957 3.054878 CCACTTGATGCTTGCTTTTCAC 58.945 45.455 0.00 0.00 0.00 3.18
911 966 5.252969 TGCTTGCTTTTCACATATCCATC 57.747 39.130 0.00 0.00 0.00 3.51
926 981 4.989279 ATCCATCATTGTAACTGGCAAC 57.011 40.909 0.00 0.00 0.00 4.17
1025 1123 1.601419 CCCATGTTCCAGCTGCTTGG 61.601 60.000 8.66 12.30 39.70 3.61
1074 1172 2.240921 TCACCACTATGCCATTTGCCTA 59.759 45.455 0.00 0.00 40.16 3.93
1090 1188 2.708861 TGCCTAGACCTGAAGAACCAAA 59.291 45.455 0.00 0.00 0.00 3.28
1188 1287 0.034896 TGAAAGAGACCTGGAACCGC 59.965 55.000 0.00 0.00 0.00 5.68
1243 1342 2.357327 TCCAATTGAGTACGTCACGG 57.643 50.000 7.12 0.00 33.71 4.94
1272 1371 5.622770 AGCAAGAAAACGGGTAATTACTG 57.377 39.130 15.05 10.47 0.00 2.74
1275 1374 5.180680 GCAAGAAAACGGGTAATTACTGTCT 59.819 40.000 15.05 2.92 0.00 3.41
1404 1511 2.034812 TGCGGGTTTTACATGTTGGAAC 59.965 45.455 2.30 6.88 0.00 3.62
1428 1537 0.400213 TGCAAAGTGGGAAGGTCGAT 59.600 50.000 0.00 0.00 0.00 3.59
1581 1695 5.120830 GCGAACAAGAAGTACAAGTGATCAT 59.879 40.000 0.00 0.00 0.00 2.45
1607 1722 1.140852 GCTCCATACACATGCCTACCA 59.859 52.381 0.00 0.00 0.00 3.25
1622 1737 3.685550 GCCTACCATACATTCTGTGGCTT 60.686 47.826 0.00 0.00 36.47 4.35
1683 1799 3.242944 CCGTGTGCTATGTTATGACTTCG 59.757 47.826 0.00 0.00 0.00 3.79
1729 1846 2.452813 GGCGTGTATGTGCCGTCTG 61.453 63.158 0.00 0.00 42.22 3.51
1742 1868 2.102420 TGCCGTCTGATATAAGTGTGGG 59.898 50.000 0.00 0.00 0.00 4.61
1745 1871 2.548067 CGTCTGATATAAGTGTGGGCCC 60.548 54.545 17.59 17.59 0.00 5.80
1815 1943 7.793927 TTATGTGTTTGTGAATGTGAGTACA 57.206 32.000 0.00 0.00 41.89 2.90
1842 1971 3.304391 GGCAGTTTGAATGCGAGTTTGTA 60.304 43.478 0.00 0.00 44.80 2.41
1843 1972 4.286910 GCAGTTTGAATGCGAGTTTGTAA 58.713 39.130 0.00 0.00 33.31 2.41
1851 1980 1.871039 TGCGAGTTTGTAAGCTTGTCC 59.129 47.619 9.86 0.00 0.00 4.02
1865 1994 3.049912 GCTTGTCCGAAATGTGGTTTTC 58.950 45.455 0.00 0.00 33.24 2.29
1893 2022 6.688637 TCTCCTGTCATATGCTTGATTTTG 57.311 37.500 0.00 0.00 0.00 2.44
1895 2024 6.317140 TCTCCTGTCATATGCTTGATTTTGTC 59.683 38.462 0.00 0.00 0.00 3.18
1897 2026 6.660521 TCCTGTCATATGCTTGATTTTGTCTT 59.339 34.615 0.00 0.00 0.00 3.01
1898 2027 6.971184 CCTGTCATATGCTTGATTTTGTCTTC 59.029 38.462 0.00 0.00 0.00 2.87
1900 2029 8.114331 TGTCATATGCTTGATTTTGTCTTCTT 57.886 30.769 0.00 0.00 0.00 2.52
1902 2031 9.415544 GTCATATGCTTGATTTTGTCTTCTTTT 57.584 29.630 0.00 0.00 0.00 2.27
1903 2032 9.985730 TCATATGCTTGATTTTGTCTTCTTTTT 57.014 25.926 0.00 0.00 0.00 1.94
1944 2075 2.187946 GAGGACGTGGCAGATGGG 59.812 66.667 0.00 0.00 0.00 4.00
2126 2261 3.819564 TGGTGATACTCCAATCCTTCG 57.180 47.619 0.00 0.00 31.50 3.79
2148 2283 3.090790 GGTCTCTCTTAACGGACTCCTT 58.909 50.000 0.00 0.00 0.00 3.36
2161 2296 3.758554 CGGACTCCTTCCATGTCAAATTT 59.241 43.478 0.00 0.00 46.29 1.82
2190 2325 1.065854 CCGCCCTCTCTTGACATTCTT 60.066 52.381 0.00 0.00 0.00 2.52
2197 2332 3.930336 TCTCTTGACATTCTTCGCATGT 58.070 40.909 0.00 0.00 37.58 3.21
2230 2365 1.209019 CTATGCACTGGAGCTTCTGGT 59.791 52.381 3.68 0.00 34.99 4.00
2312 2447 3.052414 TGGTGCTACCCCAACTCTATCTA 60.052 47.826 3.33 0.00 37.50 1.98
2332 2467 9.343539 CTATCTAGTATATCATCATTCCGGACA 57.656 37.037 1.83 0.00 0.00 4.02
2333 2468 8.774546 ATCTAGTATATCATCATTCCGGACAT 57.225 34.615 1.83 0.00 0.00 3.06
2408 2543 2.159841 CCTAACTGTTGAACATGTCGCG 60.160 50.000 0.00 0.00 0.00 5.87
2450 2585 0.530288 GCCATACAACATTGCGGGTT 59.470 50.000 0.00 0.00 0.00 4.11
2500 2636 1.949525 GCTTTTGTGGCACTCTCTTGA 59.050 47.619 19.83 0.00 0.00 3.02
2501 2637 2.031333 GCTTTTGTGGCACTCTCTTGAG 60.031 50.000 19.83 8.02 45.43 3.02
2502 2638 3.470709 CTTTTGTGGCACTCTCTTGAGA 58.529 45.455 19.83 0.13 42.73 3.27
2503 2639 3.777106 TTTGTGGCACTCTCTTGAGAT 57.223 42.857 19.83 0.00 42.73 2.75
2504 2640 2.756840 TGTGGCACTCTCTTGAGATG 57.243 50.000 19.83 3.91 42.73 2.90
2505 2641 1.277273 TGTGGCACTCTCTTGAGATGG 59.723 52.381 19.83 0.00 42.73 3.51
2506 2642 0.907486 TGGCACTCTCTTGAGATGGG 59.093 55.000 0.41 0.00 42.73 4.00
2507 2643 0.908198 GGCACTCTCTTGAGATGGGT 59.092 55.000 0.41 0.00 42.73 4.51
2508 2644 1.280421 GGCACTCTCTTGAGATGGGTT 59.720 52.381 0.41 0.00 42.73 4.11
2509 2645 2.354259 GCACTCTCTTGAGATGGGTTG 58.646 52.381 0.41 0.00 42.73 3.77
2510 2646 2.027745 GCACTCTCTTGAGATGGGTTGA 60.028 50.000 0.41 0.00 42.73 3.18
2511 2647 3.557898 GCACTCTCTTGAGATGGGTTGAA 60.558 47.826 0.41 0.00 42.73 2.69
2512 2648 4.645535 CACTCTCTTGAGATGGGTTGAAA 58.354 43.478 0.41 0.00 42.73 2.69
2513 2649 4.453819 CACTCTCTTGAGATGGGTTGAAAC 59.546 45.833 0.41 0.00 42.73 2.78
2514 2650 4.006319 CTCTCTTGAGATGGGTTGAAACC 58.994 47.826 3.47 3.47 44.32 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.751924 GCACTTCTGACGGTATCCTCT 59.248 52.381 0.00 0.00 0.00 3.69
115 116 3.192212 AGCCTTAACATCAAGCTCAAAGC 59.808 43.478 0.00 0.00 42.84 3.51
346 369 2.749076 TGTCCAAACATGAGCTGTATGC 59.251 45.455 0.00 0.00 36.98 3.14
401 424 0.105039 GGCAAGATCACCTAGGTCGG 59.895 60.000 12.84 1.45 0.00 4.79
408 431 0.534412 CAGACTCGGCAAGATCACCT 59.466 55.000 0.00 0.00 0.00 4.00
575 599 1.507141 CGCGGCAAAGTGTTTCCTCT 61.507 55.000 0.00 0.00 0.00 3.69
585 609 2.546645 AATCACCATGCGCGGCAAAG 62.547 55.000 8.83 5.04 43.62 2.77
623 649 8.037382 ACAATGAGAAGAAACACTCACATATG 57.963 34.615 0.00 0.00 44.18 1.78
711 746 2.620115 CCACATGAAACAGCTGTCACTT 59.380 45.455 21.95 11.26 0.00 3.16
768 807 5.009010 AGTGAAGTTGCCACATAAGTTGAAG 59.991 40.000 0.00 0.00 37.01 3.02
902 957 6.039605 TGTTGCCAGTTACAATGATGGATATG 59.960 38.462 0.00 0.00 34.60 1.78
979 1063 8.974060 AACATGACCTACAAGTAAAAAGAGAA 57.026 30.769 0.00 0.00 30.00 2.87
983 1081 6.072119 GGGGAACATGACCTACAAGTAAAAAG 60.072 42.308 0.00 0.00 30.00 2.27
1025 1123 1.347707 TGTCATCTGGGTTGTCTGGTC 59.652 52.381 0.00 0.00 0.00 4.02
1074 1172 5.261216 TCAAAACTTTGGTTCTTCAGGTCT 58.739 37.500 2.49 0.00 38.66 3.85
1090 1188 5.279156 GGATTGAATCAAGCACCTCAAAACT 60.279 40.000 13.45 0.00 30.75 2.66
1131 1229 7.331791 AGAATTCAACATGAGTAGTAAGGTCC 58.668 38.462 8.44 0.00 0.00 4.46
1188 1287 4.517453 TGGACCTTTGAGTTTTCGTAATGG 59.483 41.667 0.00 0.00 0.00 3.16
1404 1511 0.675633 CCTTCCCACTTTGCAAGGTG 59.324 55.000 29.26 29.26 32.17 4.00
1428 1537 2.040359 TGTGACCACAGGGACCCA 60.040 61.111 14.60 0.00 36.21 4.51
1581 1695 2.291365 GCATGTGTATGGAGCATCACA 58.709 47.619 0.00 0.00 43.30 3.58
1683 1799 1.992538 ATACTACAGCTACGGGGGAC 58.007 55.000 0.00 0.00 0.00 4.46
1729 1846 2.490991 GTTCGGGCCCACACTTATATC 58.509 52.381 24.92 0.00 0.00 1.63
1742 1868 0.250597 ACACCTAAACAGGTTCGGGC 60.251 55.000 0.00 0.00 40.85 6.13
1745 1871 2.828877 TGTCACACCTAAACAGGTTCG 58.171 47.619 0.00 0.00 40.85 3.95
1815 1943 3.243839 ACTCGCATTCAAACTGCCAATTT 60.244 39.130 0.00 0.00 36.24 1.82
1842 1971 1.981256 ACCACATTTCGGACAAGCTT 58.019 45.000 0.00 0.00 0.00 3.74
1843 1972 1.981256 AACCACATTTCGGACAAGCT 58.019 45.000 0.00 0.00 0.00 3.74
1851 1980 6.144402 CAGGAGAATTTGAAAACCACATTTCG 59.856 38.462 0.00 0.00 41.24 3.46
1865 1994 6.688637 TCAAGCATATGACAGGAGAATTTG 57.311 37.500 6.97 0.00 0.00 2.32
1944 2075 6.858993 TGTTGTTGTTGTTGTAGAGTTTCAAC 59.141 34.615 0.00 0.00 42.62 3.18
2126 2261 1.750206 GGAGTCCGTTAAGAGAGACCC 59.250 57.143 0.00 0.00 0.00 4.46
2148 2283 4.340617 GGGTAGACCAAATTTGACATGGA 58.659 43.478 19.86 0.00 39.85 3.41
2161 2296 3.674050 GAGAGGGCGGGGTAGACCA 62.674 68.421 0.21 0.00 43.43 4.02
2190 2325 1.355796 CGGACGGCTAAAACATGCGA 61.356 55.000 0.00 0.00 0.00 5.10
2230 2365 2.188829 GCATATTCAGCGCAGGCCA 61.189 57.895 11.47 0.00 41.24 5.36
2312 2447 6.857437 TCATGTCCGGAATGATGATATACT 57.143 37.500 19.20 0.00 0.00 2.12
2332 2467 0.179000 GCCACACGAGGAAGGATCAT 59.821 55.000 0.00 0.00 0.00 2.45
2333 2468 1.596934 GCCACACGAGGAAGGATCA 59.403 57.895 0.00 0.00 0.00 2.92
2408 2543 2.215196 TGAGTGTTGGCCGACTAAAAC 58.785 47.619 23.87 13.39 0.00 2.43
2450 2585 1.899814 AGTTCTACAGGACGGCATTCA 59.100 47.619 0.00 0.00 0.00 2.57



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

AutoCloner maintained by Alex Coulton.