Multiple sequence alignment - TraesCS3B01G431300

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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 TraesCS3B01G431300 chr3B 100.000 3107 0 0 580 3686 670345916 670349022 0.000000e+00 5738.0
1 TraesCS3B01G431300 chr3B 90.221 1176 103 11 2514 3686 413565287 413564121 0.000000e+00 1524.0
2 TraesCS3B01G431300 chr3B 89.664 1190 116 6 2501 3686 461803121 461804307 0.000000e+00 1509.0
3 TraesCS3B01G431300 chr3B 82.267 344 44 13 2402 2738 495284139 495284472 7.790000e-72 281.0
4 TraesCS3B01G431300 chr3B 100.000 117 0 0 1 117 670345337 670345453 2.230000e-52 217.0
5 TraesCS3B01G431300 chr3B 92.958 142 8 2 2152 2292 498500278 498500418 4.830000e-49 206.0
6 TraesCS3B01G431300 chr3B 92.308 117 9 0 1 117 739186814 739186930 2.280000e-37 167.0
7 TraesCS3B01G431300 chr3B 86.364 154 11 7 2404 2552 495284815 495284963 3.810000e-35 159.0
8 TraesCS3B01G431300 chr3B 87.255 102 13 0 2002 2103 162317885 162317784 2.330000e-22 117.0
9 TraesCS3B01G431300 chr2B 96.855 1240 37 2 1279 2517 289631817 289633055 0.000000e+00 2073.0
10 TraesCS3B01G431300 chr2B 95.487 842 32 4 1279 2118 289633090 289633927 0.000000e+00 1339.0
11 TraesCS3B01G431300 chr2B 89.571 815 67 11 2001 2809 363238362 363239164 0.000000e+00 1018.0
12 TraesCS3B01G431300 chr2B 91.469 715 36 6 580 1294 289630818 289631507 0.000000e+00 959.0
13 TraesCS3B01G431300 chr2B 93.944 611 28 8 2192 2798 289633922 289634527 0.000000e+00 915.0
14 TraesCS3B01G431300 chr2B 87.472 447 47 8 1350 1790 107587639 107588082 1.180000e-139 507.0
15 TraesCS3B01G431300 chr2B 93.249 237 15 1 1051 1286 772257389 772257625 7.580000e-92 348.0
16 TraesCS3B01G431300 chr5B 89.589 1191 112 10 2501 3686 708404470 708405653 0.000000e+00 1502.0
17 TraesCS3B01G431300 chr5B 86.217 341 22 10 2001 2335 620049054 620049375 2.720000e-91 346.0
18 TraesCS3B01G431300 chrUn 88.992 1181 103 11 2512 3686 324100296 324101455 0.000000e+00 1435.0
19 TraesCS3B01G431300 chrUn 88.960 933 94 7 2758 3686 243888142 243887215 0.000000e+00 1144.0
20 TraesCS3B01G431300 chrUn 90.909 264 20 4 782 1043 342002615 342002354 5.860000e-93 351.0
21 TraesCS3B01G431300 chrUn 90.909 264 20 4 782 1043 358505888 358505627 5.860000e-93 351.0
22 TraesCS3B01G431300 chrUn 90.152 264 22 4 782 1043 314193864 314194125 1.270000e-89 340.0
23 TraesCS3B01G431300 chrUn 90.152 264 22 4 782 1043 320966952 320966691 1.270000e-89 340.0
24 TraesCS3B01G431300 chrUn 89.773 264 23 4 782 1043 314190140 314190401 5.900000e-88 335.0
25 TraesCS3B01G431300 chrUn 93.162 117 8 0 1 117 229634771 229634887 4.890000e-39 172.0
26 TraesCS3B01G431300 chr4A 87.721 1189 133 12 2501 3686 25135462 25136640 0.000000e+00 1375.0
27 TraesCS3B01G431300 chr4A 90.639 876 73 8 2815 3686 93497146 93498016 0.000000e+00 1155.0
28 TraesCS3B01G431300 chr4A 96.330 109 4 0 9 117 715586815 715586707 2.920000e-41 180.0
29 TraesCS3B01G431300 chr4A 85.000 80 10 2 2029 2107 199922361 199922283 3.050000e-11 80.5
30 TraesCS3B01G431300 chr7D 88.673 1130 110 13 2501 3622 154587888 154586769 0.000000e+00 1362.0
31 TraesCS3B01G431300 chr7D 82.979 188 11 10 1051 1237 527923684 527923851 2.290000e-32 150.0
32 TraesCS3B01G431300 chr1B 95.495 777 30 5 2913 3686 143600759 143599985 0.000000e+00 1236.0
33 TraesCS3B01G431300 chr1B 94.074 810 41 6 2001 2809 403001776 403002579 0.000000e+00 1223.0
34 TraesCS3B01G431300 chr1B 87.926 323 19 5 2001 2320 416144750 416145055 2.710000e-96 363.0
35 TraesCS3B01G431300 chr1B 88.976 254 22 5 1350 1597 613236696 613236443 3.580000e-80 309.0
36 TraesCS3B01G431300 chr1B 93.277 119 6 1 1 117 205363849 205363731 1.360000e-39 174.0
37 TraesCS3B01G431300 chr7A 90.786 814 60 8 2001 2809 422575109 422574306 0.000000e+00 1074.0
38 TraesCS3B01G431300 chr5D 89.619 867 56 20 2002 2856 193970075 193969231 0.000000e+00 1072.0
39 TraesCS3B01G431300 chr6B 89.394 462 47 2 582 1043 154908759 154909218 6.860000e-162 580.0
40 TraesCS3B01G431300 chr7B 94.690 113 6 0 5 117 587928371 587928259 3.780000e-40 176.0
41 TraesCS3B01G431300 chr7B 93.913 115 7 0 1 115 700748675 700748789 1.360000e-39 174.0
42 TraesCS3B01G431300 chr7B 93.162 117 8 0 1 117 70947492 70947376 4.890000e-39 172.0
43 TraesCS3B01G431300 chr7B 93.860 114 7 0 1 114 741030325 741030438 4.890000e-39 172.0
44 TraesCS3B01G431300 chr7B 92.373 118 8 1 1 117 611169095 611168978 2.280000e-37 167.0
45 TraesCS3B01G431300 chr7B 79.832 238 37 11 601 835 579437979 579438208 2.950000e-36 163.0
46 TraesCS3B01G431300 chr4B 91.262 103 9 0 2001 2103 340789399 340789297 1.380000e-29 141.0
47 TraesCS3B01G431300 chr4B 77.830 212 35 7 1594 1805 47117022 47116823 1.800000e-23 121.0
48 TraesCS3B01G431300 chr2A 81.579 152 22 6 624 772 617936683 617936535 1.800000e-23 121.0
49 TraesCS3B01G431300 chr1A 90.000 90 9 0 1482 1571 543951532 543951443 2.330000e-22 117.0


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 TraesCS3B01G431300 chr3B 670345337 670349022 3685 False 2977.5 5738 100.00000 1 3686 2 chr3B.!!$F5 3685
1 TraesCS3B01G431300 chr3B 413564121 413565287 1166 True 1524.0 1524 90.22100 2514 3686 1 chr3B.!!$R2 1172
2 TraesCS3B01G431300 chr3B 461803121 461804307 1186 False 1509.0 1509 89.66400 2501 3686 1 chr3B.!!$F1 1185
3 TraesCS3B01G431300 chr3B 495284139 495284963 824 False 220.0 281 84.31550 2402 2738 2 chr3B.!!$F4 336
4 TraesCS3B01G431300 chr2B 289630818 289634527 3709 False 1321.5 2073 94.43875 580 2798 4 chr2B.!!$F4 2218
5 TraesCS3B01G431300 chr2B 363238362 363239164 802 False 1018.0 1018 89.57100 2001 2809 1 chr2B.!!$F2 808
6 TraesCS3B01G431300 chr5B 708404470 708405653 1183 False 1502.0 1502 89.58900 2501 3686 1 chr5B.!!$F2 1185
7 TraesCS3B01G431300 chrUn 324100296 324101455 1159 False 1435.0 1435 88.99200 2512 3686 1 chrUn.!!$F2 1174
8 TraesCS3B01G431300 chrUn 243887215 243888142 927 True 1144.0 1144 88.96000 2758 3686 1 chrUn.!!$R1 928
9 TraesCS3B01G431300 chrUn 314190140 314194125 3985 False 337.5 340 89.96250 782 1043 2 chrUn.!!$F3 261
10 TraesCS3B01G431300 chr4A 25135462 25136640 1178 False 1375.0 1375 87.72100 2501 3686 1 chr4A.!!$F1 1185
11 TraesCS3B01G431300 chr4A 93497146 93498016 870 False 1155.0 1155 90.63900 2815 3686 1 chr4A.!!$F2 871
12 TraesCS3B01G431300 chr7D 154586769 154587888 1119 True 1362.0 1362 88.67300 2501 3622 1 chr7D.!!$R1 1121
13 TraesCS3B01G431300 chr1B 143599985 143600759 774 True 1236.0 1236 95.49500 2913 3686 1 chr1B.!!$R1 773
14 TraesCS3B01G431300 chr1B 403001776 403002579 803 False 1223.0 1223 94.07400 2001 2809 1 chr1B.!!$F1 808
15 TraesCS3B01G431300 chr7A 422574306 422575109 803 True 1074.0 1074 90.78600 2001 2809 1 chr7A.!!$R1 808
16 TraesCS3B01G431300 chr5D 193969231 193970075 844 True 1072.0 1072 89.61900 2002 2856 1 chr5D.!!$R1 854


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
93 94 0.030773 TCACCATCGTCATCGCTAGC 59.969 55.0 4.06 4.06 36.96 3.42 F
94 95 0.941463 CACCATCGTCATCGCTAGCC 60.941 60.0 9.66 0.00 36.96 3.93 F
1706 2152 0.592637 TCCGACGAAACAGCGAACTA 59.407 50.0 0.00 0.00 34.83 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 2152 0.827368 GCGGAGAGGAGGAATGAAGT 59.173 55.000 0.00 0.00 0.00 3.01 R
1870 2317 3.213506 ACATCAAAACTGTAGTGCTGCA 58.786 40.909 0.00 0.00 0.00 4.41 R
3284 5384 0.174389 ACGATGAGTGGCAGCTACTG 59.826 55.000 17.44 4.23 34.12 2.74 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
80 81 4.033776 CGCCCCCACTGTCACCAT 62.034 66.667 0.00 0.00 0.00 3.55
81 82 2.044946 GCCCCCACTGTCACCATC 60.045 66.667 0.00 0.00 0.00 3.51
82 83 2.268920 CCCCCACTGTCACCATCG 59.731 66.667 0.00 0.00 0.00 3.84
83 84 2.592993 CCCCCACTGTCACCATCGT 61.593 63.158 0.00 0.00 0.00 3.73
84 85 1.079127 CCCCACTGTCACCATCGTC 60.079 63.158 0.00 0.00 0.00 4.20
85 86 1.671166 CCCACTGTCACCATCGTCA 59.329 57.895 0.00 0.00 0.00 4.35
86 87 0.250234 CCCACTGTCACCATCGTCAT 59.750 55.000 0.00 0.00 0.00 3.06
87 88 1.645034 CCACTGTCACCATCGTCATC 58.355 55.000 0.00 0.00 0.00 2.92
88 89 1.271876 CACTGTCACCATCGTCATCG 58.728 55.000 0.00 0.00 38.55 3.84
89 90 0.458543 ACTGTCACCATCGTCATCGC 60.459 55.000 0.00 0.00 36.96 4.58
90 91 0.179127 CTGTCACCATCGTCATCGCT 60.179 55.000 0.00 0.00 36.96 4.93
91 92 1.065551 CTGTCACCATCGTCATCGCTA 59.934 52.381 0.00 0.00 36.96 4.26
92 93 1.065551 TGTCACCATCGTCATCGCTAG 59.934 52.381 0.00 0.00 36.96 3.42
93 94 0.030773 TCACCATCGTCATCGCTAGC 59.969 55.000 4.06 4.06 36.96 3.42
94 95 0.941463 CACCATCGTCATCGCTAGCC 60.941 60.000 9.66 0.00 36.96 3.93
95 96 1.730902 CCATCGTCATCGCTAGCCG 60.731 63.158 9.66 6.56 36.96 5.52
96 97 2.049985 ATCGTCATCGCTAGCCGC 60.050 61.111 9.66 0.00 36.73 6.53
97 98 3.559657 ATCGTCATCGCTAGCCGCC 62.560 63.158 9.66 0.00 36.73 6.13
99 100 4.971125 GTCATCGCTAGCCGCCCC 62.971 72.222 9.66 0.00 36.73 5.80
620 621 1.955080 CCCACCTCTATCTACCACGAC 59.045 57.143 0.00 0.00 0.00 4.34
631 632 2.220786 TACCACGACTCCCCTCCTCC 62.221 65.000 0.00 0.00 0.00 4.30
724 725 1.369625 CGATTCACCTTCTTTCCCCG 58.630 55.000 0.00 0.00 0.00 5.73
757 758 1.615262 CCCCAATCCACCTTCTCCC 59.385 63.158 0.00 0.00 0.00 4.30
938 939 3.896133 GCCGCGACGAGACCCATA 61.896 66.667 8.23 0.00 0.00 2.74
939 940 3.039988 CCGCGACGAGACCCATAT 58.960 61.111 8.23 0.00 0.00 1.78
980 981 2.558359 CACATCCTCACCTTTTTCACCC 59.442 50.000 0.00 0.00 0.00 4.61
1044 1046 1.229359 CTGGATCCATGCAGCCCTT 59.771 57.895 16.63 0.00 39.36 3.95
1054 1056 4.355720 CAGCCCTTGCCTGCTCCA 62.356 66.667 0.00 0.00 38.69 3.86
1055 1057 4.357279 AGCCCTTGCCTGCTCCAC 62.357 66.667 0.00 0.00 38.69 4.02
1058 1060 2.357836 CCTTGCCTGCTCCACCAT 59.642 61.111 0.00 0.00 0.00 3.55
1059 1061 1.304713 CCTTGCCTGCTCCACCATT 60.305 57.895 0.00 0.00 0.00 3.16
1060 1062 1.601419 CCTTGCCTGCTCCACCATTG 61.601 60.000 0.00 0.00 0.00 2.82
1061 1063 1.601419 CTTGCCTGCTCCACCATTGG 61.601 60.000 0.00 0.00 45.56 3.16
1064 1066 3.136123 CTGCTCCACCATTGGCCG 61.136 66.667 1.54 0.00 43.56 6.13
1147 1149 2.280389 CACCCATCGCTGGATCCG 60.280 66.667 6.92 3.14 46.37 4.18
1148 1150 3.550431 ACCCATCGCTGGATCCGG 61.550 66.667 16.98 16.98 46.37 5.14
1151 1153 2.355126 CATCGCTGGATCCGGTCG 60.355 66.667 21.88 22.76 0.00 4.79
1316 1762 1.444250 GTGAGGTTCACCGACCACA 59.556 57.895 11.72 0.00 41.37 4.17
1360 1806 3.451556 ATGTGCAGCGAGATCCCCG 62.452 63.158 0.00 1.20 0.00 5.73
1383 1829 3.114616 CTCTCCCGCAAGTGCACG 61.115 66.667 12.01 0.00 42.21 5.34
1446 1892 1.215673 TCTCTCTCGCTAGAACCCCAT 59.784 52.381 0.00 0.00 0.00 4.00
1454 1900 1.584724 CTAGAACCCCATGTCCCAGT 58.415 55.000 0.00 0.00 0.00 4.00
1539 1985 3.023949 GCTGTCCGACATCCAGGCT 62.024 63.158 0.62 0.00 0.00 4.58
1676 2122 2.854963 TGTTCAGATGCAGCTCACTTT 58.145 42.857 0.00 0.00 0.00 2.66
1706 2152 0.592637 TCCGACGAAACAGCGAACTA 59.407 50.000 0.00 0.00 34.83 2.24
1833 2279 2.417651 CGCCGGTGTTCTGGTTCTATTA 60.418 50.000 6.91 0.00 41.89 0.98
1834 2280 2.934553 GCCGGTGTTCTGGTTCTATTAC 59.065 50.000 1.90 0.00 41.89 1.89
1870 2317 5.596836 TTTTCTTCAGATTTTGCCTGTGT 57.403 34.783 0.00 0.00 33.57 3.72
2316 2775 5.163642 ACTCTCGACAACGCAGTATAGATTT 60.164 40.000 0.00 0.00 45.00 2.17
2346 2805 4.244862 GTGCGGATTTGGAACATGAAAAT 58.755 39.130 0.00 0.00 39.30 1.82
2846 4926 2.499197 TGCAGTGCGGTTTTCATTCTA 58.501 42.857 11.20 0.00 0.00 2.10
2863 4943 0.949105 CTAAAGCAGTGCGGTCGGTT 60.949 55.000 10.00 0.00 0.00 4.44
2943 5028 9.201989 AGTAATGTGGATCACTTCTTGATAGTA 57.798 33.333 0.00 0.00 45.67 1.82
3076 5163 1.588674 TTTTTCGTCCGATGCAGTGT 58.411 45.000 0.00 0.00 0.00 3.55
3426 6127 1.262950 CATGCCTCGTTTCGACAAACA 59.737 47.619 1.26 0.00 41.94 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.647019 GCGATGACGATGGTGACAGTG 61.647 57.143 0.00 0.00 41.62 3.66
70 71 0.458543 GCGATGACGATGGTGACAGT 60.459 55.000 0.00 0.00 41.62 3.55
71 72 0.179127 AGCGATGACGATGGTGACAG 60.179 55.000 0.00 0.00 41.62 3.51
72 73 1.065551 CTAGCGATGACGATGGTGACA 59.934 52.381 0.00 0.00 42.66 3.58
73 74 1.759994 CTAGCGATGACGATGGTGAC 58.240 55.000 0.00 0.00 42.66 3.67
74 75 0.030773 GCTAGCGATGACGATGGTGA 59.969 55.000 0.00 0.00 42.66 4.02
75 76 0.941463 GGCTAGCGATGACGATGGTG 60.941 60.000 9.00 0.00 42.66 4.17
76 77 1.364171 GGCTAGCGATGACGATGGT 59.636 57.895 9.00 0.00 42.66 3.55
77 78 1.730902 CGGCTAGCGATGACGATGG 60.731 63.158 9.00 0.00 42.66 3.51
78 79 2.368105 GCGGCTAGCGATGACGATG 61.368 63.158 13.48 0.00 42.66 3.84
79 80 2.049985 GCGGCTAGCGATGACGAT 60.050 61.111 13.48 0.00 42.66 3.73
620 621 2.203714 GGATCGGGAGGAGGGGAG 60.204 72.222 0.00 0.00 0.00 4.30
631 632 2.190578 GGGCAGAAGGTGGATCGG 59.809 66.667 0.00 0.00 0.00 4.18
730 731 4.529731 GGATTGGGGGAGGGCAGC 62.530 72.222 0.00 0.00 0.00 5.25
732 733 3.346734 GTGGATTGGGGGAGGGCA 61.347 66.667 0.00 0.00 0.00 5.36
779 780 2.014068 GCAGGGGAAGAAGTTGGATCG 61.014 57.143 0.00 0.00 0.00 3.69
921 922 3.208884 ATATGGGTCTCGTCGCGGC 62.209 63.158 6.13 1.93 0.00 6.53
1054 1056 4.740822 GGGACAGCGGCCAATGGT 62.741 66.667 2.24 0.00 0.00 3.55
1221 1223 4.078516 GGGTCTCGGGGGTGAACG 62.079 72.222 0.00 0.00 0.00 3.95
1335 1781 2.046023 TCGCTGCACATGAAGGGG 60.046 61.111 0.00 0.00 34.62 4.79
1422 1868 1.314730 GTTCTAGCGAGAGAGAGGGG 58.685 60.000 0.00 0.00 31.77 4.79
1424 1870 1.314730 GGGTTCTAGCGAGAGAGAGG 58.685 60.000 0.00 0.00 31.77 3.69
1446 1892 3.644966 ACAGAAGAAACAACTGGGACA 57.355 42.857 0.00 0.00 36.17 4.02
1454 1900 9.730705 ATTGAGATCAAGATACAGAAGAAACAA 57.269 29.630 1.32 0.00 39.47 2.83
1530 1976 2.046988 TGCACGTCAGCCTGGATG 60.047 61.111 5.38 5.38 0.00 3.51
1539 1985 2.415491 CGATTTAGACTCCTGCACGTCA 60.415 50.000 8.29 0.00 32.68 4.35
1579 2025 3.817084 CCAACACAGAAATTGCAGAGAGA 59.183 43.478 0.00 0.00 0.00 3.10
1659 2105 1.718396 CGAAAGTGAGCTGCATCTGA 58.282 50.000 1.02 0.00 0.00 3.27
1662 2108 1.300971 TGGCGAAAGTGAGCTGCATC 61.301 55.000 1.02 0.00 0.00 3.91
1676 2122 4.394078 CGTCGGACGACTTGGCGA 62.394 66.667 25.29 0.00 46.05 5.54
1706 2152 0.827368 GCGGAGAGGAGGAATGAAGT 59.173 55.000 0.00 0.00 0.00 3.01
1870 2317 3.213506 ACATCAAAACTGTAGTGCTGCA 58.786 40.909 0.00 0.00 0.00 4.41
1882 2329 3.363280 GGTACACCGAACGACATCAAAAC 60.363 47.826 0.00 0.00 0.00 2.43
1922 2369 9.793259 TTTTCTTAAGTGAACAACATAGGAGAT 57.207 29.630 1.63 0.00 0.00 2.75
1923 2370 9.621629 TTTTTCTTAAGTGAACAACATAGGAGA 57.378 29.630 1.63 0.00 0.00 3.71
2316 2775 0.950836 CCAAATCCGCACACAAGTCA 59.049 50.000 0.00 0.00 0.00 3.41
2346 2805 3.254657 CCAAACTTTCCGGAACTGCATTA 59.745 43.478 18.64 0.00 0.00 1.90
2846 4926 2.203153 AACCGACCGCACTGCTTT 60.203 55.556 0.00 0.00 0.00 3.51
2943 5028 3.757270 TCGGGTGTAAATGAACCACAAT 58.243 40.909 0.00 0.00 38.27 2.71
3076 5163 3.485463 ACTTCATCCGACTGAAAACCA 57.515 42.857 2.06 0.00 34.86 3.67
3284 5384 0.174389 ACGATGAGTGGCAGCTACTG 59.826 55.000 17.44 4.23 34.12 2.74
3285 5385 0.457851 GACGATGAGTGGCAGCTACT 59.542 55.000 11.92 11.92 0.00 2.57
3426 6127 6.152831 ACTGTTTTTGCTCCAGTTTTCTAACT 59.847 34.615 0.00 0.00 45.40 2.24
3555 6727 4.575236 GGATAGATATCGTCGAGGTGCATA 59.425 45.833 4.85 0.00 33.52 3.14
3560 6732 3.436015 CGTTGGATAGATATCGTCGAGGT 59.564 47.826 4.85 0.00 33.52 3.85



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

AutoCloner maintained by Alex Coulton.