Multiple sequence alignment - TraesCS4A01G444700

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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 TraesCS4A01G444700 chr4A 100.000 3146 0 0 1 3146 713013959 713017104 0.000000e+00 5810
1 TraesCS4A01G444700 chr4A 87.484 2317 253 17 848 3140 713032310 713034613 0.000000e+00 2638
2 TraesCS4A01G444700 chr4A 87.942 821 65 15 3 818 713031524 713032315 0.000000e+00 937
3 TraesCS4A01G444700 chr4A 90.682 601 42 9 3 590 494467550 494468149 0.000000e+00 787
4 TraesCS4A01G444700 chr4A 92.222 360 28 0 3 362 617108919 617109278 7.780000e-141 510
5 TraesCS4A01G444700 chr7D 87.744 3182 339 31 1 3146 20484762 20487928 0.000000e+00 3668
6 TraesCS4A01G444700 chr7D 89.062 2377 240 16 3 2371 20520398 20522762 0.000000e+00 2931
7 TraesCS4A01G444700 chr7D 86.719 2402 282 26 770 3146 20310770 20313159 0.000000e+00 2634
8 TraesCS4A01G444700 chr7D 84.891 2429 315 28 742 3144 20598269 20600671 0.000000e+00 2405
9 TraesCS4A01G444700 chr7D 83.682 2341 344 23 833 3146 20404284 20406613 0.000000e+00 2172
10 TraesCS4A01G444700 chr7D 82.581 2394 373 32 783 3146 20947076 20949455 0.000000e+00 2071
11 TraesCS4A01G444700 chr7A 88.337 2375 252 20 783 3146 20588683 20591043 0.000000e+00 2828
12 TraesCS4A01G444700 chr7A 87.238 2390 272 9 779 3146 20650734 20653112 0.000000e+00 2693
13 TraesCS4A01G444700 chr7A 85.599 2604 330 27 561 3146 20910419 20912995 0.000000e+00 2689
14 TraesCS4A01G444700 chr7A 86.373 2407 288 26 770 3146 20482718 20485114 0.000000e+00 2591
15 TraesCS4A01G444700 chr7A 86.029 2405 295 32 770 3146 20966196 20968587 0.000000e+00 2542
16 TraesCS4A01G444700 chr7A 87.586 2175 260 7 975 3146 20457865 20460032 0.000000e+00 2512
17 TraesCS4A01G444700 chr7A 83.675 2389 348 27 787 3146 20659584 20661959 0.000000e+00 2213
18 TraesCS4A01G444700 chr7A 87.250 549 58 9 13 555 20909752 20910294 1.600000e-172 616
19 TraesCS4A01G444700 chr7A 80.569 211 30 7 314 518 20697595 20697800 5.430000e-33 152
20 TraesCS4A01G444700 chr6B 91.892 333 27 0 3 335 534958038 534958370 1.710000e-127 466
21 TraesCS4A01G444700 chr6B 91.156 147 11 2 329 473 534977438 534977584 6.880000e-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 TraesCS4A01G444700 chr4A 713013959 713017104 3145 False 5810.0 5810 100.0000 1 3146 1 chr4A.!!$F3 3145
1 TraesCS4A01G444700 chr4A 713031524 713034613 3089 False 1787.5 2638 87.7130 3 3140 2 chr4A.!!$F4 3137
2 TraesCS4A01G444700 chr4A 494467550 494468149 599 False 787.0 787 90.6820 3 590 1 chr4A.!!$F1 587
3 TraesCS4A01G444700 chr7D 20484762 20487928 3166 False 3668.0 3668 87.7440 1 3146 1 chr7D.!!$F3 3145
4 TraesCS4A01G444700 chr7D 20520398 20522762 2364 False 2931.0 2931 89.0620 3 2371 1 chr7D.!!$F4 2368
5 TraesCS4A01G444700 chr7D 20310770 20313159 2389 False 2634.0 2634 86.7190 770 3146 1 chr7D.!!$F1 2376
6 TraesCS4A01G444700 chr7D 20598269 20600671 2402 False 2405.0 2405 84.8910 742 3144 1 chr7D.!!$F5 2402
7 TraesCS4A01G444700 chr7D 20404284 20406613 2329 False 2172.0 2172 83.6820 833 3146 1 chr7D.!!$F2 2313
8 TraesCS4A01G444700 chr7D 20947076 20949455 2379 False 2071.0 2071 82.5810 783 3146 1 chr7D.!!$F6 2363
9 TraesCS4A01G444700 chr7A 20588683 20591043 2360 False 2828.0 2828 88.3370 783 3146 1 chr7A.!!$F3 2363
10 TraesCS4A01G444700 chr7A 20650734 20653112 2378 False 2693.0 2693 87.2380 779 3146 1 chr7A.!!$F4 2367
11 TraesCS4A01G444700 chr7A 20482718 20485114 2396 False 2591.0 2591 86.3730 770 3146 1 chr7A.!!$F2 2376
12 TraesCS4A01G444700 chr7A 20966196 20968587 2391 False 2542.0 2542 86.0290 770 3146 1 chr7A.!!$F7 2376
13 TraesCS4A01G444700 chr7A 20457865 20460032 2167 False 2512.0 2512 87.5860 975 3146 1 chr7A.!!$F1 2171
14 TraesCS4A01G444700 chr7A 20659584 20661959 2375 False 2213.0 2213 83.6750 787 3146 1 chr7A.!!$F5 2359
15 TraesCS4A01G444700 chr7A 20909752 20912995 3243 False 1652.5 2689 86.4245 13 3146 2 chr7A.!!$F8 3133


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
955 1100 1.070445 GCAGATCAGGCCAGCGTAT 59.930 57.895 5.01 0.0 0.0 3.06 F
1342 1489 0.895100 TGGGGATGCAAGCAACTCAC 60.895 55.000 4.57 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1949 0.543749 AAGCATCACTCTACTGCCCC 59.456 55.000 0.0 0.0 36.56 5.80 R
2249 2402 1.144936 CTCGATGAACCCCTCTGCC 59.855 63.158 0.0 0.0 0.00 4.85 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
35 36 4.792057 GCAAATCTCATATGCTCTTGTGGC 60.792 45.833 0.00 0.00 37.12 5.01
55 56 6.667414 TGTGGCAAATTCTACCCTCATAAAAT 59.333 34.615 0.00 0.00 0.00 1.82
147 156 9.725019 TGTAATCATGGGAGTACATATTGATTC 57.275 33.333 11.74 7.24 46.28 2.52
151 160 2.993899 GGGAGTACATATTGATTCGCCG 59.006 50.000 0.00 0.00 0.00 6.46
344 354 3.114527 TGCATATTGGCAAGCCGAT 57.885 47.368 17.47 17.47 41.65 4.18
398 408 4.898265 TGGTTCAGATTTCAACATTTGGGA 59.102 37.500 0.00 0.00 0.00 4.37
413 424 9.581099 CAACATTTGGGATGTTTAACCTAATAC 57.419 33.333 1.88 0.00 39.94 1.89
461 472 7.701539 ACATGAGCATTTATTTGGTGAAGTA 57.298 32.000 0.00 0.00 0.00 2.24
485 497 5.054477 TCACTGGTCTTGTTGCTAGTTAAC 58.946 41.667 0.00 0.00 0.00 2.01
488 500 5.883673 ACTGGTCTTGTTGCTAGTTAACAAA 59.116 36.000 20.35 12.79 44.58 2.83
501 513 6.129194 GCTAGTTAACAAAATTCTGTTTGCCG 60.129 38.462 8.61 0.00 41.33 5.69
688 821 5.355910 TGTGGTTGGAGAGTTTTTAAGTGTC 59.644 40.000 0.00 0.00 0.00 3.67
719 857 4.764823 AGTGTTTGGTGAGTTTTGAAGTGA 59.235 37.500 0.00 0.00 0.00 3.41
738 876 4.523943 AGTGATTTTGCAGGTGCTTCATAA 59.476 37.500 3.18 0.00 42.66 1.90
740 878 6.377996 AGTGATTTTGCAGGTGCTTCATAATA 59.622 34.615 3.18 0.00 42.66 0.98
843 986 2.910688 ATACAACTAGGCCACCATCG 57.089 50.000 5.01 0.00 0.00 3.84
942 1087 2.570181 GCAAAAGCAGCGGCAGAT 59.430 55.556 12.44 0.00 44.61 2.90
955 1100 1.070445 GCAGATCAGGCCAGCGTAT 59.930 57.895 5.01 0.00 0.00 3.06
1044 1189 2.284952 TCGCGTAATGCATGATGTTCTG 59.715 45.455 5.77 0.00 46.97 3.02
1081 1226 3.916172 TCGTAGTCGCAACAATCAAGTAC 59.084 43.478 0.00 0.00 36.96 2.73
1148 1293 3.034635 AGGACATGGTGGATGAGTACTC 58.965 50.000 16.32 16.32 35.80 2.59
1216 1363 2.868899 AGAAGGGTTTCAAGAAGCCAG 58.131 47.619 16.00 0.00 42.60 4.85
1235 1382 3.940221 CCAGGATCTCTGCTTTCTTTGAG 59.060 47.826 5.86 0.00 42.05 3.02
1319 1466 3.249986 CCATTGGGTTGCCACAATAAG 57.750 47.619 0.00 0.00 35.67 1.73
1332 1479 2.431419 CACAATAAGCAATGGGGATGCA 59.569 45.455 0.00 0.00 46.22 3.96
1342 1489 0.895100 TGGGGATGCAAGCAACTCAC 60.895 55.000 4.57 0.00 0.00 3.51
1419 1566 1.763545 GAAGATCTAGTGGGGGTGGAC 59.236 57.143 0.00 0.00 0.00 4.02
1462 1609 3.289836 CAATGGTTGGCAGGTGATGATA 58.710 45.455 0.00 0.00 0.00 2.15
1485 1632 3.054139 TGGAATGCTCTGTGATAAGCCTT 60.054 43.478 0.00 0.00 37.73 4.35
1594 1741 6.760770 GGTCTCCATCTCTCAAACTTATTCTG 59.239 42.308 0.00 0.00 0.00 3.02
1601 1748 7.546250 TCTCTCAAACTTATTCTGGAGAAGT 57.454 36.000 0.00 0.00 37.48 3.01
1603 1750 9.090103 TCTCTCAAACTTATTCTGGAGAAGTTA 57.910 33.333 9.00 0.00 41.39 2.24
1662 1812 4.720649 TGTCAGTGTTCTATCTAGCACC 57.279 45.455 0.00 0.00 32.75 5.01
1680 1830 3.499202 GCACCCTGGATATGGACATCATT 60.499 47.826 0.00 0.00 37.30 2.57
1714 1864 8.017418 AGAGACACTAAAGAAATATCTGGAGG 57.983 38.462 0.00 0.00 35.59 4.30
1823 1973 4.446371 GGCAGTAGAGTGATGCTTACAAT 58.554 43.478 0.00 0.00 39.88 2.71
1832 1982 6.067217 AGTGATGCTTACAATAAGGGAAGT 57.933 37.500 0.00 0.00 0.00 3.01
1839 1989 1.287425 CAATAAGGGAAGTCCGCGTC 58.713 55.000 4.92 0.00 41.52 5.19
1905 2055 1.026718 CCGAAGACAAGGCATGGGAC 61.027 60.000 0.00 0.00 0.00 4.46
1987 2137 5.308825 AGCCATTATCCGAGGAAATAGTTG 58.691 41.667 0.00 0.00 0.00 3.16
2004 2154 0.540923 TTGGCAAGTGCAAAGGCTTT 59.459 45.000 6.68 6.68 44.36 3.51
2114 2266 9.273016 GAGTTGGGAGATGATTAATAATTCGAA 57.727 33.333 0.00 0.00 0.00 3.71
2133 2286 4.404394 TCGAAGCTTGACCACATAGGAATA 59.596 41.667 2.10 0.00 41.22 1.75
2141 2294 8.129211 GCTTGACCACATAGGAATATTTTGTAC 58.871 37.037 0.00 0.00 41.22 2.90
2168 2321 6.006275 AGCTTCATATACCTTCCAACACAT 57.994 37.500 0.00 0.00 0.00 3.21
2240 2393 3.472652 ACATAGGAAACAACTTGCACGA 58.527 40.909 0.00 0.00 0.00 4.35
2249 2402 4.621068 ACAACTTGCACGATTATGGATG 57.379 40.909 0.00 0.00 0.00 3.51
2323 2476 4.438148 GAAGGCTATCTGAAGGAGTTGAC 58.562 47.826 0.00 0.00 0.00 3.18
2429 2582 2.796593 GGCAGTTGATTTGTGCAAGAAC 59.203 45.455 0.00 0.00 39.05 3.01
2431 2584 3.243643 GCAGTTGATTTGTGCAAGAACAC 59.756 43.478 0.00 0.00 41.10 3.32
2485 2639 1.419387 GGGTCTCTTGAGATGGATGGG 59.581 57.143 3.50 0.00 0.00 4.00
2489 2643 1.139654 CTCTTGAGATGGATGGGCGAA 59.860 52.381 0.00 0.00 0.00 4.70
2565 2737 4.225042 AGTCATTACACTGGGCAATAGTGA 59.775 41.667 18.51 2.42 46.52 3.41
2566 2738 5.104360 AGTCATTACACTGGGCAATAGTGAT 60.104 40.000 18.51 8.53 46.52 3.06
2567 2739 6.099701 AGTCATTACACTGGGCAATAGTGATA 59.900 38.462 18.51 8.88 46.52 2.15
2568 2740 6.425114 GTCATTACACTGGGCAATAGTGATAG 59.575 42.308 18.51 8.42 46.52 2.08
2569 2741 5.950544 TTACACTGGGCAATAGTGATAGT 57.049 39.130 18.51 0.00 46.52 2.12
2592 2767 3.884895 TGCCATCAACCACTATACCTTG 58.115 45.455 0.00 0.00 0.00 3.61
2782 2960 6.174720 ACACTTGACCTTTGTAGATCTGAA 57.825 37.500 5.18 0.00 0.00 3.02
2881 3059 2.293519 TGGGATAGAGTTGACATGGGGA 60.294 50.000 0.00 0.00 0.00 4.81
2908 3086 5.250543 TGGTATATGTATCCCCAATGGTCTG 59.749 44.000 0.00 0.00 34.77 3.51
3022 3200 3.591527 TGAGGTTATGGAATGTGAAGGGT 59.408 43.478 0.00 0.00 0.00 4.34
3103 3281 5.708697 AGATGTGAATGCAAGTGATGAGAAA 59.291 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.913335 ATTTGCCACAAGAGCATATGAG 57.087 40.909 6.97 0.00 40.59 2.90
55 56 4.522114 TCCTCACACAACAAGAATGTTCA 58.478 39.130 0.00 0.00 46.78 3.18
118 119 8.367911 TCAATATGTACTCCCATGATTACAGTC 58.632 37.037 0.00 0.00 39.22 3.51
147 156 2.472861 GTGTCATAGATGTCATTCGGCG 59.527 50.000 0.00 0.00 0.00 6.46
179 188 8.623903 AGCGCAATCAAGAAATGAATAATAGAA 58.376 29.630 11.47 0.00 42.54 2.10
303 313 9.595823 TGCATATTCTACTTCCAAGTTACTTAC 57.404 33.333 0.00 0.00 40.37 2.34
309 319 9.071276 CCAATATGCATATTCTACTTCCAAGTT 57.929 33.333 25.71 1.70 34.44 2.66
344 354 3.785887 AGGAAACCAATCTGGCATACCTA 59.214 43.478 0.00 0.00 42.67 3.08
461 472 4.357918 AACTAGCAACAAGACCAGTGAT 57.642 40.909 0.00 0.00 0.00 3.06
485 497 5.173131 GTCAACTACGGCAAACAGAATTTTG 59.827 40.000 0.00 0.00 39.15 2.44
488 500 4.134563 AGTCAACTACGGCAAACAGAATT 58.865 39.130 0.00 0.00 0.00 2.17
688 821 2.101249 ACTCACCAAACACTTTGCCATG 59.899 45.455 0.00 0.00 39.31 3.66
719 857 5.361857 AGCTATTATGAAGCACCTGCAAAAT 59.638 36.000 0.00 0.00 45.16 1.82
843 986 4.631813 AGAATTGCTAATGTCTCGGTGTTC 59.368 41.667 0.00 0.00 0.00 3.18
942 1087 1.134521 CCAAACTATACGCTGGCCTGA 60.135 52.381 14.77 0.00 0.00 3.86
955 1100 4.720046 TGTGTGCCATACTTTCCAAACTA 58.280 39.130 0.00 0.00 0.00 2.24
1081 1226 1.077212 CCTCCAACCAGCCCTCATG 60.077 63.158 0.00 0.00 0.00 3.07
1148 1293 1.997606 GTTCCCGACCAACAAGATACG 59.002 52.381 0.00 0.00 0.00 3.06
1216 1363 3.341823 TGCTCAAAGAAAGCAGAGATCC 58.658 45.455 0.00 0.00 44.51 3.36
1235 1382 4.142513 CCTTCACCTTGAAAGCTATCTTGC 60.143 45.833 0.00 0.00 35.73 4.01
1301 1448 2.255406 TGCTTATTGTGGCAACCCAAT 58.745 42.857 6.97 6.97 44.33 3.16
1313 1460 3.724374 CTTGCATCCCCATTGCTTATTG 58.276 45.455 0.00 0.00 40.77 1.90
1319 1466 0.741927 GTTGCTTGCATCCCCATTGC 60.742 55.000 0.00 0.00 40.55 3.56
1332 1479 6.262944 TCTTGACAATGTAATGTGAGTTGCTT 59.737 34.615 0.00 0.00 32.57 3.91
1342 1489 6.825213 TCTTGGGATCTCTTGACAATGTAATG 59.175 38.462 0.00 0.00 0.00 1.90
1371 1518 0.723981 GAGAGCGTGAGATGTTTGCC 59.276 55.000 0.00 0.00 0.00 4.52
1419 1566 4.204581 GCTCGAGTTTTTCTCTGTTTTCG 58.795 43.478 15.13 0.00 40.75 3.46
1462 1609 3.137913 AGGCTTATCACAGAGCATTCCAT 59.862 43.478 0.00 0.00 40.63 3.41
1485 1632 1.075374 CCAAGACCACCCATTCCAAGA 59.925 52.381 0.00 0.00 0.00 3.02
1662 1812 4.226846 AGGCTAATGATGTCCATATCCAGG 59.773 45.833 0.00 0.00 34.45 4.45
1680 1830 6.665992 TTCTTTAGTGTCTCTTCAAGGCTA 57.334 37.500 0.00 0.00 0.00 3.93
1714 1864 8.964476 TCCAATATGATCAAGTACTTCCTTTC 57.036 34.615 4.77 1.33 0.00 2.62
1799 1949 0.543749 AAGCATCACTCTACTGCCCC 59.456 55.000 0.00 0.00 36.56 5.80
1823 1973 2.879907 CGACGCGGACTTCCCTTA 59.120 61.111 12.47 0.00 0.00 2.69
1839 1989 1.572085 CTGGAGAAGCAAGTGTGGCG 61.572 60.000 0.00 0.00 36.08 5.69
1843 1993 1.131638 TGTCCTGGAGAAGCAAGTGT 58.868 50.000 0.00 0.00 0.00 3.55
1851 2001 8.059461 TCTAGTGTTAAGATATGTCCTGGAGAA 58.941 37.037 0.00 0.00 0.00 2.87
1945 2095 4.202461 TGGCTTCAACTCTGTAGGACATTT 60.202 41.667 0.00 0.00 0.00 2.32
1987 2137 0.601046 GGAAAGCCTTTGCACTTGCC 60.601 55.000 3.59 0.00 41.13 4.52
2004 2154 4.701651 CCAATTGACACAATAGCAAGAGGA 59.298 41.667 7.12 0.00 0.00 3.71
2100 2252 7.693952 TGTGGTCAAGCTTCGAATTATTAATC 58.306 34.615 0.00 0.00 0.00 1.75
2114 2266 6.891908 ACAAAATATTCCTATGTGGTCAAGCT 59.108 34.615 0.00 0.00 37.07 3.74
2133 2286 7.806180 AGGTATATGAAGCTCAGGTACAAAAT 58.194 34.615 0.00 0.00 0.00 1.82
2141 2294 4.963318 TGGAAGGTATATGAAGCTCAGG 57.037 45.455 0.00 0.00 0.00 3.86
2168 2321 5.804979 GCAGTACAAGAAGCAACTTTTCAAA 59.195 36.000 0.00 0.00 0.00 2.69
2240 2393 1.838611 ACCCCTCTGCCATCCATAAT 58.161 50.000 0.00 0.00 0.00 1.28
2249 2402 1.144936 CTCGATGAACCCCTCTGCC 59.855 63.158 0.00 0.00 0.00 4.85
2323 2476 5.008019 ACAAGTTGTAGCATGTTTCTGTCAG 59.992 40.000 6.75 0.00 0.00 3.51
2429 2582 6.631238 CGTCATAAGTAACACCAAAACAAGTG 59.369 38.462 0.00 0.00 39.93 3.16
2431 2584 6.950545 TCGTCATAAGTAACACCAAAACAAG 58.049 36.000 0.00 0.00 0.00 3.16
2564 2736 7.042335 GGTATAGTGGTTGATGGCATACTATC 58.958 42.308 18.43 12.28 32.80 2.08
2565 2737 6.730977 AGGTATAGTGGTTGATGGCATACTAT 59.269 38.462 18.74 18.74 33.95 2.12
2566 2738 6.082031 AGGTATAGTGGTTGATGGCATACTA 58.918 40.000 0.00 4.66 0.00 1.82
2567 2739 4.907875 AGGTATAGTGGTTGATGGCATACT 59.092 41.667 0.00 2.15 0.00 2.12
2568 2740 5.228945 AGGTATAGTGGTTGATGGCATAC 57.771 43.478 0.00 0.00 0.00 2.39
2569 2741 5.456042 CCAAGGTATAGTGGTTGATGGCATA 60.456 44.000 0.00 0.00 0.00 3.14
2592 2767 8.150945 TCAAATATCTTGACTCCTTACATAGCC 58.849 37.037 0.00 0.00 0.00 3.93
2782 2960 2.105477 CCCACTAGGCAGCTCATGTATT 59.895 50.000 0.00 0.00 0.00 1.89
2865 3043 2.571653 CCACTTCCCCATGTCAACTCTA 59.428 50.000 0.00 0.00 0.00 2.43
2881 3059 5.615261 ACCATTGGGGATACATATACCACTT 59.385 40.000 7.78 0.00 38.51 3.16
2908 3086 5.447818 CGTCTGCAGATTTGTTAGATTTCCC 60.448 44.000 21.47 0.00 0.00 3.97
3022 3200 5.261216 TCACTGATGAGTCCACAGTACATA 58.739 41.667 15.55 3.91 41.93 2.29
3103 3281 2.709213 GCATTCAGCAAGAGAACCTCT 58.291 47.619 0.00 0.00 43.37 3.69



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

AutoCloner maintained by Alex Coulton.