Multiple sequence alignment - TraesCS1B01G449100

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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 TraesCS1B01G449100 chr1B 100.000 1818 0 0 1 1818 667929932 667931749 0.000000e+00 3358.0
1 TraesCS1B01G449100 chr1B 94.026 837 44 6 987 1818 668031092 668030257 0.000000e+00 1264.0
2 TraesCS1B01G449100 chr1B 93.590 858 32 5 971 1815 667975787 667974940 0.000000e+00 1258.0
3 TraesCS1B01G449100 chr1B 89.863 878 41 15 987 1818 667997259 667996384 0.000000e+00 1085.0
4 TraesCS1B01G449100 chr1B 88.650 511 30 9 25 535 667976868 667976386 4.360000e-167 597.0
5 TraesCS1B01G449100 chr1B 100.000 319 0 0 2052 2370 667931983 667932301 7.300000e-165 590.0
6 TraesCS1B01G449100 chr1B 86.914 512 43 4 25 535 668032018 668031530 9.570000e-154 553.0
7 TraesCS1B01G449100 chr1B 86.041 394 34 10 541 927 668031480 668031101 1.020000e-108 403.0
8 TraesCS1B01G449100 chr1B 85.025 394 34 11 541 927 667997641 667997266 6.180000e-101 377.0
9 TraesCS1B01G449100 chr1B 86.339 366 26 6 25 390 667998709 667998368 6.180000e-101 377.0
10 TraesCS1B01G449100 chr1B 90.288 278 15 6 2091 2368 667996249 667995984 1.040000e-93 353.0
11 TraesCS1B01G449100 chr1B 91.093 247 21 1 2092 2338 667974929 667974684 1.360000e-87 333.0
12 TraesCS1B01G449100 chr1B 91.393 244 19 2 2096 2338 668029993 668029751 1.360000e-87 333.0
13 TraesCS1B01G449100 chr1B 90.625 160 15 0 376 535 667997851 667997692 1.850000e-51 213.0
14 TraesCS1B01G449100 chr1B 89.262 149 8 3 538 679 667976326 667976179 1.870000e-41 180.0
15 TraesCS1B01G449100 chr1B 88.462 130 12 3 798 926 667975901 667975774 1.130000e-33 154.0
16 TraesCS1B01G449100 chr1D 91.134 1252 65 14 538 1772 479759853 479758631 0.000000e+00 1655.0
17 TraesCS1B01G449100 chr1D 87.074 1261 118 30 573 1818 479751245 479750015 0.000000e+00 1384.0
18 TraesCS1B01G449100 chr1D 91.194 511 33 7 25 535 479760412 479759914 0.000000e+00 684.0
19 TraesCS1B01G449100 chr1D 87.867 511 39 3 25 535 479751818 479751331 1.580000e-161 579.0
20 TraesCS1B01G449100 chr1D 93.145 248 16 1 2091 2338 479750004 479749758 1.730000e-96 363.0
21 TraesCS1B01G449100 chr1D 89.655 261 24 1 1018 1278 479737852 479737595 1.760000e-86 329.0
22 TraesCS1B01G449100 chr1D 93.151 146 10 0 2165 2310 479722321 479722176 5.130000e-52 215.0
23 TraesCS1B01G449100 chr1D 94.915 59 3 0 1760 1818 479758612 479758554 2.510000e-15 93.5
24 TraesCS1B01G449100 chr1D 80.488 123 19 5 1545 1663 479737354 479737233 3.240000e-14 89.8
25 TraesCS1B01G449100 chr1D 83.333 84 6 3 2295 2370 479722161 479722078 1.180000e-08 71.3
26 TraesCS1B01G449100 chr1A 89.016 1311 71 25 538 1818 576204012 576202745 0.000000e+00 1555.0
27 TraesCS1B01G449100 chr1A 89.043 1150 77 21 538 1661 576139619 576138493 0.000000e+00 1380.0
28 TraesCS1B01G449100 chr1A 88.824 510 33 11 26 533 576204561 576204074 2.610000e-169 604.0
29 TraesCS1B01G449100 chr1A 88.889 477 41 3 69 533 576140157 576139681 5.680000e-161 577.0
30 TraesCS1B01G449100 chr1A 85.833 360 43 6 1018 1370 576078231 576077873 2.220000e-100 375.0
31 TraesCS1B01G449100 chr1A 89.606 279 18 4 2092 2370 576138376 576138109 6.270000e-91 344.0
32 TraesCS1B01G449100 chr1A 91.600 250 20 1 2089 2338 576202736 576202488 6.270000e-91 344.0
33 TraesCS1B01G449100 chr1A 86.667 120 4 7 1699 1818 576138494 576138387 3.200000e-24 122.0
34 TraesCS1B01G449100 chr1A 81.452 124 16 7 1545 1663 576077757 576077636 6.970000e-16 95.3


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 TraesCS1B01G449100 chr1B 667929932 667932301 2369 False 1974.000000 3358 100.000000 1 2370 2 chr1B.!!$F1 2369
1 TraesCS1B01G449100 chr1B 668029751 668032018 2267 True 638.250000 1264 89.593500 25 2338 4 chr1B.!!$R3 2313
2 TraesCS1B01G449100 chr1B 667974684 667976868 2184 True 504.400000 1258 90.211400 25 2338 5 chr1B.!!$R1 2313
3 TraesCS1B01G449100 chr1B 667995984 667998709 2725 True 481.000000 1085 88.428000 25 2368 5 chr1B.!!$R2 2343
4 TraesCS1B01G449100 chr1D 479758554 479760412 1858 True 810.833333 1655 92.414333 25 1818 3 chr1D.!!$R4 1793
5 TraesCS1B01G449100 chr1D 479749758 479751818 2060 True 775.333333 1384 89.362000 25 2338 3 chr1D.!!$R3 2313
6 TraesCS1B01G449100 chr1D 479737233 479737852 619 True 209.400000 329 85.071500 1018 1663 2 chr1D.!!$R2 645
7 TraesCS1B01G449100 chr1A 576202488 576204561 2073 True 834.333333 1555 89.813333 26 2338 3 chr1A.!!$R3 2312
8 TraesCS1B01G449100 chr1A 576138109 576140157 2048 True 605.750000 1380 88.551250 69 2370 4 chr1A.!!$R2 2301
9 TraesCS1B01G449100 chr1A 576077636 576078231 595 True 235.150000 375 83.642500 1018 1663 2 chr1A.!!$R1 645


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
381 934 0.178068 AGATTATCACGCCCGCAAGT 59.822 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 2322 1.165284 TGCACGCACATGCTTCTTCA 61.165 50.0 1.82 0.0 46.28 3.02 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
196 197 4.320608 TTGTAGATAGCGACATGATGCA 57.679 40.909 14.54 0.00 29.63 3.96
273 295 7.786030 TCTTTATCTTGGTGTTATCCTCTCTG 58.214 38.462 0.00 0.00 0.00 3.35
381 934 0.178068 AGATTATCACGCCCGCAAGT 59.822 50.000 0.00 0.00 0.00 3.16
448 1004 7.126398 GCTATTTTGCGGAGTAAATAAGAGTG 58.874 38.462 0.00 0.00 42.52 3.51
535 1091 6.438425 AGCTTTGATTCACTAACCATGGATTT 59.562 34.615 21.47 5.69 0.00 2.17
548 1163 6.089249 ACCATGGATTTTTGTCTCAACTTC 57.911 37.500 21.47 0.00 0.00 3.01
689 1321 3.010250 AGGGCCGAAAAGATAGAAAGGTT 59.990 43.478 0.00 0.00 0.00 3.50
691 1323 3.128764 GGCCGAAAAGATAGAAAGGTTGG 59.871 47.826 0.00 0.00 0.00 3.77
794 1429 6.072452 CCGCTTGAAAATTCCTCTAGTTTTCT 60.072 38.462 13.53 0.00 40.62 2.52
833 1630 0.936764 CATCGTCCATCTTCTCCGCG 60.937 60.000 0.00 0.00 0.00 6.46
912 1770 1.798626 TCCTCATCCATCTCACCAGG 58.201 55.000 0.00 0.00 0.00 4.45
913 1771 1.008815 TCCTCATCCATCTCACCAGGT 59.991 52.381 0.00 0.00 0.00 4.00
914 1772 1.415659 CCTCATCCATCTCACCAGGTC 59.584 57.143 0.00 0.00 0.00 3.85
916 1774 1.206878 CATCCATCTCACCAGGTCCA 58.793 55.000 0.00 0.00 0.00 4.02
918 1776 1.279496 TCCATCTCACCAGGTCCAAG 58.721 55.000 0.00 0.00 0.00 3.61
919 1777 0.393537 CCATCTCACCAGGTCCAAGC 60.394 60.000 0.00 0.00 0.00 4.01
924 1782 1.133181 TCACCAGGTCCAAGCATCCA 61.133 55.000 0.00 0.00 0.00 3.41
927 1785 1.318158 CCAGGTCCAAGCATCCAAGC 61.318 60.000 0.00 0.00 0.00 4.01
928 1786 0.609957 CAGGTCCAAGCATCCAAGCA 60.610 55.000 0.00 0.00 36.85 3.91
930 1788 1.565759 AGGTCCAAGCATCCAAGCATA 59.434 47.619 0.00 0.00 36.85 3.14
931 1789 1.952296 GGTCCAAGCATCCAAGCATAG 59.048 52.381 0.00 0.00 36.85 2.23
932 1790 2.648059 GTCCAAGCATCCAAGCATAGT 58.352 47.619 0.00 0.00 36.85 2.12
933 1791 3.019564 GTCCAAGCATCCAAGCATAGTT 58.980 45.455 0.00 0.00 36.85 2.24
934 1792 3.065925 GTCCAAGCATCCAAGCATAGTTC 59.934 47.826 0.00 0.00 36.85 3.01
935 1793 3.018856 CCAAGCATCCAAGCATAGTTCA 58.981 45.455 0.00 0.00 36.85 3.18
936 1794 3.066342 CCAAGCATCCAAGCATAGTTCAG 59.934 47.826 0.00 0.00 36.85 3.02
937 1795 2.928334 AGCATCCAAGCATAGTTCAGG 58.072 47.619 0.00 0.00 36.85 3.86
938 1796 2.240667 AGCATCCAAGCATAGTTCAGGT 59.759 45.455 0.00 0.00 36.85 4.00
939 1797 2.615912 GCATCCAAGCATAGTTCAGGTC 59.384 50.000 0.00 0.00 0.00 3.85
940 1798 3.877559 CATCCAAGCATAGTTCAGGTCA 58.122 45.455 0.00 0.00 0.00 4.02
941 1799 4.458397 CATCCAAGCATAGTTCAGGTCAT 58.542 43.478 0.00 0.00 0.00 3.06
942 1800 5.614308 CATCCAAGCATAGTTCAGGTCATA 58.386 41.667 0.00 0.00 0.00 2.15
943 1801 5.692115 TCCAAGCATAGTTCAGGTCATAA 57.308 39.130 0.00 0.00 0.00 1.90
944 1802 5.428253 TCCAAGCATAGTTCAGGTCATAAC 58.572 41.667 0.00 0.00 0.00 1.89
945 1803 5.189736 TCCAAGCATAGTTCAGGTCATAACT 59.810 40.000 0.00 0.00 39.25 2.24
946 1804 5.882557 CCAAGCATAGTTCAGGTCATAACTT 59.117 40.000 0.00 0.00 37.19 2.66
947 1805 7.047891 CCAAGCATAGTTCAGGTCATAACTTA 58.952 38.462 0.00 0.00 37.19 2.24
948 1806 7.552687 CCAAGCATAGTTCAGGTCATAACTTAA 59.447 37.037 0.00 0.00 37.19 1.85
949 1807 8.607459 CAAGCATAGTTCAGGTCATAACTTAAG 58.393 37.037 0.00 0.00 37.19 1.85
950 1808 7.275920 AGCATAGTTCAGGTCATAACTTAAGG 58.724 38.462 7.53 0.00 37.19 2.69
951 1809 7.048512 GCATAGTTCAGGTCATAACTTAAGGT 58.951 38.462 7.53 2.03 37.19 3.50
952 1810 8.202137 GCATAGTTCAGGTCATAACTTAAGGTA 58.798 37.037 1.94 1.94 37.19 3.08
974 1832 8.985922 AGGTATATAATAGCAGCTGATTGATCA 58.014 33.333 20.43 0.00 35.16 2.92
985 1845 5.591472 CAGCTGATTGATCAAGGAACCAATA 59.409 40.000 8.42 0.00 36.18 1.90
1020 1880 1.550327 TGGCTTCTCTGTCGATGAGT 58.450 50.000 14.99 0.00 33.59 3.41
1392 2287 1.202770 AGGCGGTAATCTGGTAATGGC 60.203 52.381 0.00 0.00 0.00 4.40
1409 2304 1.638070 TGGCCAAGGGATGATACACAA 59.362 47.619 0.61 0.00 0.00 3.33
1524 2432 6.366332 GTCAATGTATACATGCACTACTAGCC 59.634 42.308 18.94 0.00 36.56 3.93
2124 3094 2.100916 GGCTTAGCATCTCGTTGAGGTA 59.899 50.000 6.53 0.00 0.00 3.08
2197 3167 2.104111 TGTGACAAAGGACGGAGAACAT 59.896 45.455 0.00 0.00 0.00 2.71
2201 3171 2.086869 CAAAGGACGGAGAACATGCAT 58.913 47.619 0.00 0.00 0.00 3.96
2289 3260 0.971447 GGGTTGCTACCTCTCCTCGT 60.971 60.000 17.03 0.00 44.38 4.18
2339 3310 3.240670 TCCCGCAGATATTGGGAGT 57.759 52.632 0.00 0.00 46.96 3.85
2340 3311 1.507140 TCCCGCAGATATTGGGAGTT 58.493 50.000 0.00 0.00 46.96 3.01
2341 3312 1.843851 TCCCGCAGATATTGGGAGTTT 59.156 47.619 0.00 0.00 46.96 2.66
2342 3313 1.949525 CCCGCAGATATTGGGAGTTTG 59.050 52.381 0.00 0.00 46.41 2.93
2343 3314 1.949525 CCGCAGATATTGGGAGTTTGG 59.050 52.381 4.34 0.00 42.02 3.28
2344 3315 1.949525 CGCAGATATTGGGAGTTTGGG 59.050 52.381 0.00 0.00 42.02 4.12
2345 3316 2.421388 CGCAGATATTGGGAGTTTGGGA 60.421 50.000 0.00 0.00 42.02 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.964934 CGACTGTGCCTATGGTTTTATTAAAC 59.035 38.462 0.00 0.00 42.34 2.01
19 20 6.655848 ACGACTGTGCCTATGGTTTTATTAAA 59.344 34.615 0.00 0.00 0.00 1.52
20 21 6.092944 CACGACTGTGCCTATGGTTTTATTAA 59.907 38.462 0.00 0.00 39.67 1.40
21 22 5.583061 CACGACTGTGCCTATGGTTTTATTA 59.417 40.000 0.00 0.00 39.67 0.98
22 23 4.394920 CACGACTGTGCCTATGGTTTTATT 59.605 41.667 0.00 0.00 39.67 1.40
23 24 3.938963 CACGACTGTGCCTATGGTTTTAT 59.061 43.478 0.00 0.00 39.67 1.40
38 39 3.469629 CAACGAATTTAGTGCACGACTG 58.530 45.455 12.01 1.66 35.96 3.51
366 388 0.533491 AACTACTTGCGGGCGTGATA 59.467 50.000 0.00 0.00 0.00 2.15
432 988 6.338146 TCCATGTTCACTCTTATTTACTCCG 58.662 40.000 0.00 0.00 0.00 4.63
435 991 9.601217 GTACATCCATGTTCACTCTTATTTACT 57.399 33.333 0.00 0.00 41.97 2.24
448 1004 6.149308 TGAACTGTTCATGTACATCCATGTTC 59.851 38.462 18.69 19.06 42.29 3.18
535 1091 6.456449 GCTTTCGTAGTTGAAGTTGAGACAAA 60.456 38.462 0.00 0.00 0.00 2.83
548 1163 7.119360 CACATACATGTATGCTTTCGTAGTTG 58.881 38.462 35.22 22.00 45.06 3.16
770 1403 6.903419 AGAAAACTAGAGGAATTTTCAAGCG 58.097 36.000 14.44 0.00 42.30 4.68
775 1408 7.119992 GTGGAGGAGAAAACTAGAGGAATTTTC 59.880 40.741 0.00 2.03 40.88 2.29
794 1429 1.409064 GATGTGCATACGAGTGGAGGA 59.591 52.381 0.00 0.00 0.00 3.71
833 1630 0.244721 GGATTCAGCTTTGTGTGGGC 59.755 55.000 0.00 0.00 0.00 5.36
912 1770 2.648059 ACTATGCTTGGATGCTTGGAC 58.352 47.619 0.00 0.00 0.00 4.02
913 1771 3.282021 GAACTATGCTTGGATGCTTGGA 58.718 45.455 0.00 0.00 0.00 3.53
914 1772 3.018856 TGAACTATGCTTGGATGCTTGG 58.981 45.455 0.00 0.00 0.00 3.61
916 1774 3.285484 CCTGAACTATGCTTGGATGCTT 58.715 45.455 0.00 0.00 0.00 3.91
918 1776 2.615912 GACCTGAACTATGCTTGGATGC 59.384 50.000 0.00 0.00 0.00 3.91
919 1777 3.877559 TGACCTGAACTATGCTTGGATG 58.122 45.455 0.00 0.00 0.00 3.51
924 1782 7.770897 CCTTAAGTTATGACCTGAACTATGCTT 59.229 37.037 0.97 0.00 34.81 3.91
947 1805 9.829507 GATCAATCAGCTGCTATTATATACCTT 57.170 33.333 9.47 0.00 0.00 3.50
948 1806 8.985922 TGATCAATCAGCTGCTATTATATACCT 58.014 33.333 9.47 0.00 32.11 3.08
949 1807 9.605275 TTGATCAATCAGCTGCTATTATATACC 57.395 33.333 9.47 0.00 38.19 2.73
951 1809 9.828039 CCTTGATCAATCAGCTGCTATTATATA 57.172 33.333 9.47 0.00 38.19 0.86
952 1810 8.546322 TCCTTGATCAATCAGCTGCTATTATAT 58.454 33.333 9.47 2.25 38.19 0.86
953 1811 7.910584 TCCTTGATCAATCAGCTGCTATTATA 58.089 34.615 9.47 0.00 38.19 0.98
954 1812 6.776744 TCCTTGATCAATCAGCTGCTATTAT 58.223 36.000 9.47 0.00 38.19 1.28
955 1813 6.178607 TCCTTGATCAATCAGCTGCTATTA 57.821 37.500 9.47 0.00 38.19 0.98
956 1814 5.045012 TCCTTGATCAATCAGCTGCTATT 57.955 39.130 9.47 1.26 38.19 1.73
957 1815 4.701651 TCCTTGATCAATCAGCTGCTAT 57.298 40.909 9.47 0.00 38.19 2.97
958 1816 4.194640 GTTCCTTGATCAATCAGCTGCTA 58.805 43.478 9.47 0.00 38.19 3.49
959 1817 3.015327 GTTCCTTGATCAATCAGCTGCT 58.985 45.455 9.47 0.00 38.19 4.24
960 1818 2.098770 GGTTCCTTGATCAATCAGCTGC 59.901 50.000 9.47 0.00 38.19 5.25
961 1819 3.349927 TGGTTCCTTGATCAATCAGCTG 58.650 45.455 8.96 7.63 38.19 4.24
962 1820 3.726557 TGGTTCCTTGATCAATCAGCT 57.273 42.857 8.96 0.00 38.19 4.24
963 1821 4.996788 ATTGGTTCCTTGATCAATCAGC 57.003 40.909 8.96 6.29 38.19 4.26
964 1822 6.018425 CGACTATTGGTTCCTTGATCAATCAG 60.018 42.308 8.96 1.31 38.19 2.90
965 1823 5.817296 CGACTATTGGTTCCTTGATCAATCA 59.183 40.000 8.96 0.00 32.81 2.57
966 1824 6.049149 TCGACTATTGGTTCCTTGATCAATC 58.951 40.000 8.96 0.00 32.81 2.67
967 1825 5.989477 TCGACTATTGGTTCCTTGATCAAT 58.011 37.500 8.96 0.00 34.65 2.57
968 1826 5.046591 ACTCGACTATTGGTTCCTTGATCAA 60.047 40.000 8.12 8.12 0.00 2.57
969 1827 4.466370 ACTCGACTATTGGTTCCTTGATCA 59.534 41.667 0.00 0.00 0.00 2.92
974 1832 3.576982 TGTCACTCGACTATTGGTTCCTT 59.423 43.478 0.00 0.00 43.06 3.36
985 1845 0.176680 GCCATGGATGTCACTCGACT 59.823 55.000 18.40 0.00 43.06 4.18
999 1859 2.159128 ACTCATCGACAGAGAAGCCATG 60.159 50.000 20.10 0.00 36.91 3.66
1204 2064 2.284112 ACGGTAGGCGGGGAAAGA 60.284 61.111 0.00 0.00 0.00 2.52
1304 2196 1.289160 ACTCCAGCTTAAGCCCATGA 58.711 50.000 23.71 13.46 43.38 3.07
1392 2287 5.436175 TGTGTATTGTGTATCATCCCTTGG 58.564 41.667 0.00 0.00 0.00 3.61
1409 2304 6.550938 TCTTCATTCAGTCCATCTGTGTAT 57.449 37.500 0.00 0.00 43.97 2.29
1427 2322 1.165284 TGCACGCACATGCTTCTTCA 61.165 50.000 1.82 0.00 46.28 3.02
1459 2360 5.236263 CCATGCACACGCTTATGAGTATTAA 59.764 40.000 0.00 0.00 39.64 1.40
1517 2425 2.614481 CCAACTTTTCTGCCGGCTAGTA 60.614 50.000 29.70 14.07 0.00 1.82
1668 2606 9.976255 GTTACAACGTGCAGACAATAATATAAA 57.024 29.630 0.00 0.00 0.00 1.40
2094 3064 2.816672 GAGATGCTAAGCCCTAAATGCC 59.183 50.000 0.00 0.00 0.00 4.40
2102 3072 1.576356 CTCAACGAGATGCTAAGCCC 58.424 55.000 0.00 0.00 0.00 5.19
2167 3137 6.411376 TCCGTCCTTTGTCACATAATATTGT 58.589 36.000 0.00 0.00 0.00 2.71
2182 3152 2.290260 TGATGCATGTTCTCCGTCCTTT 60.290 45.455 2.46 0.00 0.00 3.11
2197 3167 4.160626 TCTGCCATTTGATCAATTGATGCA 59.839 37.500 25.37 22.74 34.37 3.96
2201 3171 3.764972 TGCTCTGCCATTTGATCAATTGA 59.235 39.130 24.96 11.26 0.00 2.57
2289 3260 3.495001 TCAACAACAACGATGAACGCATA 59.505 39.130 0.00 0.00 46.94 3.14



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

AutoCloner maintained by Alex Coulton.