Sample THEME output is provided below.
For each hypothesis tested THEME provides:

1. A text logo of the unrefined hypothesis.
2. A text logo of the best refined hypothesis and the optimal value of the hypothesis weighting (Beta) determined by cross-validation 
3. The mean cross-validation error achieved by the best refined hypothesis
4. The log-likelihood ratio score used as a matching threshold by the SVM classifier and the number of true and false positives in the input set at this threshold
5. A list of matches to the motif in the input set

Matches are output in the following format:
sequence_name------> offset_1: matching_sequence .... offset_n: matching_sequence


-------BEGIN SAMPLE OUTPUT---------


Loading Markov background file from /cluster/macisaac/con/Utilities/human_6th_order.bg
Processing input sequences....
---------------New Hypothesis---------------
Unrefined Hypothesis: ..RGGTCA (0)
Refined Hypothesis: ..rGGtCA (88) Optimal Beta: 0.333333
Mean 3-fold cv error: 0.418485
LLR match threshold: 0.773461 True positives: 51 False Negatives: 13
Motif matches in positive input set:
NM_004590------>  139: GGAGGTCA 697: CAAGGTCA 
NM_001622------>  118: TGCCCTTG 
NM_013952------>  90: CAAGGTCA 421: TGACCTTT 584: TGACCTTC 666: AGAGGTCA 755: AGGGGTCA 
NM_004768------>  192: TGCCCTTG 
NM_000040------>  737: TGACCTTT 794: ACAGGTCA 
NM_025032------>  483: TGCCCTTG 779: AAGGGTCA 915: TGACCCTT 1092: CAGGGTCA 
NM_000773------>  560: CCAGGTCA 
NM_006402------>  765: AGGGGTCA 
NM_000638------>  512: AAAGGTCA 582: TTAGGTCA 
NM_002490------>  132: TGACCCTC 179: TGACCTCA 1258: ATAGGTCA 1322: CTAGGTCA 
NM_018045------>  418: TGACCTTT 1103: TAAGGTCA 
NM_005513------>  1161: TGACCCCG 
NM_018295------>  651: TGACCTGG 1339: TGACCCTC 
NM_004512------>  52: TGACCTGG 
NM_015471------>  373: GAGGGTCA 762: TGACCTTG 
NM_031479------>  429: CAGGGTCA 979: CCAGGTCA 1006: GAGGGTCA 
NM_030579------>  14: TGAGGTCA 
NM_002633------>  85: TGACCTTG 613: TGACCCTC 
NM_006895------>  366: TGACCTTC 487: TGACCTCG 943: TGACCTTT 
NM_002790------>  114: TGACCCTT 
NM_000504------>  250: GAAGGTCA 1196: AGAGGTCA 
NM_018129------>  735: TGACCTCT 
NM_021969------>  141: AAAGGTCA 767: CAAGGTCA 1271: TGAGGTCA 
NM_015940------>  31: TGACCTCA 1121: TAGGGTCA 
NM_016327------>  107: TGACCTTC 1288: TGACCTTT 
NM_016953------>  33: TGACCCTG 
NM_000029------>  477: TGACCCTG 505: TGACCTTC 
NM_001671------>  778: TGACCCTG 978: TCAGGTCA 1074: CAGGGTCA 
NM_000606------>  543: AGAGGTCA 
NM_014748------>  486: AGGGGTCA 
NM_000602------>  510: TGACCTGG 664: AAAGGTCA 
NM_001610------>  153: CCAGGTCA 
NM_001914------>  191: ACAGGTCA 1087: TGACCCCG 
NM_000106------>  511: TGACCCTT 839: TGACCTTG 880: TGACCTTC 
NM_004433------>  569: TCAGGTCA 1208: GAGGGTCA 
NM_001155------>  308: GAGGGTCA 858: TGACCTGT 
NM_138482------>  1021: TGACCCCG 1226: CAAGGGCA 
NM_002217------>  194: TAAGGTCA 881: TGACCCTG 1341: TGACCTCT 
NM_002218------>  489: TGACCTCA 
NM_018148------>  958: TGACCTGG 1390: TGCCCTTG 
NM_001859------>  490: CAGGGTCA 1142: TGACCTGG 1329: TGACCTTG 
NM_016518------>  514: TGACCTCA 
NM_013249------>  324: TGACCCTC 784: TGACCCTC 
NM_015950------>  5: CAAGGTCA 735: TGACCTCG 
NM_019043------>  397: CGGGGTCA 
NM_000416------>  482: CGGGGTCA 
NG_000853------>  501: TGACCCTT 829: TGACCTTG 870: TGACCTTC 
NM_032562------>  77: TGACCTCT 874: AAGGGTCA 1375: TGAGGTCA 
NM_005952------>  8: TGACCCTG 
NM_015216------>  257: TGACCTCA 
NM_005951------>  102: CAGGGTCA 164: AGAGGTCA 1066: GGAGGTCA