Table 1. Training set composition of the different HMM models.

Name of HMM	Test Set	Number of match states	Average length of LTRs in training set	Average score of training set	Number of LTRs in training set	Human beta	Mouse beta	Chicken alpha beta	Alpha	Lenti	Delta	Human gamma	Exogenous gamma
Hml	Jackknifing	170	728	40	23	23
Gamma	Jackknifing	110	630	22	72							69	3
Beta	Lenti (8 sequences)	110	611	11	175	23	138	2	4		8
Lenti	Jackknifing	190	386	45	37					37
General	Lenti (8 sequences)	130	624	5.5	178	23	69	2	4		8	69	3