outnolp bug

[martin-raden]

bugs for the following example:

• right-most is lonely
• right-most bp of seed is not in interaction

 --> ./IntaRNA --mode=M --outNoLP --tAccW=0 --qAccW=0 --tAccL=0 --qAccL=0 --qIntLenMax=80 --tIntLenMax=80 --qIntLoopMax=10 --tIntLoopMax=10 --seedNoGU -q uggucggugcaugugauuacgucguacggggggggauggcauagccgacg  -t cgcgggcccgcgcguugcgcgcgcgcccgcggcccccuuugagugugagucccccccccc --outmode=D

target
            44                 58
             |                 |
5'-CGC...UGAG    A        C     CC-3'
             UGUG GUCCCCCC     C
             |||| :+++++++     |
             ACGG UAGGGGGG     G
3'-GCA...CGAU             GGCAU CUGC...GGU-5'
             |                 |
            41                 24
query

interaction seq1   = 44--58
interaction seq2   = 24--41

interaction energy = -1.07374e+07 kcal/mol
  = E(init)        = 4.1
  + E(loops)       = -1.07375e+07
  + E(dangleLeft)  = -0.57
  + E(dangleRight) = -0.92
  + E(endLeft)     = 0.5
  + E(endRight)    = 0
    : E(hybrid)    = -1.07375e+07
  + ED(seq1)       = 0.56
    : Pu(seq1)     = 0.403081
  + ED(seq2)       = 12.01
    : Pu(seq2)     = 3.44409e-09

seed seq1   = 51--57 | 50--56
seed seq2   = 29--35 | 30--36
seed energy = -9.57 | -7.74
seed ED1    = 0.21 | 0.26
seed ED2    = 6.49 | 7.19
seed Pu1    = 0.71125 | 0.655827
seed Pu2    = 2.67165e-05 | 8.58063e-06