HMM length of domain: 22 aa

c-Evalue (conditional Evalue): It is an attempt to measure the statistical significance of each domain, given that we’ve already decided that the target sequence is a true homolog. It is the expected number of additional domains we’d find with a domain score this big in the set of sequences reported in the top hits list, if those sequences consisted only of random nonhomologous sequence outside the region that sufficed to define them as homologs.
i-Evalue (independent Evalue): The significance of the sequence in the whole database search, if this were the only domain we had identified. 
Domain annotation for each sequence:
#	score	bias	c-Evalue	i-Evalue	hmmfrom	hmm to	alifrom	ali to
--	-----	----	--------	--------	-------	------	-------	------
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
1	2.6	3.2	0.0062	1.1e+02	11	16	13	18
2	-1.2	2.1	0.092	1.5e+03	12	15	32	35
3	25.6	2.2	3.9e-10	6.6e-06	4	21	52	69
4	-3.8	6.9	0.61	1e+04	10	15	79	84
5	-5.3	1.3	1	1.7e+04	6	9	89	92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0062
           HMGA 11 PRGRPK 16
                    RGRPK
  KWMTBOMO13303 13 GRGRPK 18
                   5****9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.092
           HMGA 12 RGRP 15
                   RGRP
  KWMTBOMO13303 32 RGRP 35
                   9**9 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 3.9e-10
           HMGA  4 gvPsPKRPRGRPKGSKNK 21
                   + P  KR RGRPKGSK+K
  KWMTBOMO13303 52 QAPVAKRGRGRPKGSKKK 69
                   56778************9 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 0.61
           HMGA 10 RPRGRP 15
                   R RGRP
  KWMTBOMO13303 79 RGRGRP 84
                   679**9 PP

  == domain 5  score: -5.3 bits;  conditional E-value: 1
           HMGA  6 PsPK 9 
                   P PK
  KWMTBOMO13303 89 PPPK 92
                   7787 PP