# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file:                         RF00001.cm
# target sequence database:              GCA_000146045.2.fasta
# tabular output of hits:                cmsearch_114_5S_Yeast.tbl
# sequence reporting threshold:          score >= 38
# number of worker threads:              56
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       5S_rRNA  [CLEN=119]
Accession:   RF00001
Description: 5S ribosomal RNA
Hit scores:
 rank     E-value  score  bias  sequence                 start    end   mdl trunc   gc  description
 ----   --------- ------ -----  ----------------------- ------ ------   --- ----- ----  -----------
  (1) !   1.6e-18   88.8   0.0  ENA|BK006945|BK006945.2 459676 459796 +  cm    no 0.52  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
  (2) !   1.6e-18   88.8   0.0  ENA|BK006945|BK006945.2 489349 489469 +  cm    no 0.52  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
  (3) !   4.4e-17   83.2   0.0  ENA|BK006945|BK006945.2 468813 468933 +  cm    no 0.53  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
  (4) !   4.4e-17   83.2   0.0  ENA|BK006945|BK006945.2 472465 472585 +  cm    no 0.53  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
  (5) !   4.4e-17   83.2   0.0  ENA|BK006945|BK006945.2 482045 482165 +  cm    no 0.53  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
  (6) !   4.4e-17   83.2   0.0  ENA|BK006945|BK006945.2 485697 485817 +  cm    no 0.53  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII


Hit alignments:
>> ENA|BK006945|BK006945.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   1.6e-18   88.8   0.0  cm        1      119 []      459676      459796 + .. 0.99    no 0.52

                                                                                                                v NC
                                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
                  5S_rRNA      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78    
                                 G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G:    GUA 
  ENA|BK006945|BK006945.2 459676 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 459755
                                 ***********************************************99***********************8756**** PP

                                 v                  vv                     NC
                                 <-----<<____>>----->>->-->>->>>))))))))): CS
                  5S_rRNA     79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119   
                                  +  +UGGGUGACC+   G  AA  :CAGGUGC:GCA::C+
  ENA|BK006945|BK006945.2 459756 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU 459796
                                 ***********************9***************** PP

>> ENA|BK006945|BK006945.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (2) !   1.6e-18   88.8   0.0  cm        1      119 []      489349      489469 + .. 0.99    no 0.52

                                                                                                                v NC
                                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
                  5S_rRNA      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78    
                                 G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G:    GUA 
  ENA|BK006945|BK006945.2 489349 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 489428
                                 ***********************************************99***********************8756**** PP

                                 v                  vv                     NC
                                 <-----<<____>>----->>->-->>->>>))))))))): CS
                  5S_rRNA     79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119   
                                  +  +UGGGUGACC+   G  AA  :CAGGUGC:GCA::C+
  ENA|BK006945|BK006945.2 489429 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU 489469
                                 ***********************9***************** PP

>> ENA|BK006945|BK006945.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (3) !   4.4e-17   83.2   0.0  cm        1      119 []      468813      468933 + .. 0.99    no 0.53

                                                                                                                v NC
                                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
                  5S_rRNA      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78    
                                  : UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G:    GUA 
  ENA|BK006945|BK006945.2 468813 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 468892
                                 ***********************************************99***********************8756**** PP

                                 v                  vv                     NC
                                 <-----<<____>>----->>->-->>->>>))))))))): CS
                  5S_rRNA     79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119   
                                  +  +UGGGUGACC+   G  AA  :CAGGUGC:GCA :  
  ENA|BK006945|BK006945.2 468893 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 468933
                                 ***********************9***************** PP

>> ENA|BK006945|BK006945.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (4) !   4.4e-17   83.2   0.0  cm        1      119 []      472465      472585 + .. 0.99    no 0.53

                                                                                                                v NC
                                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
                  5S_rRNA      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78    
                                  : UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G:    GUA 
  ENA|BK006945|BK006945.2 472465 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 472544
                                 ***********************************************99***********************8756**** PP

                                 v                  vv                     NC
                                 <-----<<____>>----->>->-->>->>>))))))))): CS
                  5S_rRNA     79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119   
                                  +  +UGGGUGACC+   G  AA  :CAGGUGC:GCA :  
  ENA|BK006945|BK006945.2 472545 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 472585
                                 ***********************9***************** PP

>> ENA|BK006945|BK006945.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (5) !   4.4e-17   83.2   0.0  cm        1      119 []      482045      482165 + .. 0.99    no 0.53

                                                                                                                v NC
                                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
                  5S_rRNA      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78    
                                  : UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G:    GUA 
  ENA|BK006945|BK006945.2 482045 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 482124
                                 ***********************************************99***********************8756**** PP

                                 v                  vv                     NC
                                 <-----<<____>>----->>->-->>->>>))))))))): CS
                  5S_rRNA     79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119   
                                  +  +UGGGUGACC+   G  AA  :CAGGUGC:GCA :  
  ENA|BK006945|BK006945.2 482125 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 482165
                                 ***********************9***************** PP

>> ENA|BK006945|BK006945.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (6) !   4.4e-17   83.2   0.0  cm        1      119 []      485697      485817 + .. 0.99    no 0.53

                                                                                                                v NC
                                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
                  5S_rRNA      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78    
                                  : UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G:    GUA 
  ENA|BK006945|BK006945.2 485697 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 485776
                                 ***********************************************99***********************8756**** PP

                                 v                  vv                     NC
                                 <-----<<____>>----->>->-->>->>>))))))))): CS
                  5S_rRNA     79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119   
                                  +  +UGGGUGACC+   G  AA  :CAGGUGC:GCA :  
  ENA|BK006945|BK006945.2 485777 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 485817
                                 ***********************9***************** PP



Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (119 consensus positions)
Target sequences:                                               16  (24142652 residues searched)
Target sequences re-searched for truncated hits:                16  (12416 residues re-searched)
Windows   passing  local HMM SSV           filter:           24991  (0.2423); expected (0.35)
Windows   passing  local HMM Viterbi       filter:            8464  (0.08504); expected (0.15)
Windows   passing  local HMM Viterbi  bias filter:            8432  (0.08473); expected (0.15)
Windows   passing  local HMM Forward       filter:             135  (0.001502); expected (0.003)
Windows   passing  local HMM Forward  bias filter:             134  (0.001493); expected (0.003)
Windows   passing glocal HMM Forward       filter:              65  (0.0007404); expected (0.003)
Windows   passing glocal HMM Forward  bias filter:              65  (0.0007404); expected (0.003)
Envelopes passing glocal HMM envelope defn filter:              61  (0.0003446); expected (0.003)
Envelopes passing  local CM  CYK           filter:              15  (6.52e-05); expected (0.0001)
Total CM hits reported:                                          6  (3.006e-05); includes 0 truncated hit(s)

# CPU time: 3.96u 0.20s 00:00:04.16 Elapsed: 00:00:00.36
//
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