ry range: 1-400  (total 400)

 Target: /data/www-rg/seblastian_results/541244304/tempfiles/temptarget.fasta
 Chromosome: KV884750.1:subseq_2720142,100000_ Strand: -
 Positions:
 -Exon 1  54668        54724
 -Exon 2  52901        52969
 -Exon 3  52218        52326
 -Exon 4  51859        51933
 -Exon 5  50374        50636
 -Exon 6  49892        50000
 -Exon 7  49762        49810
 -Exon 8  49488        49668
 -Exon 9  49200        49379
 -Exon 10 49009        49113

 Redox box: no

Query   MALYHYVTQEQLSGFDKYK <---Intron---> YSAVDSNPLSIYVMHPFWNSVVK <---Intron---> VLPTWLAPNLITFTGFMFLVLTFTML
        | || |||||||/|||||| <   1698bp   > ||||||||||||/|||||| ||| <   574bp    >  |||||||||||||||| ||  | ||
Target  MDLYEYVTQEQLAGFDKYK                YSAVDSNPLSIYIMHPFWNFVVK                FLPTWLAPNLITFTGFMLLVFNFLML
        agctgtgacgccggtgata                tagggtacttataaccttatgga                tccattgcacaatagtatcgtatcat
        tataaatcaaatcgtaaaa                agctacactctattactgattta                ttccgtccattctcgttttttatttt
        gttcatctgggtgactacg                ccagcctcgactcgctcgttggg                taaaggtacctacactggtgccttgg
                                                                                                            

Query   SFFDFDFYASG <---Intron---> EGHTHVPSWVWIAAGLFNFLAYTLD <---Intron---> GVDGKQARRTNSSTPLGELFDHGLDSWACVFF
        /|||||| ||  <   284bp    >     |||||||/|||/||||||||| <   1222bp   > |||||||||||||||||||||||||||||/||
Target  AFFDFDFTASA                AMQEHVPSWVWVAAGIFNFLAYTLD                GVDGKQARRTNSSTPLGELFDHGLDSWACLFF
        gttgtgtagtg                gacgcgcatgtggggatattgtacg                ggggacgccaattaccggctgcgcgatgtctt
        cttatatccc                cctaaatcggtgtccgttattcact                agtagaacggcacccctgattaagtaggcgttt
        cctctccatt                taggacgttgcgttagccccgctat                tttttagaaccccggagggttctcgccgcccct
                                                                                                            

Query   VATVYSVFGRGETGVSVVTLYYLLWVVLFSFILSHWEKYNTGILFLPWGYDISQV <---Intron---> TISIVYIITAVVGVETWYKPVFLNIHYRD
        ||||||/|||||/|| | ||||/|||||||||||||||||||||||||||||||| <   373bp    > |/|/|///||||||||||/|/  // |/|
Target  VATVYSIFGRGESGVDVATLYYILWVVLFSFILSHWEKYNTGILFLPWGYDISQV                TVSVVFLVTAVVGVETWYQPIVWHVLYKD
        ggagttatgcggagggggatttactggctttactctgataagattcctgtgaacg                agtggttgaggggggattccagtcgctag
        tcctacttgggaggtatcctaattgttttctttcagaaaacgttttcggaatgat                ctctttttccttgtacgaacttgattaaa
        gccgccatgtggtcgcgccgtccgggggccccgtcggatctgcgtgcgatcccag                cccttcgcttgttgatgcgacggccctac
                                                                                                            

Query   LFTVMIIG <---Intron---> CLFVVTLPMSLYNVFK <---Intron---> AYRNNTLKHSSLYEALLPFFSPVLLFVLSTLWISFSPTNIVQKQ
        ||| /||  <    81bp    > | | /||||||||/ | <    93bp    > |/|/||||||||||| ||| ||||||/|||/|/ /||/||// |
Target  LFTFLIIV                CSFTITLPMSLYNILK                AHRSNTLKHSSLYEAFLPFLSPVLLFILSTIWVVYSPSNILELQ
        ctatcaag                tttaaatcaactaaca                gccaaacacaattggtcctctcgcctattaatggttctaacgcc
        ttctttt                tgctctctctgtaatta                caggactaaggtaacttcttccttttttcctgttacccattata
        tcttgcc                ctcctagacgcccccg                gctctctggtccgtatcgccctccccccgcctgggttaccccgga
                                                                                                            

Query   PRIFYLMVGTAFSNVT <---Intron---> CKLIVCQMSNTRCKPLSLLLLPMSIVVLLVISGTVQGGESLVLFIWTAVVLLTHIHYGVSV <---In
        |||||/||||||/||| <   108bp    > |||||||||||||/ |/ |||||| |||| //  |   |/|/|//|||||/| |||/|/|| <    8
Target  PRIFYIMVGTAFANVT                CKLIVCQMSNTRCQALNCLLLPMSAVVLLAVTRVVT-NETLLLYLWTAVVILAHIHFGISV       
        ccattaaggagtgaga                tacagtcaaaactcgcatccccatgggttggacgga-agaccctctagggacgcactgatg       
        cgttatttgcctcatc                gatttgatgacggactagtttctccttttctcgttc-aactttatgccttttcatatgtct       
        cgccccgggagcctca                tggtgtggtccccaaacccagcgaggggatccggcc-taaggttagattcaaacactcaag       
                                                                                                            

Query   tron---> VKQLSDHFNIFAFSLKKPNSDUQDEEKIGLKAAEV
        6bp    > |/||| || |||||||||/||||/||/|||| |||
Target           VQQLSSHFKIFAFSLKKPSSDUQEEEQIGLKGAEV
                 gcccaactaatgttcaacaagtcgggcagtagggg
                 taatggatattctctaacggagaaaaatgtagcat
                 aagcccccactcctgggcctcagggaatcgaatgt
                                      *             
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 1042 ; UGA-SECIS: 1081

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV884750.1:subseq_2720142,100000_ Strand = - Positions = 47966 - 47892
 Found by:  Infernal (score=36.39) Covels (score=26.93)
 Stem2 length = 9   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -20.91

         ..(((((((.......(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(({({(((---((..([[(((((({((((...................))))}))))))]])..--..)))))})})).
 target  CUCAGCGCU---UGAAUGAAGAGUGUGUCCAAAAGCCAUUAAAUGGAGCGGACUCACUCUGAGGA--AACAAGCACAGGA
                         ****          ^^^                          ****