Locus 7338

Sequence ID 3L_DroMel_CAF1
Location 19,696,969 – 19,697,128
Length 159
Max. P 0.986181
window11914 window11915 window11916 window11917

overview

Window 4

Location 19,696,969 – 19,697,088
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.85
Mean single sequence MFE -21.15
Consensus MFE -16.04
Energy contribution -15.84
Covariance contribution -0.20
Combinations/Pair 1.11
Mean z-score -2.53
Structure conservation index 0.76
SVM decision value 1.63
SVM RNA-class probability 0.968931
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19696969 119 + 23771897
UGCACGUGUGUAUACACACAUACAUUCAUAC-UUAUGUAUGUGCGUACAAAUUGUCGAGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAU
.(((((((((....)))))((((((......-..))))))))))......(((((((.(((((((.................................))))...))).))))))).... ( -26.11)
>DroSec_CAF1 11355 116 + 1
UGCACGUGUGUAUACACACACACACACACACAUUU----CAUACAUACAAAUUGUCGGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAU
.....((((((......))))))............----.................((((((((............(((....(((....)))....)))..(......))))))))).. ( -19.50)
>DroSim_CAF1 13293 113 + 1
UGCACGUGUGUAUACACACACACACACAC---UUU----CGUACAUACAAAUUGUCGGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAU
.....((((((......))))))......---...----.(.(((.......))))((((((((............(((....(((....)))....)))..(......))))))))).. ( -19.60)
>DroEre_CAF1 11850 101 + 1
UGCACGUGUGUAUACACAUACU-------------------GACGUACAAAUUGUCUGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAU
.((..((((((....)))))).-------------------............((((((((.((((........................))))))))))))))................ ( -20.26)
>DroYak_CAF1 11957 101 + 1
UGCACGUGUGUACACACAUACU-------------------AACAUACAAAUUGUCUGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAU
.((..((((((....)))))).-------------------............((((((((.((((........................))))))))))))))................ ( -20.26)
>consensus
UGCACGUGUGUAUACACACACACA__CA____UU_______UACAUACAAAUUGUCGGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAU
.((..((((((....))))))................................(((.((((.((((........................)))))))).)))))................ (-16.04 = -15.84 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,696,969 – 19,697,088
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.85
Mean single sequence MFE -32.34
Consensus MFE -23.52
Energy contribution -23.88
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -3.06
Structure conservation index 0.73
SVM decision value 2.03
SVM RNA-class probability 0.986181
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19696969 119 - 23771897
AUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACUCGACAAUUUGUACGCACAUACAUAA-GUAUGAAUGUAUGUGUGUAUACACACGUGCA
(..((((((((.(((.((((((((.........)))).))))..((((.......))))))).))))))))..).....(((((....-)))))..((((((((((....)))))))))) ( -36.90)
>DroSec_CAF1 11355 116 - 1
AUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCCGACAAUUUGUAUGUAUG----AAAUGUGUGUGUGUGUGUGUGUAUACACACGUGCA
(..((((((((.(((.((((((((.........)))).))))..((((.......))))))).))))))))..).......----...((..((((((((((....))))))))))..)) ( -34.60)
>DroSim_CAF1 13293 113 - 1
AUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCCGACAAUUUGUAUGUACG----AAA---GUGUGUGUGUGUGUGUAUACACACGUGCA
(..((((((((.(((.((((((((.........)))).))))..((((.......))))))).))))))))..)(..(((.----...---)))..)(..((((((....))))))..). ( -35.60)
>DroEre_CAF1 11850 101 - 1
AUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCAGACAAUUUGUACGUC-------------------AGUAUGUGUAUACACACGUGCA
......((.((((.....((((((((((((.....((((.........))))..)))).))))))))......)))).)-------------------)((((((((....)))))))). ( -26.90)
>DroYak_CAF1 11957 101 - 1
AUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCAGACAAUUUGUAUGUU-------------------AGUAUGUGUGUACACACGUGCA
(..(((((((......((((((((.........)))).)))).(((((((....))))..))).)))))))..).....-------------------.((((((((....)))))))). ( -27.70)
>consensus
AUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCCGACAAUUUGUAUGUA_______AA____UG__UGUGUGUGUGUAUACACACGUGCA
(..((((((((.(((.((((((((.........)))).))))..((((.......))))))).))))))))..).........................((((((((....)))))))). (-23.52 = -23.88 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,697,008 – 19,697,128
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.41
Mean single sequence MFE -23.37
Consensus MFE -18.12
Energy contribution -18.72
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.78
SVM decision value 0.35
SVM RNA-class probability 0.700027
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19697008 120 + 23771897
GUGCGUACAAAUUGUCGAGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAUUGGCCGUUGGAUAAACCAACACGACAUUACAUUGCACAUA
(((((.......(((((.((((((............(((....(((....)))....)))..(......))))))).........(((((.....))))).)))))......)))))... ( -24.52)
>DroSec_CAF1 11391 120 + 1
AUACAUACAAAUUGUCGGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAUUGGCCGUUGGAUAAACCAACACGACAUUACAUUGCACAUA
............((((((((((((............(((....(((....)))....)))..(......))))))))).......(((((.....)))))..)))).............. ( -22.20)
>DroSim_CAF1 13326 120 + 1
GUACAUACAAAUUGUCGGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAUUGGCCGUUGGAUAAACCAACACGACAUUACAUUGCACAUA
((.((.......((((((((((((............(((....(((....)))....)))..(......))))))))).......(((((.....)))))..))))......)).))... ( -23.52)
>DroEre_CAF1 11872 119 + 1
-GACGUACAAAUUGUCUGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAUUGGCCGUUGGAUAAACCAACACGACAUUACGUUGCACAUG
-((((((......((((((((.((((........................)))))))))))).......((.(((....)))...(((((.....))))).))....))))))....... ( -24.36)
>DroYak_CAF1 11979 119 + 1
-AACAUACAAAUUGUCUGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAUUGGCCGUUGGAUAAACCAACACGACAUUACAUUGCACAUA
-............((((((((.((((........................))))))))))))((((......(((....)))...(((((.....)))))...........))))..... ( -22.26)
>consensus
_UACAUACAAAUUGUCGGGUUGUCUAAAAAUAAAACCUGCAUACUAAAAAUAGAAACCAGACGCGAACACGACAAUCCAUUGGCCGUUGGAUAAACCAACACGACAUUACAUUGCACAUA
............((((((((((((............(((....(((....)))....)))..(......))))))))).......(((((.....)))))..)))).............. (-18.12 = -18.72 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,697,008 – 19,697,128
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.41
Mean single sequence MFE -29.88
Consensus MFE -26.46
Energy contribution -26.26
Covariance contribution -0.20
Combinations/Pair 1.06
Mean z-score -1.40
Structure conservation index 0.89
SVM decision value 0.55
SVM RNA-class probability 0.779441
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19697008 120 - 23771897
UAUGUGCAAUGUAAUGUCGUGUUGGUUUAUCCAACGGCCAAUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACUCGACAAUUUGUACGCAC
...((((........(((((..(((.....))))))))..(..((((((((.(((.((((((((.........)))).))))..((((.......))))))).))))))))..)..)))) ( -31.90)
>DroSec_CAF1 11391 120 - 1
UAUGUGCAAUGUAAUGUCGUGUUGGUUUAUCCAACGGCCAAUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCCGACAAUUUGUAUGUAU
...(((((.......(((((..(((.....))))))))..(..((((((((.(((.((((((((.........)))).))))..((((.......))))))).))))))))..).))))) ( -28.70)
>DroSim_CAF1 13326 120 - 1
UAUGUGCAAUGUAAUGUCGUGUUGGUUUAUCCAACGGCCAAUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCCGACAAUUUGUAUGUAC
...(((((.......(((((..(((.....))))))))..(..((((((((.(((.((((((((.........)))).))))..((((.......))))))).))))))))..).))))) ( -29.80)
>DroEre_CAF1 11872 119 - 1
CAUGUGCAACGUAAUGUCGUGUUGGUUUAUCCAACGGCCAAUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCAGACAAUUUGUACGUC-
.((((((((((....(((.((((((((........)))))))))))...)))......((((((((((((.....((((.........))))..)))).))))))))....))))))).- ( -30.90)
>DroYak_CAF1 11979 119 - 1
UAUGUGCAAUGUAAUGUCGUGUUGGUUUAUCCAACGGCCAAUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCAGACAAUUUGUAUGUU-
((((.(((((.((.((.(.((((((.....))))))).)).)).))))))))).....((((((((((((.....((((.........))))..)))).))))))))............- ( -28.10)
>consensus
UAUGUGCAAUGUAAUGUCGUGUUGGUUUAUCCAACGGCCAAUGGAUUGUCGUGUUCGCGUCUGGUUUCUAUUUUUAGUAUGCAGGUUUUAUUUUUAGACAACCCGACAAUUUGUAUGUA_
.((((((((.....((((.((((((.....))))))......((.(((((((....)).((((....(((....)))....))))...........))))))).))))..)))))))).. (-26.46 = -26.26 +  -0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:19 2006