Locus 3544

Sequence ID 3L_DroMel_CAF1
Location 10,379,825 – 10,379,927
Length 102
Max. P 0.919932
window5533 window5534

overview

Window 3

Location 10,379,825 – 10,379,927
Length 102
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 78.13
Mean single sequence MFE -26.20
Consensus MFE -18.79
Energy contribution -19.65
Covariance contribution 0.86
Combinations/Pair 1.19
Mean z-score -1.75
Structure conservation index 0.72
SVM decision value 1.13
SVM RNA-class probability 0.919932
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10379825 102 + 23771897
UAUAUACAUGCUGCUGAUAUGAAGAGCAUGUGU--UGUAGUGAAGUCACUUUCUACCCUCUCGCUCAAAUAGAGGGAUCACAUGACUUGAUUGCUUACACAGCC
...(((((((((.((.......)))))))))))--.(((((.((((((.......((((((.........))))))......)))))).))))).......... ( -31.02)
>DroPse_CAF1 278653 87 + 1
UGUAAG-GGA---U------G-----GUGGUGU--GGCAGUAAAGUCACUUUCUACCCUCUCGCUUAAAUAGAGGGAUCACAUGACUUGAUUGCUUGCACAGAC
((((((-.((---(------(-----((((.((--(((......)))))...)))))(((((.........))))).............))).))))))..... ( -25.80)
>DroEre_CAF1 268815 99 + 1
UACAUACAUA---CUGAUAUGGGGAGCAUGUGU--UGUAGUGAAGUCACUUUCUACCCUCUCGCUCAAAUAGAGGGAUCACAUGACUUGAUUGCUUACACAGCC
..(((((...---..).))))....((.(((((--.(((((.((((((.......((((((.........))))))......)))))).)))))..))))))). ( -28.62)
>DroWil_CAF1 405270 90 + 1
U--AUG-UUU---GUUAU--UUGGGGCU--AGC----UGCUAAAGUCACUUUCUACCCUCUCGCUUAAAUAGAGGGAUCACAUGACUUGAUUGCUUACACAGCC
.--...-...---.....--....((((--(((----.....((((((.......((((((.........))))))......))))))....))).....)))) ( -20.02)
>DroYak_CAF1 266180 99 + 1
UAAAUACAUA---CCGAUAUGAAGAGCAUGUGU--UGUAGUGAAGUCACUUUCUACCCUCUCGCUCAAAUAGAGGGAUCACAUGACUUGAUUGCUUACACAGCC
......((((---....))))....((.(((((--.(((((.((((((.......((((((.........))))))......)))))).)))))..))))))). ( -28.32)
>DroAna_CAF1 259482 97 + 1
UGUAAA-GGA---UUCAU--G-GGGGGAUGAGAUACGGAGUUGAGUCACUUUCUACCCUCUCGCUCAAAUAGAGGGAUCACAUGACUUGAUUGCUUACACAGCC
(((((.-...---(((((--.-.....)))))....(.(((..(((((.......((((((.........))))))......)))))..))).))))))..... ( -23.42)
>consensus
UAUAUA_AUA___CUGAU__G_GGAGCAUGUGU__UGUAGUGAAGUCACUUUCUACCCUCUCGCUCAAAUAGAGGGAUCACAUGACUUGAUUGCUUACACAGCC
.............................((((...(((((.((((((.......((((((.........))))))......)))))).)))))..)))).... (-18.79 = -19.65 +   0.86)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,379,825 – 10,379,927
Length 102
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 78.13
Mean single sequence MFE -23.93
Consensus MFE -18.02
Energy contribution -18.18
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.75
SVM decision value 0.66
SVM RNA-class probability 0.813181
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10379825 102 - 23771897
GGCUGUGUAAGCAAUCAAGUCAUGUGAUCCCUCUAUUUGAGCGAGAGGGUAGAAAGUGACUUCACUACA--ACACAUGCUCUUCAUAUCAGCAGCAUGUAUAUA
.(((.....)))....(((((((.....((((((.........))))))......))))))).......--..(((((((((.......)).)))))))..... ( -27.80)
>DroPse_CAF1 278653 87 - 1
GUCUGUGCAAGCAAUCAAGUCAUGUGAUCCCUCUAUUUAAGCGAGAGGGUAGAAAGUGACUUUACUGCC--ACACCAC-----C------A---UCC-CUUACA
...((((...(((.(.(((((((.....((((((.........))))))......))))))).).))))--)))....-----.------.---...-...... ( -21.90)
>DroEre_CAF1 268815 99 - 1
GGCUGUGUAAGCAAUCAAGUCAUGUGAUCCCUCUAUUUGAGCGAGAGGGUAGAAAGUGACUUCACUACA--ACACAUGCUCCCCAUAUCAG---UAUGUAUGUA
.(((.....)))....(((((((.....((((((.........))))))......)))))))...((((--..(((((((.........))---))))).)))) ( -25.60)
>DroWil_CAF1 405270 90 - 1
GGCUGUGUAAGCAAUCAAGUCAUGUGAUCCCUCUAUUUAAGCGAGAGGGUAGAAAGUGACUUUAGCA----GCU--AGCCCCAA--AUAAC---AAA-CAU--A
(((((.((..((....(((((((.....((((((.........))))))......)))))))..)).----)))--))))....--.....---...-...--. ( -24.40)
>DroYak_CAF1 266180 99 - 1
GGCUGUGUAAGCAAUCAAGUCAUGUGAUCCCUCUAUUUGAGCGAGAGGGUAGAAAGUGACUUCACUACA--ACACAUGCUCUUCAUAUCGG---UAUGUAUUUA
.(((.....)))....(((((((.....((((((.........))))))......))))))).......--..(((((((.........))---)))))..... ( -24.60)
>DroAna_CAF1 259482 97 - 1
GGCUGUGUAAGCAAUCAAGUCAUGUGAUCCCUCUAUUUGAGCGAGAGGGUAGAAAGUGACUCAACUCCGUAUCUCAUCCCCC-C--AUGAA---UCC-UUUACA
.(((.....))).....((((((.....((((((.........))))))......)))))).......(((..((((.....-.--)))).---...-..))). ( -19.30)
>consensus
GGCUGUGUAAGCAAUCAAGUCAUGUGAUCCCUCUAUUUGAGCGAGAGGGUAGAAAGUGACUUCACUACA__ACACAUGCUCC_C__AUCAG___UAU_UAUAUA
(..(((....)))..)(((((((.....((((((.........))))))......))))))).......................................... (-18.02 = -18.18 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:42 2006