Locus 3954

Sequence ID 3L_DroMel_CAF1
Location 11,491,008 – 11,491,102
Length 94
Max. P 0.791452
window6154 window6155

overview

Window 4

Location 11,491,008 – 11,491,102
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 67.26
Mean single sequence MFE -25.23
Consensus MFE -13.43
Energy contribution -13.65
Covariance contribution 0.22
Combinations/Pair 1.20
Mean z-score -1.51
Structure conservation index 0.53
SVM decision value 0.59
SVM RNA-class probability 0.791452
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491008 94 + 23771897
----CGCUUUUU-U--------UCAAUUU---UUA-UGCUUCCAAAAUAGGCCCAGCACUCGCCGCAGGCCAUCUUCACCAGCUUUAAGCUGGAGAGAAGCGAAUAUUCCG---------
----((((((((-(--------.......---...-.............((((..((.......)).)))).......(((((.....)))))))))))))).........--------- ( -26.50)
>DroPse_CAF1 12291 93 + 1
----AGACC-----------------UCU---UUC-UGUUGCC--CGCAGGCUCAGCAUUCGCCCCAGGCCAUCUUCACCAGCUUCAAAUUGGAAAGAAAUGAGCACUCAAGUGCGCCUG
----.....-----------------...---..(-((..(((--....))).))).........(((((..((((..((((.......)))).)))).....((((....))))))))) ( -22.30)
>DroSec_CAF1 6068 101 + 1
UGUACGCGUUUU-U---------CGAUUUAUUUUAUUUAUCCCAAAACAGGCCCAGCACUCACCGCAGGCCAUCUUCACCAGCUUUAAGCUGGAGAGAAGCGAAUACGCCG---------
.(((..((((((-(---------(.........................((((..((.......)).)))).......(((((.....))))).))))))))..)))....--------- ( -30.10)
>DroPer_CAF1 2528 93 + 1
----AGACC-----------------UCU---UUC-UGUUGCC--AGCAGGCUCAGCAUUCGCCCCAGGCCAUCUUCACCAGCUUUAAAUUGGAAAGAAAUGAGCACUCAAGUGCGCCUG
----.....-----------------...---..(-((..(((--....))).))).........(((((..((((..((((.......)))).)))).....((((....))))))))) ( -22.80)
>DroEre_CAF1 1732 95 + 1
UAU--GCGUUUU----------UCUAUUU---UUA-UGAUGCCCAUACAGGCGCAGCACUCGCCGCAGGCCAUCUUCACCAGCUUCAAGCUGGAGCGAAGCGAAUACUCCG---------
...--.((((((----------.((....---...-.((((.((.....((((.......))))...)).))))....(((((.....))))))).)))))).........--------- ( -25.80)
>DroYak_CAF1 2322 105 + 1
UAU--ACGUUUUUUCCAUUUUUUUUUUUU---UUA-CGAUCCCCCCACAGGCCCAGCACUCGCCGCAGGCCAUCUUCACCAGCUUCAAGCUGGAGAGAAGCGAAUACUCUG---------
...--.((((((((...............---...-.............((((..((.......)).)))).......(((((.....))))).)))))))).........--------- ( -23.90)
>consensus
_____GCGUUUU___________C_AUUU___UUA_UGAUGCC_AAACAGGCCCAGCACUCGCCGCAGGCCAUCUUCACCAGCUUCAAGCUGGAGAGAAGCGAAUACUCCG_________
.................................................((((..((....))....)))).((((..(((((.....))))).))))...................... (-13.43 = -13.65 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,491,008 – 11,491,102
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 67.26
Mean single sequence MFE -29.22
Consensus MFE -17.55
Energy contribution -17.75
Covariance contribution 0.20
Combinations/Pair 1.19
Mean z-score -1.09
Structure conservation index 0.60
SVM decision value -0.01
SVM RNA-class probability 0.529101
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11491008 94 - 23771897
---------CGGAAUAUUCGCUUCUCUCCAGCUUAAAGCUGGUGAAGAUGGCCUGCGGCGAGUGCUGGGCCUAUUUUGGAAGCA-UAA---AAAUUGA--------A-AAAAAGCG----
---------..........(((((((.(((((.....))))).)(((((((((..((((....)))))))).))))))))))).-...---.......--------.-........---- ( -29.00)
>DroPse_CAF1 12291 93 - 1
CAGGCGCACUUGAGUGCUCAUUUCUUUCCAAUUUGAAGCUGGUGAAGAUGGCCUGGGGCGAAUGCUGAGCCUGCG--GGCAACA-GAA---AGA-----------------GGUCU----
.((((((((....))))....(((((((..........((.....))...(((((((((.........)))).))--)))....-)))---)))-----------------)))))---- ( -27.90)
>DroSec_CAF1 6068 101 - 1
---------CGGCGUAUUCGCUUCUCUCCAGCUUAAAGCUGGUGAAGAUGGCCUGCGGUGAGUGCUGGGCCUGUUUUGGGAUAAAUAAAAUAAAUCG---------A-AAAACGCGUACA
---------..((((.((((((((...(((((.....))))).))))..((((((((.....))).)))))(((((((.......)))))))...))---------)-)..))))..... ( -31.30)
>DroPer_CAF1 2528 93 - 1
CAGGCGCACUUGAGUGCUCAUUUCUUUCCAAUUUAAAGCUGGUGAAGAUGGCCUGGGGCGAAUGCUGAGCCUGCU--GGCAACA-GAA---AGA-----------------GGUCU----
(((((((((....)))).....((((((((.........))).)))))..)))))((((.........)))).((--(....))-)..---...-----------------.....---- ( -28.80)
>DroEre_CAF1 1732 95 - 1
---------CGGAGUAUUCGCUUCGCUCCAGCUUGAAGCUGGUGAAGAUGGCCUGCGGCGAGUGCUGCGCCUGUAUGGGCAUCA-UAA---AAAUAGA----------AAAACGC--AUA
---------.(((((....)))))((.(((((.....)))))....((((.(((((((((.......)))).))).)).)))).-...---.......----------.....))--... ( -31.90)
>DroYak_CAF1 2322 105 - 1
---------CAGAGUAUUCGCUUCUCUCCAGCUUGAAGCUGGUGAAGAUGGCCUGCGGCGAGUGCUGGGCCUGUGGGGGGAUCG-UAA---AAAAAAAAAAAAUGGAAAAAACGU--AUA
---------..((...(((((.((((.(((((.....))))).).))).((((..((((....)))))))).)))))....)).-...---........................--... ( -26.40)
>consensus
_________CGGAGUAUUCGCUUCUCUCCAGCUUAAAGCUGGUGAAGAUGGCCUGCGGCGAGUGCUGGGCCUGUUU_GGCAUCA_UAA___AAAU_G___________AAAACGC_____
............(((((((.((((...(((((.....))))).))))...(((...))))))))))...((......))......................................... (-17.55 = -17.75 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:51 2006