Locus 7248

Sequence ID	3L_DroMel_CAF1
Location	19,407,771 – 19,407,874
Length	103
Max. P	0.956115

overview

Window 3

Location	19,407,771 – 19,407,874
Length	103
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.41
Mean single sequence MFE	-25.61
Consensus MFE	-17.65
Energy contribution	-17.77
Covariance contribution	0.12
Combinations/Pair	1.25
Mean z-score	-1.70
Structure conservation index	0.69
SVM decision value	1.09
SVM RNA-class probability	0.913892
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19407771 103 + 23771897
-----AUAUUCAAAUA---UAGCAGAUAUAGAUAUUUCUUUGAGUGUU--AGUUUCACUCCGUUUCCGUUACACGCCGAUGCGCGUGUAAGGAGCAUGUAAAUAUGAAAGGCA
-----...((((..((---((((..................(((((..--.....)))))....(((.((((((((......))))))))))))).))))....))))..... ( -24.00)
>DroSec_CAF1 46640 100 + 1
-----UUAUGGAAAUA---UAGAA--UAUUGCU-UUUCUCUGAGUGUA--CGUUUCACUCCGUUUCCGUUACACGCCGAUGCGCGUGUAAGGAGCAUGUAAAUAUGAAAGGCA
-----...........---.....--...((((-((((...(((((..--.....)))))(((((((.((((((((......)))))))))))).))).......)))))))) ( -29.70)
>DroSim_CAF1 46803 100 + 1
-----UUAUGCAAAUA---UAGAA--UAAUGCU-UUUCUCUGAGUGUA--CGUUUCACUCCGUUUCCGUUACACGCCGAUGCGCGUGUAAGGAGCAUGUAAAUAUGAAAGGCA
-----...........---.....--...((((-((((...(((((..--.....)))))(((((((.((((((((......)))))))))))).))).......)))))))) ( -29.80)
>DroEre_CAF1 43114 95 + 1
-----AAAUUCCAACA---AACAC-------AA-UUUCGCUGCGUGUA--AAUAGCGCUCCGUCUCCGUUACACGCCGAUGCGCGUGUAAGGAGCAUGUAAAUAUGAAAGGCA
-----...........---.....-------..-....(((((((...--....))))..(((((((.((((((((......)))))))))))).)))...........))). ( -26.20)
>DroYak_CAF1 72772 95 + 1
-----AAAUCCCAAUA---AACAC-------AU-UUUCGCUGCGUGUA--AAUGGCACUCCUUCUCUGUUACACGCCGAUGCGCGUGUAAGGAGCAUGUAAAUAUGAAAGGCA
-----...........---.....-------..-....(((.(((((.--....((((((((.......(((((((......))))))))))))..)))..)))))...))). ( -22.21)
>DroAna_CAF1 45456 107 + 1
AUGAAAACUUCCUACAUCUUAGUC--UA---AU-UUUUUUUCAAUGCCAGAAUUCUACUCAAUUUCCGUUACACGCCAAUGCGCGUGUAAGGAGCAUGUAAAUAUGAAAGGCA
.((((((......((......)).--..---..-...)))))).((((...............((((.((((((((......))))))))))))((((....))))...)))) ( -21.74)
>consensus
_____AAAUUCAAAUA___UAGAA__UA___AU_UUUCUCUGAGUGUA__AAUUUCACUCCGUUUCCGUUACACGCCGAUGCGCGUGUAAGGAGCAUGUAAAUAUGAAAGGCA
..................................((((...(((((.........)))))(((((((.((((((((......)))))))))))).))).......)))).... (-17.65 = -17.77 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	19,407,771 – 19,407,874
Length	103
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	77.41
Mean single sequence MFE	-26.34
Consensus MFE	-17.39
Energy contribution	-17.33
Covariance contribution	-0.05
Combinations/Pair	1.20
Mean z-score	-2.07
Structure conservation index	0.66
SVM decision value	1.46
SVM RNA-class probability	0.956115
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19407771 103 - 23771897
UGCCUUUCAUAUUUACAUGCUCCUUACACGCGCAUCGGCGUGUAACGGAAACGGAGUGAAACU--AACACUCAAAGAAAUAUCUAUAUCUGCUA---UAUUUGAAUAU-----
........(((((((.(((.(((((((((((......)))))))).)))....(((((.....--..)))))......................---))).)))))))----- ( -23.40)
>DroSec_CAF1 46640 100 - 1
UGCCUUUCAUAUUUACAUGCUCCUUACACGCGCAUCGGCGUGUAACGGAAACGGAGUGAAACG--UACACUCAGAGAAA-AGCAAUA--UUCUA---UAUUUCCAUAA-----
(((.((((............(((((((((((......)))))))).)))....(((((.....--..)))))...))))-.)))...--.....---...........----- ( -27.00)
>DroSim_CAF1 46803 100 - 1
UGCCUUUCAUAUUUACAUGCUCCUUACACGCGCAUCGGCGUGUAACGGAAACGGAGUGAAACG--UACACUCAGAGAAA-AGCAUUA--UUCUA---UAUUUGCAUAA-----
(((.((((............(((((((((((......)))))))).)))....(((((.....--..)))))...))))-.)))...--.....---...........----- ( -26.80)
>DroEre_CAF1 43114 95 - 1
UGCCUUUCAUAUUUACAUGCUCCUUACACGCGCAUCGGCGUGUAACGGAGACGGAGCGCUAUU--UACACGCAGCGAAA-UU-------GUGUU---UGUUGGAAUUU-----
....(((((((..((((.(((((((((((((......)))))))).(....))))))(((...--.......)))....-.)-------)))..---)).)))))...----- ( -28.70)
>DroYak_CAF1 72772 95 - 1
UGCCUUUCAUAUUUACAUGCUCCUUACACGCGCAUCGGCGUGUAACAGAGAAGGAGUGCCAUU--UACACGCAGCGAAA-AU-------GUGUU---UAUUGGGAUUU-----
..................(((((((((((((......))))))).......)))))).(((..--((.(((((......-.)-------)))).---)).))).....----- ( -24.21)
>DroAna_CAF1 45456 107 - 1
UGCCUUUCAUAUUUACAUGCUCCUUACACGCGCAUUGGCGUGUAACGGAAAUUGAGUAGAAUUCUGGCAUUGAAAAAAA-AU---UA--GACUAAGAUGUAGGAAGUUUUCAU
((((.(((.((((((.((..(((((((((((......)))))))).))).)))))))))))....)))).((((((...-.(---(.--.((......))..))..)))))). ( -27.90)
>consensus
UGCCUUUCAUAUUUACAUGCUCCUUACACGCGCAUCGGCGUGUAACGGAAACGGAGUGAAACU__UACACUCAGAGAAA_AU___UA__GUCUA___UAUUGGAAUAU_____
.................((((((((((((((......)))))))).(....)))))))....................................................... (-17.39 = -17.33 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:06 2006