Locus 5257

Sequence ID	3L_DroMel_CAF1
Location	14,526,453 – 14,526,585
Length	132
Max. P	0.965189

overview

Window 2

Location	14,526,453 – 14,526,552
Length	99
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	76.64
Mean single sequence MFE	-25.34
Consensus MFE	-15.32
Energy contribution	-15.98
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.60
SVM decision value	1.58
SVM RNA-class probability	0.965189
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14526453 99 + 23771897
UGCAACCCCUUUUCUCC--GC----UCGCCACU--------UGUACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUU
......((((((..((.--((----..((....--------..........))..)).))..)).))))..((((((((......)))))))).................... ( -17.84)
>DroVir_CAF1 1090 101 + 1
UGCACCCCUUUUGGGGCAGCCUUGUCAGCCAGU--------UGUACAAAUUGCUCGCUGAUUAGCAGGCAAGCGCAUGAAAUUAAUCAUAUGCAAAUA----CGAGUAUGCUA
.(((((((....))))..((((.((((((.(((--------.((....)).))).))))))....))))..(((.((((......)))).))).....----......))).. ( -30.90)
>DroPse_CAF1 1027 107 + 1
-CUAACCCCUUUUUGCCUGCC----UUGCCACUCACUCAGUCGUACAAA-UGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGCCACUUUUUCCG
-...........((((((((.----.((.....)).((((.((..(...-.)..))))))...))))))))((((((((......)))))))).................... ( -26.10)
>DroGri_CAF1 1129 93 + 1
UGCAACCCCUUUCGG----------UUGGCAGU--------UGUACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAG--CCAAGUAUCCUU
(((((((......))----------))(((...--------........((((..(((....)))..))))((((((((......)))))))).....)--))..)))..... ( -27.10)
>DroAna_CAF1 977 99 + 1
GCUAACCCCUUUUUUGU--GC----UCGCCACU--------UGUACAAAUUGCUGGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUUGUCGACUUUUCUU
(((((..((...(((((--((----........--------.))))))).....))....))))).(((((((((((((......)))))))).....))))).......... ( -24.00)
>DroPer_CAF1 1027 107 + 1
-CUAACCCCUUUUUGCCUGCC----UUGCCACUCACUCAGUCGUACAAA-UGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGCCACUUUUUCCG
-...........((((((((.----.((.....)).((((.((..(...-.)..))))))...))))))))((((((((......)))))))).................... ( -26.10)
>consensus
UCCAACCCCUUUUUGCC__CC____UUGCCACU________UGUACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGCCAACUUUUCUU
.................................................((((..(((....)))..))))((((((((......)))))))).................... (-15.32 = -15.98 +   0.67)

alignment

secondary structure

dotplot

Window 3

Location	14,526,480 – 14,526,585
Length	105
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	79.24
Mean single sequence MFE	-28.52
Consensus MFE	-17.06
Energy contribution	-17.08
Covariance contribution	0.03
Combinations/Pair	1.06
Mean z-score	-2.09
Structure conservation index	0.60
SVM decision value	0.84
SVM RNA-class probability	0.865047
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14526480 105 + 23771897
UG-UACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUU-----CCUUGACGCG--AAUUUGUUGCUGUCGUGGGAG
..-.........(((((.(((.(((((.(((((((((((......))))))))......((((............-----....))))..--..))).))))))))))))).. ( -26.39)
>DroGri_CAF1 1152 90 + 1
UG-UACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAG--CCAAGUAUCCUUCC-----AUUUGGCGCA--A-UGUGUCU------------
..-((((..((((..(((....)))..))))((((((((......)))))))).....(--((((((........-----)))))))...--.-))))...------------ ( -27.60)
>DroEre_CAF1 978 110 + 1
UG-GGCAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUUUCCUUGAAGCG--AAUUUGUUGCUGUCGUGGGAG
((-(((...((((..(((....)))..))))((((((((......)))))))).......))))).............((((.(((((((--(.....))))).))).)))). ( -34.20)
>DroWil_CAF1 35310 105 + 1
UGGGACAAAUUGCUCGCUGAUUAGCAAGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUUGCAAACUUUCUCUUU-----CUUUUUUUAU--AGCUUCUUUCUGUG-UCGCAA
((.((((..(((((.(((....))).)))))((((((((......))))))))......................-----..........--............))-)).)). ( -24.70)
>DroYak_CAF1 984 105 + 1
UG-UGCAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUU-----CCUUGACGCG--AAUUUGUUGCUGUCGUGGGAG
.(-((....((((..(((....)))..))))((((((((......))))))))..........))).......((-----((.(((((((--(.....)))).)))).)))). ( -30.60)
>DroAna_CAF1 1004 107 + 1
UG-UACAAAUUGCUGGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUUGUCGACUUUUCUUUU-----CCUUGACGCCCAAUGUUGUUGCUGUCGUGGGAG
.(-.((((.(((((.(((....))).)))))((((((((......)))))))).....)))))..........((-----((.((((((.((....))..)).)))).)))). ( -27.60)
>consensus
UG_UACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUU_____CCUUGACGCG__AAUUUGUUGCUGUCGUGGGAG
.........(((((.(((....))).)))))((((((((......))))))))............................................................ (-17.06 = -17.08 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:40 2006