Locus 5567

Sequence ID	3L_DroMel_CAF1
Location	15,257,733 – 15,257,885
Length	152
Max. P	0.953579

overview

Window 5

Location	15,257,733 – 15,257,845
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	78.42
Mean single sequence MFE	-23.18
Consensus MFE	-15.24
Energy contribution	-15.48
Covariance contribution	0.24
Combinations/Pair	1.09
Mean z-score	-1.92
Structure conservation index	0.66
SVM decision value	0.92
SVM RNA-class probability	0.881785
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15257733 112 + 23771897
UCGAAGUUUACUACUCAUUCUUCUUUAUUAUUCUUGAUUGUUCCCAACAAAGCUUUGAAAACCAUCAUACCCCAUUGGCCGUAACGGCCCCAGGGUAUGUAACGAACCGAAU
(((((((((.....(((.................))).(((.....)))))))))))).......(((((((....(((((...)))))...)))))))............. ( -24.53)
>DroSec_CAF1 146910 107 + 1
UUAAAGUUUAGUACUAAUUUUUUUUUA----UCUUGUUUAUUCCCAACGUUGAA-UAAAAAUCAUCAUACCCCAUUUGCCUUAAAGGCUCCAGGGUAUGUAACGAACCGAAU
.....((((..(((.............----.....(((((((........)))-)))).......((((((.....(((.....)))....)))))))))..))))..... ( -19.50)
>DroSim_CAF1 155140 112 + 1
UUAAAGUUUACUACGCAUUCUUUUUUAAUAUUCUUGUUUAUUCCCAACGUAGCUUUGAAAACCAUCAUACCCCAUUGGCCUUAAAGGCCCCAGGGUAUGUAACGAACCGAAU
((((((....(((((...........((((....)))).........))))))))))).......(((((((....((((.....))))...)))))))............. ( -22.85)
>DroEre_CAF1 147174 109 + 1
CUAAAUUCC---UCUGAUUCUUUUUUAUUACUCUUGCACAUUCCAAACGAUGCUGUGAAAACCAUCAUGCCCCAUUGGCCGUAAAAGCCACAGGGUAUGUAACGAACCGAAU
.........---....((((...((..((((.................((((..((....))))))((((((...((((.......))))..))))))))))..))..)))) ( -20.40)
>DroYak_CAF1 153365 107 + 1
CUAAAGUUC-----ACAUUCUUUCGCAUUUUUCUUUUGCAUUCCAAGCGAUGCCUUGAAAAACAUCAUACCCCAGUGGCCCUAGAGGCCCCAGGGUAUGUAACGAACCGAAU
.....((((-----.............((((((....(((((......)))))...))))))...(((((((..(.((((.....)))))..)))))))....))))..... ( -28.60)
>consensus
UUAAAGUUUA_UACUCAUUCUUUUUUAUUAUUCUUGUUUAUUCCCAACGAUGCUUUGAAAACCAUCAUACCCCAUUGGCCGUAAAGGCCCCAGGGUAUGUAACGAACCGAAU
.................................................................(((((((....((((.....))))...)))))))............. (-15.24 = -15.48 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	15,257,733 – 15,257,845
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	78.42
Mean single sequence MFE	-30.04
Consensus MFE	-19.82
Energy contribution	-19.78
Covariance contribution	-0.04
Combinations/Pair	1.17
Mean z-score	-2.15
Structure conservation index	0.66
SVM decision value	1.43
SVM RNA-class probability	0.953579
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15257733 112 - 23771897
AUUCGGUUCGUUACAUACCCUGGGGCCGUUACGGCCAAUGGGGUAUGAUGGUUUUCAAAGCUUUGUUGGGAACAAUCAAGAAUAAUAAAGAAGAAUGAGUAGUAAACUUCGA
....((((..(((((((((((..(((((...)))))...)))))))(((.(((..(((.......)))..))).))).....................))))..)))).... ( -33.30)
>DroSec_CAF1 146910 107 - 1
AUUCGGUUCGUUACAUACCCUGGAGCCUUUAAGGCAAAUGGGGUAUGAUGAUUUUUA-UUCAACGUUGGGAAUAAACAAGA----UAAAAAAAAAUUAGUACUAAACUUUAA
....(((.((((((((((((((..(((.....)))...))))))))).)))).((((-(((........))))))).....----.............).)))......... ( -22.50)
>DroSim_CAF1 155140 112 - 1
AUUCGGUUCGUUACAUACCCUGGGGCCUUUAAGGCCAAUGGGGUAUGAUGGUUUUCAAAGCUACGUUGGGAAUAAACAAGAAUAUUAAAAAAGAAUGCGUAGUAAACUUUAA
....((((..(((((((((((..((((.....))))...)))))))....(((..(((.......)))..))).........................))))..)))).... ( -28.50)
>DroEre_CAF1 147174 109 - 1
AUUCGGUUCGUUACAUACCCUGUGGCUUUUACGGCCAAUGGGGCAUGAUGGUUUUCACAGCAUCGUUUGGAAUGUGCAAGAGUAAUAAAAAAGAAUCAGA---GGAAUUUAG
.((((((((....(((.((((((((((.....)))).)))))).))).((.((((((((...((.....)).)))).)))).))........))))).))---)........ ( -26.00)
>DroYak_CAF1 153365 107 - 1
AUUCGGUUCGUUACAUACCCUGGGGCCUCUAGGGCCACUGGGGUAUGAUGUUUUUCAAGGCAUCGCUUGGAAUGCAAAAGAAAAAUGCGAAAGAAUGU-----GAACUUUAG
((((..(((((..(((((((..(((((.....)))).)..))))))).(((.(((((((......))))))).)))..........))))).))))..-----......... ( -39.90)
>consensus
AUUCGGUUCGUUACAUACCCUGGGGCCUUUAAGGCCAAUGGGGUAUGAUGGUUUUCAAAGCAUCGUUGGGAAUAAACAAGAAUAAUAAAAAAGAAUGAGUA_UAAACUUUAA
.....((((....((((((((..((((.....))))...)))))))).............((.....))))))....................................... (-19.82 = -19.78 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	15,257,773 – 15,257,885
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.34
Mean single sequence MFE	-30.88
Consensus MFE	-15.30
Energy contribution	-15.27
Covariance contribution	-0.02
Combinations/Pair	1.16
Mean z-score	-3.03
Structure conservation index	0.50
SVM decision value	1.14
SVM RNA-class probability	0.921623
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15257773 112 + 23771897
UUCCCAACAAAGCUUUGAAAACCAUCAUACCCCAUU----GGCCGUAACGG----CCCCAGGGUAUGUAACGAACCGAAUUACAAGGCGUACAACCCUCAGGACAACUGUCCAACUUGGA
...((((....((((((........(((((((....----(((((...)))----))...)))))))...((...)).....))))))............((((....))))...)))). ( -33.50)
>DroSec_CAF1 146946 111 + 1
UUCCCAACGUUGAA-UAAAAAUCAUCAUACCCCAUU----UGCCUUAAAGG----CUCCAGGGUAUGUAACGAACCGAAUUACAAGGCGUACAACCCUCAGGACAACUGUCCAACUUGGA
...((((.((((..-..........(((((((....----.(((.....))----)....)))))))..(((..((.........))))).)))).....((((....))))...)))). ( -28.50)
>DroSim_CAF1 155180 112 + 1
UUCCCAACGUAGCUUUGAAAACCAUCAUACCCCAUU----GGCCUUAAAGG----CCCCAGGGUAUGUAACGAACCGAAUUACAAGGCGUACAACCCUCAGGACAACUGUCCAACUUGGA
...((((.(((((((((........(((((((....----((((.....))----))...)))))))...((...)).....)))))).)))........((((....))))...)))). ( -34.80)
>DroEre_CAF1 147211 112 + 1
UUCCAAACGAUGCUGUGAAAACCAUCAUGCCCCAUU----GGCCGUAAAAG----CCACAGGGUAUGUAACGAACCGAAUUACAAGGCGUACAACCCUCAGGACAACUGUCCAACUUGGA
.(((((...(((((((....))...(((((((...(----(((.......)----)))..)))))))..................)))))..........((((....))))...))))) ( -30.20)
>DroYak_CAF1 153400 112 + 1
UUCCAAGCGAUGCCUUGAAAAACAUCAUACCCCAGU----GGCCCUAGAGG----CCCCAGGGUAUGUAACGAACCGAAUUACAAGGCGUACAACCCUCAGGACAACUGUCCAACUUGGC
..(((((..((((((((........(((((((..(.----((((.....))----)))..)))))))...((...)).....))))))))..........((((....))))..))))). ( -39.50)
>DroAna_CAF1 139208 104 + 1
---------------UAAAAAAUAAUAUCCCUCAGUUUAUGGCCA-AUACACCUUUUCUAGGGUAAAAAACGUAACGAAUUACAAGGAGUACACCCCUUAGGACAACUGUCCAAUUUGGA
---------------.....................(((((....-.(((.(((.....)))))).....)))))((((((..((((.(....).)))).((((....)))))))))).. ( -18.80)
>consensus
UUCCCAACGAUGCUUUGAAAACCAUCAUACCCCAUU____GGCCGUAAAGG____CCCCAGGGUAUGUAACGAACCGAAUUACAAGGCGUACAACCCUCAGGACAACUGUCCAACUUGGA
.........................(((((((............................))))))).......((((......(((.(.....))))..((((....))))...)))). (-15.30 = -15.27 +  -0.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:36 2006