Locus 2215

Sequence ID	3R_DroMel_CAF1
Location	6,322,843 – 6,323,004
Length	161
Max. P	0.999970

overview

Window 7

Location	6,322,843 – 6,322,953
Length	110
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	98.55
Mean single sequence MFE	-27.63
Consensus MFE	-27.22
Energy contribution	-27.22
Covariance contribution	-0.00
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.98
SVM decision value	2.75
SVM RNA-class probability	0.996778
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6322843 110 + 27905053
GUCGUCCUUGCGCACUUUCCAGUCGACAGGAUUUCUCAAAGAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCU
(((((....))).)).........((((((..(((((........)))))...).)))))..(((((.(((.....(((((....)))))))).)))))........... ( -25.60)
>DroPse_CAF1 83824 110 + 1
AGCGUCCUUGCGUACUUUCCAGUCGACAGGAUUUCUCAAAGAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCU
.((((....))))...........((((((..(((((........)))))...).)))))..(((((.(((.....(((((....)))))))).)))))........... ( -26.60)
>DroGri_CAF1 112648 110 + 1
CGCGUCCUUGCGCACUUUCCAGUCGACAGGAUUUCUCAAAGAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCU
.((((....))))...........((((((..(((((........)))))...).)))))..(((((.(((.....(((((....)))))))).)))))........... ( -29.00)
>DroWil_CAF1 172646 110 + 1
CGCGUCCUUGCGCACUUUCCAGUCGACAGGAUUUCUCAAAGAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCU
.((((....))))...........((((((..(((((........)))))...).)))))..(((((.(((.....(((((....)))))))).)))))........... ( -29.00)
>DroMoj_CAF1 135788 110 + 1
CGCGUCCUUGCGCACUUUCCAGUCGACAGGAUUUCUCAAAGAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCU
.((((....))))...........((((((..(((((........)))))...).)))))..(((((.(((.....(((((....)))))))).)))))........... ( -29.00)
>DroPer_CAF1 90106 110 + 1
AGCGUCCUUGCGUACUUUCCAGUCGACAGGAUUUCUCAAAGAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCU
.((((....))))...........((((((..(((((........)))))...).)))))..(((((.(((.....(((((....)))))))).)))))........... ( -26.60)
>consensus
CGCGUCCUUGCGCACUUUCCAGUCGACAGGAUUUCUCAAAGAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCU
.((((....))))...........((((((..(((((........)))))...).)))))..(((((.(((.....(((((....)))))))).)))))........... (-27.22 = -27.22 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	6,322,883 – 6,322,989
Length	106
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	95.13
Mean single sequence MFE	-25.10
Consensus MFE	-25.05
Energy contribution	-25.05
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	1.00
SVM decision value	5.04
SVM RNA-class probability	0.999970
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6322883 106 + 27905053
GAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUU-CGCUACUUUUUGCGUUUGCUUUUUUUCC
(((((((((((((((......))))).((((.....(((((....))))).....)))).....)))))))))).--...-(((........))).............. ( -25.00)
>DroVir_CAF1 93510 106 + 1
GAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUUCCGCUACUUUUUGCGUUUUUCUG-UAUGC
(((((((((((((((......))))).((((.....(((((....))))).....)))).....)))))))))).--....(((........)))........-..... ( -25.20)
>DroGri_CAF1 112688 106 + 1
GAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUUCCGCUACUUUUUGCGUUUUUCUG-UAUGC
(((((((((((((((......))))).((((.....(((((....))))).....)))).....)))))))))).--....(((........)))........-..... ( -25.20)
>DroEre_CAF1 94884 104 + 1
GAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUU-CGCUACUUUUUGCGUUUGCUUU--UUCC
(((((((((((((((......))))).((((.....(((((....))))).....)))).....)))))))))).--...-(((........)))........--.... ( -25.00)
>DroWil_CAF1 172686 107 + 1
GAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUUUUUUU-CGCUACUUUUUGCGUUUUUCUG-UUUGC
(((((((((((((((......))))).((((.....(((((....))))).....)))).....))))))))))......-(((........)))........-..... ( -25.00)
>DroMoj_CAF1 135828 106 + 1
GAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUUCCGCUACUUUUUGCGUUUUUCUG-UAUGC
(((((((((((((((......))))).((((.....(((((....))))).....)))).....)))))))))).--....(((........)))........-..... ( -25.20)
>consensus
GAUAAGGGAAUUGCUCUGUCAAGUAAAGUGAUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU__UUU_CGCUACUUUUUGCGUUUUUCUG_UAUGC
(((((((((((((((......))))).((((.....(((((....))))).....)))).....)))))))))).......(((........))).............. (-25.05 = -25.05 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	6,322,913 – 6,323,004
Length	91
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	81.39
Mean single sequence MFE	-13.83
Consensus MFE	-12.25
Energy contribution	-12.25
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.43
Structure conservation index	0.89
SVM decision value	1.49
SVM RNA-class probability	0.958621
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6322913 91 + 27905053
AUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUU-CGCUACUUUUUGCGUUUGCUUUUUUUC-CC---AAGCCCC----CCA--UCCC---
......(((((....))))).........................--...-(((........)))...((((......-..---))))...----...--....--- ( -14.00)
>DroGri_CAF1 112718 101 + 1
AUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUUCCGCUACUUUUUGCGUUUUUCUG-UAUG-CUUGCUAUCCCUCUCUCUC--UCUCACA
.((((((((((....))))).........................--....(((........))).......)-))))-...................--....... ( -13.40)
>DroEre_CAF1 94914 86 + 1
AUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUU-CGCUACUUUUUGCGUUUGCUUU--UUC-CC---AAGCCCC----CCUU--------
......(((((....))))).........................--...-(((........)))...((((.--...-..---))))...----....-------- ( -14.20)
>DroWil_CAF1 172716 98 + 1
AUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUUUUUUU-CGCUACUUUUUGCGUUUUUCUG-UUUG-CUUUCUCGCUCU----CUC--UCUCACA
......(((((....)))))..............................-(((........)))........-...(-(......))...----...--....... ( -12.90)
>DroYak_CAF1 87531 92 + 1
AUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUU-CGCUACUUUUUGCGUUUGCUUU-UUUC-CC---AAGUCCC----CCCCCUCCC---
......(((((....))))).........................--...-(((........)))........-....-..---.......----.........--- ( -12.30)
>DroAna_CAF1 91668 92 + 1
AUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU--UUU-CGCUACUUUUUGCGUUUGCUUU-UUUCGCC---CCGCC------CCU--GCCCGGC
......(((((....))))).........................--...-(((........)))........-....(((---..((.------...--))..))) ( -16.20)
>consensus
AUAUAUGGUCCGAAAGGACUUCAAUUUAUACAAUUUCUCUUAUUU__UUU_CGCUACUUUUUGCGUUUGCUUU_UUUC_CC___AAGCCCC____CCC__UCCC___
......(((((....)))))...............................(((........))).......................................... (-12.25 = -12.25 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:04 2006