Locus 8769

Sequence ID	3R_DroMel_CAF1
Location	23,405,203 – 23,405,294
Length	91
Max. P	0.968006

overview

Window 0

Location	23,405,203 – 23,405,294
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	83.55
Mean single sequence MFE	-20.58
Consensus MFE	-11.70
Energy contribution	-12.14
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-2.04
Structure conservation index	0.57
SVM decision value	-0.03
SVM RNA-class probability	0.519305
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23405203 91 + 27905053
AAAUCGAGGGCCUUGUCACCGCGAUGACAGCUACAGCUACAUAUAUCUAUAUAGAGCUAAAGUUGUUCUGCCCCUUCGAAUUGAUUUACCA
...((((((((...(((.....)))(((((((..((((..((((....))))..))))..)))))))..))))..))))............ ( -22.90)
>DroSec_CAF1 19662 84 + 1
AAAUCGAGGGCCUUGUCACCGCGAUGACAGCUACAGCU----AUAUCUAUAUAGAGCUAUAG---UUCUGCCCCUUCGAAUUGAUUUACCA
...((((((((..(((((......)))))((((.((((----.(((....))).)))).)))---)...))))..))))............ ( -21.50)
>DroSim_CAF1 19883 84 + 1
AAAUCGAGGGCCUUGUCACCGCGAUGACAGCUACAGCU----AUAUCUAUAUAGAGCUAUAG---UUCUGCCCCUUCGAAUUGAUUUACCA
...((((((((..(((((......)))))((((.((((----.(((....))).)))).)))---)...))))..))))............ ( -21.50)
>DroEre_CAF1 23034 72 + 1
AAAUCAAGGGCCUUGUCACAGGGAUGACAGCUACAGCU---------------GAGCUAUAG---UUGUGC-CCAACGAAUUGAUUUACCA
(((((((((((((((...))))....(((((((.(((.---------------..))).)))---))))))-))......))))))).... ( -20.00)
>DroYak_CAF1 21009 73 + 1
AAAUCAAGGGCCUUGUCACCGCGAUGACAGCUACAGCU---------------GAACUAUAG---UUCUACUCCAUCGAAUUGAUUUACCA
.......((.....((((...(((((..(((....)))---------------((((....)---))).....)))))...))))...)). ( -17.00)
>consensus
AAAUCGAGGGCCUUGUCACCGCGAUGACAGCUACAGCU____AUAUCUAUAUAGAGCUAUAG___UUCUGCCCCUUCGAAUUGAUUUACCA
(((((((((((.((((((......))))))(((.((((................)))).))).......)))).......))))))).... (-11.70 = -12.14 +   0.44)

alignment

secondary structure

dotplot

Window 1

Location	23,405,203 – 23,405,294
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	83.55
Mean single sequence MFE	-24.58
Consensus MFE	-19.57
Energy contribution	-19.41
Covariance contribution	-0.16
Combinations/Pair	1.14
Mean z-score	-2.34
Structure conservation index	0.80
SVM decision value	1.62
SVM RNA-class probability	0.968006
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23405203 91 - 27905053
UGGUAAAUCAAUUCGAAGGGGCAGAACAACUUUAGCUCUAUAUAGAUAUAUGUAGCUGUAGCUGUCAUCGCGGUGACAAGGCCCUCGAUUU
............((((.(((.(.......((.(((((.(((((....))))).))))).)).((((((....)))))).).)))))))... ( -26.10)
>DroSec_CAF1 19662 84 - 1
UGGUAAAUCAAUUCGAAGGGGCAGAA---CUAUAGCUCUAUAUAGAUAU----AGCUGUAGCUGUCAUCGCGGUGACAAGGCCCUCGAUUU
............((((.(((.(....---((((((((.(((....))).----)))))))).((((((....)))))).).)))))))... ( -28.50)
>DroSim_CAF1 19883 84 - 1
UGGUAAAUCAAUUCGAAGGGGCAGAA---CUAUAGCUCUAUAUAGAUAU----AGCUGUAGCUGUCAUCGCGGUGACAAGGCCCUCGAUUU
............((((.(((.(....---((((((((.(((....))).----)))))))).((((((....)))))).).)))))))... ( -28.50)
>DroEre_CAF1 23034 72 - 1
UGGUAAAUCAAUUCGUUGG-GCACAA---CUAUAGCUC---------------AGCUGUAGCUGUCAUCCCUGUGACAAGGCCCUUGAUUU
....(((((((......((-((....---(((((((..---------------.))))))).((((((....))))))..))))))))))) ( -21.70)
>DroYak_CAF1 21009 73 - 1
UGGUAAAUCAAUUCGAUGGAGUAGAA---CUAUAGUUC---------------AGCUGUAGCUGUCAUCGCGGUGACAAGGCCCUUGAUUU
....(((((((.....((.(((.(((---(....))))---------------.))).))((((((((....)))))..)))..))))))) ( -18.10)
>consensus
UGGUAAAUCAAUUCGAAGGGGCAGAA___CUAUAGCUCUAUAUAGAUAU____AGCUGUAGCUGUCAUCGCGGUGACAAGGCCCUCGAUUU
............((((.((.((.......((((((((................)))))))).((((((....))))))..))))))))... (-19.57 = -19.41 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:23 2006