Locus 3174

Sequence ID	2R_DroMel_CAF1
Location	10,836,968 – 10,837,087
Length	119
Max. P	0.997476

overview

Window 4

Location	10,836,968 – 10,837,087
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	91.98
Mean single sequence MFE	-27.87
Consensus MFE	-23.22
Energy contribution	-23.62
Covariance contribution	0.40
Combinations/Pair	1.10
Mean z-score	-2.63
Structure conservation index	0.83
SVM decision value	2.87
SVM RNA-class probability	0.997476
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10836968 119 + 20766785
UAAAACAAUACAAAAGAAGGAAACUGAAAUCAAUCGACUUGAUUUCAAUCAUCGGUUUCAGUGUGGCCGCCCUAGGGCUUUGUAAGUUCACCAGGGCUACAUUAAAAUACCAAAUCACU
...............((((....))((((((((.....))))))))..))...(((...((((((((((((....)))..((......))....))))))))).....)))........ ( -30.40)
>DroSec_CAF1 44330 118 + 1
UAAAACAAUACAAAAGAAGGAAACUGAAAUCAAUCGACUUGAUUUCAAUCAUCGGUUUCAGUGUGGCCGACCUAGGGCUUUAUAAUUUUAUCAGGGCUCCAUUAAAAUACCGAAUU-CU
..............(((((....)(((((((((.....)))))))))....(((((......((((((......))((((((((....))).))))).))))......))))).))-)) ( -24.80)
>DroSim_CAF1 44578 118 + 1
UAAAACAAUACAAAAGAAGGAAACUGAAAUCAAUCGACUUGAUUUCAAUCAUCGGUUUCAGUGUGGCCGCCCUAGGGCUUUAUAAUUUUAUCAGGGCUCCAUUAAAAUACCGAAUU-CU
..............(((((....)(((((((((.....)))))))))....(((((...((((..((((((....)))..((......))....)))..)))).....))))).))-)) ( -29.10)
>DroEre_CAF1 49970 118 + 1
UAAAACAAUACAAAAGAAGCAAACUGAAAUCAAUCGACUUGAUUUCAAUCAUCGGUUUCAGUGUGACCGUCCUGGGGCAUUAUAAAUUUACCAGGGCUACAUUAAUAUACCAAAUU-AU
...............(((((....(((((((((.....))))))))).......)))))((((((...(((((((...............))))))))))))).............-.. ( -26.46)
>DroYak_CAF1 50209 118 + 1
UAAAACAAUACAAAAGAAGGAAACUGAAAUCAAUCGACUUGAUUUCAAUCAUCGGUUUGAGUGUGACCGCCCUGGGGCAUUAUAAAUUUGCUAGGGCUACAUUAAUAUACCAAAUU-AU
...............((((....))((((((((.....))))))))..))...(((...((((((...(((((..((((.........))))))))))))))).....))).....-.. ( -28.60)
>consensus
UAAAACAAUACAAAAGAAGGAAACUGAAAUCAAUCGACUUGAUUUCAAUCAUCGGUUUCAGUGUGGCCGCCCUAGGGCUUUAUAAAUUUACCAGGGCUACAUUAAAAUACCAAAUU_CU
...............((((....))((((((((.....))))))))..))...(((...((((((((((((....)))..((......))....))))))))).....)))........ (-23.22 = -23.62 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	10,836,968 – 10,837,087
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	91.98
Mean single sequence MFE	-27.10
Consensus MFE	-22.76
Energy contribution	-23.32
Covariance contribution	0.56
Combinations/Pair	1.15
Mean z-score	-1.30
Structure conservation index	0.84
SVM decision value	0.10
SVM RNA-class probability	0.583400
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10836968 119 - 20766785
AGUGAUUUGGUAUUUUAAUGUAGCCCUGGUGAACUUACAAAGCCCUAGGGCGGCCACACUGAAACCGAUGAUUGAAAUCAAGUCGAUUGAUUUCAGUUUCCUUCUUUUGUAUUGUUUUA
......(((((..((((.(((.(((..((....))......(((....)))))).))).))))))))).((((((((((((.....))))))))))))..................... ( -29.60)
>DroSec_CAF1 44330 118 - 1
AG-AAUUCGGUAUUUUAAUGGAGCCCUGAUAAAAUUAUAAAGCCCUAGGUCGGCCACACUGAAACCGAUGAUUGAAAUCAAGUCGAUUGAUUUCAGUUUCCUUCUUUUGUAUUGUUUUA
((-((.(((((..((((.((..(((..(((..................))))))..)).))))))))).((((((((((((.....))))))))))))...)))).............. ( -24.27)
>DroSim_CAF1 44578 118 - 1
AG-AAUUCGGUAUUUUAAUGGAGCCCUGAUAAAAUUAUAAAGCCCUAGGGCGGCCACACUGAAACCGAUGAUUGAAAUCAAGUCGAUUGAUUUCAGUUUCCUUCUUUUGUAUUGUUUUA
((-((.(((((.((....(((.((((((.................))))))..)))....)).))))).((((((((((((.....))))))))))))...)))).............. ( -30.73)
>DroEre_CAF1 49970 118 - 1
AU-AAUUUGGUAUAUUAAUGUAGCCCUGGUAAAUUUAUAAUGCCCCAGGACGGUCACACUGAAACCGAUGAUUGAAAUCAAGUCGAUUGAUUUCAGUUUGCUUCUUUUGUAUUGUUUUA
.(-((..(((((((.....(.((((((((...((.....))...))))).((((.........))))..((((((((((((.....)))))))))))).))).)...)))))))..))) ( -25.40)
>DroYak_CAF1 50209 118 - 1
AU-AAUUUGGUAUAUUAAUGUAGCCCUAGCAAAUUUAUAAUGCCCCAGGGCGGUCACACUCAAACCGAUGAUUGAAAUCAAGUCGAUUGAUUUCAGUUUCCUUCUUUUGUAUUGUUUUA
.(-((..(((((((........(((((.(((.........)))...)))))(((.........)))((.((((((((((((.....))))))))))))....))...)))))))..))) ( -25.50)
>consensus
AG_AAUUUGGUAUUUUAAUGUAGCCCUGGUAAAAUUAUAAAGCCCUAGGGCGGCCACACUGAAACCGAUGAUUGAAAUCAAGUCGAUUGAUUUCAGUUUCCUUCUUUUGUAUUGUUUUA
......(((((..((((.(((.(((...(((....)))...(((....)))))).))).))))))))).((((((((((((.....))))))))))))..................... (-22.76 = -23.32 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:15 2006