Locus 3557

Sequence ID	2R_DroMel_CAF1
Location	11,872,473 – 11,872,641
Length	168
Max. P	0.880516

overview

Window 0

Location	11,872,473 – 11,872,573
Length	100
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	81.09
Mean single sequence MFE	-23.57
Consensus MFE	-15.36
Energy contribution	-15.95
Covariance contribution	0.59
Combinations/Pair	1.09
Mean z-score	-1.81
Structure conservation index	0.65
SVM decision value	0.39
SVM RNA-class probability	0.715683
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11872473 100 - 20766785
AAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGCAGGCGCAUAC------ACACUCGCAUUCG---CCCGCC
...((((((((..((((.(((..(((((((((......)))))).)-))..))).))))))))))))...((.((((.((.(------......).)).))---)).)). ( -27.40)
>DroSec_CAF1 13046 106 - 1
AAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGCGGGCGCACACACACACACACUCGCACUCA---ACCGCC
...((((((((..((((.(((..(((((((((......)))))).)-))..))).))))))))))))...(((((.(............).))))).....---...... ( -25.40)
>DroSim_CAF1 12548 106 - 1
AAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGCAGGCACACACACACACACACUCGCACUCA---ACCGCC
...((((((((..((((.(((..(((((((((......)))))).)-))..))).))))))))))))...((((.................)).)).....---...... ( -20.33)
>DroEre_CAF1 15043 97 - 1
AAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGC------------ACACACACAUACACUCGACGGCCGCC
......((((((.((((.(((..(((((((((......)))))).)-))..))).))))...(((....)))------------................)))))).... ( -20.00)
>DroYak_CAF1 12943 106 - 1
AAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGCUGACGCACACACACACACGCAUACACUCG---CCCGCC
...((((((((..((((.(((..(((((((((......)))))).)-))..))).))))))))))))...((....))............((........)---)..... ( -20.80)
>DroAna_CAF1 11669 94 - 1
AAUUCUGCUGUCAAAAUACUUGACAUUUGAUUAAUUGAAAUCGACUUUGGAAAGUA-----AGUUGAUAAGCAGGCUGGCGCACACGGACA--------CG---CACGCC
...(((((((((((..(((((..((.((((((......))))))...))..)))))-----..))))).))))))..((((....((....--------))---..)))) ( -27.50)
>consensus
AAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU_UGGAAAGUUACUACAGUUGAUAAGCAGGCGCACACACACACACACUCGCACUCG___CCCGCC
...((((((((..((((.(((..((.((((((......))))))...))..))).))))))))))))........................................... (-15.36 = -15.95 +   0.59)

alignment

secondary structure

dotplot

Window 1

Location	11,872,499 – 11,872,613
Length	114
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	78.58
Mean single sequence MFE	-26.03
Consensus MFE	-12.40
Energy contribution	-14.40
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.48
SVM decision value	0.37
SVM RNA-class probability	0.708736
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11872499 114 - 20766785
CGCUUCCACUUUGGGACUGCUGCCACCCAAAUAAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGCAGG
.((((....((((((..........))))))............((((((((..((((.(((..(((((((((......)))))).)-))..))).)))))))))))).))))... ( -28.20)
>DroSim_CAF1 12580 112 - 1
--CUUCCACUUUGGAACUGCUGCUCCCCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGCAGG
--.((((.....))))(((((((((.......)))).......((((((((..((((.(((..(((((((((......)))))).)-))..))).))))))))))))..))))). ( -31.30)
>DroEre_CAF1 15069 108 - 1
CCCCUCCACU-UGGGACUGCUGCU--CCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGC---
.(((......-.)))...((((((--(.....)))).......((((((((..((((.(((..(((((((((......)))))).)-))..))).))))))))))))..)))--- ( -26.80)
>DroYak_CAF1 12975 111 - 1
CCCUUUUACU-UGGGACUGCUGCU--UCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU-UGGAAAGUUACUACAGUUGAUAAGCUGA
(((.......-.)))...((((((--(.....)))).......((((((((..((((.(((..(((((((((......)))))).)-))..))).))))))))))))..)))... ( -26.10)
>DroAna_CAF1 11693 93 - 1
--------------GAG---UUCUCCCCAAAUGAGUUAUAAAUUCUGCUGUCAAAAUACUUGACAUUUGAUUAAUUGAAAUCGACUUUGGAAAGUA-----AGUUGAUAAGCAGG
--------------...---..(((.......))).........((((((((((..(((((..((.((((((......))))))...))..)))))-----..))))).))))). ( -22.00)
>DroPer_CAF1 12536 93 - 1
--------------CCGUGCGACU--CCAAAUGAGUUAUAAACUCUCUUGUCAAAAUACUUGACAAUUGAUUAAUUGAAAUCGACU-UUGAAAGUA-----AGUUGAUAAGCAGG
--------------((.(((((((--(.....)))))..........(((((((..(((((..(((((((((......))))))..-))).)))))-----..)))))))))))) ( -21.80)
>consensus
__CUUCCACU_UGGGACUGCUGCU__CCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAUUGAAAUCGACU_UGGAAAGUUACUACAGUUGAUAAGCAGG
..................(((..........(.(((((.....((((.((((((.....)))))).)))).))))).).(((((((.(((.......))).))))))).)))... (-12.40 = -14.40 +   2.00)

alignment

secondary structure

dotplot

Window 2

Location	11,872,538 – 11,872,641
Length	103
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	77.60
Mean single sequence MFE	-25.92
Consensus MFE	-14.87
Energy contribution	-15.76
Covariance contribution	0.89
Combinations/Pair	1.15
Mean z-score	-2.00
Structure conservation index	0.57
SVM decision value	0.90
SVM RNA-class probability	0.878657
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11872538 103 + 20766785
AUUAAUCAAUUGUCAAAAUACUUGACAGCUGAAUUUAUAACUUAUUUGGGUGGCAGCAGUCCCAAAGUGGAAGCGAAGCAGGAGACAGCAGGAUGUUGCUGCG
.....(((.(((((((.....))))))).))).................(..((((((.(((....((....))...((.(....).)).)))))))))..). ( -28.40)
>DroSec_CAF1 13117 88 + 1
AUUAAUCAAUUGUCAAAAUACUUGACAGCUGAAUUUAUAACUCAUUUGGGGAGCAGCAGUUCCAAAGUGGAAG---------------CAGGAUGUUGCUGCG
.....(((.(((((((.....))))))).))).........((((((..(((((....))))).))))))..(---------------(((.......)))). ( -24.00)
>DroSim_CAF1 12619 88 + 1
AUUAAUCAAUUGUCAAAAUACUUGACAGCUGAAUUUAUAACUCAUUUGGGGAGCAGCAGUUCCAAAGUGGAAG---------------CAGGAUGUUGCUGCG
.....(((.(((((((.....))))))).))).........((((((..(((((....))))).))))))..(---------------(((.......)))). ( -24.00)
>DroEre_CAF1 15105 100 + 1
AUUAAUCAAUUGUCAAAAUACUUGACAGCUGAAUUUAUAACUCAUUUGG--AGCAGCAGUCCCA-AGUGGAGGGGAAACGGGCGACAGCAGGAUGUUGCUGCG
.....(((.(((((((.....))))))).)))........(((((((((--..(....)..)))-))).))).(....).(((((((......)))))))... ( -29.70)
>DroYak_CAF1 13014 100 + 1
AUUAAUCAAUUGUCAAAAUACUUGACAGCUGAAUUUAUAACUCAUUUGA--AGCAGCAGUCCCA-AGUAAAAGGGAAGCAGGCGACAGCAGGAUGUUGCUGCG
.....(((.(((((((.....))))))).))).................--.(((((..((((.-.......))))((((.((....))....))))))))). ( -27.90)
>DroPer_CAF1 12570 83 + 1
AUUAAUCAAUUGUCAAGUAUUUUGACAAGAGAGUUUAUAACUCAUUUGG--AGUCGCACGG----------------ACAGGCG--GGCAGGAUGUGUCUGCG
.....((((((((((((...))))))))..((((.....))))..))))--.(((.....)----------------))..(((--((((.....))))))). ( -21.50)
>consensus
AUUAAUCAAUUGUCAAAAUACUUGACAGCUGAAUUUAUAACUCAUUUGG__AGCAGCAGUCCCA_AGUGGAAG_____CAGGCG__AGCAGGAUGUUGCUGCG
.....(((.(((((((.....))))))).)))....................((((((((((............................))))..)))))). (-14.87 = -15.76 +   0.89)

alignment

secondary structure

dotplot

Window 3

Location	11,872,538 – 11,872,641
Length	103
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	77.60
Mean single sequence MFE	-20.82
Consensus MFE	-12.90
Energy contribution	-14.23
Covariance contribution	1.33
Combinations/Pair	1.05
Mean z-score	-1.84
Structure conservation index	0.62
SVM decision value	0.91
SVM RNA-class probability	0.880516
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11872538 103 - 20766785
CGCAGCAACAUCCUGCUGUCUCCUGCUUCGCUUCCACUUUGGGACUGCUGCCACCCAAAUAAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAU
.((((((...(((((..((.....((...))....))..))))).))))))....................((((.(((((((...))))))).))))..... ( -21.50)
>DroSec_CAF1 13117 88 - 1
CGCAGCAACAUCCUG---------------CUUCCACUUUGGAACUGCUGCUCCCCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAU
.((((((...(((..---------------..........)))..))))))....................((((.(((((((...))))))).))))..... ( -19.70)
>DroSim_CAF1 12619 88 - 1
CGCAGCAACAUCCUG---------------CUUCCACUUUGGAACUGCUGCUCCCCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAU
.((((((...(((..---------------..........)))..))))))....................((((.(((((((...))))))).))))..... ( -19.70)
>DroEre_CAF1 15105 100 - 1
CGCAGCAACAUCCUGCUGUCGCCCGUUUCCCCUCCACU-UGGGACUGCUGCU--CCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAU
.((((((.......((....)).....((((.......-.)))).)))))).--.................((((.(((((((...))))))).))))..... ( -22.60)
>DroYak_CAF1 13014 100 - 1
CGCAGCAACAUCCUGCUGUCGCCUGCUUCCCUUUUACU-UGGGACUGCUGCU--UCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAU
.((((((......)))))).((..((.((((.......-.))))..)).)).--((((.(((((.....)))))..(((((((...))))))).))))..... ( -25.50)
>DroPer_CAF1 12570 83 - 1
CGCAGACACAUCCUGCC--CGCCUGU----------------CCGUGCGACU--CCAAAUGAGUUAUAAACUCUCUUGUCAAAAUACUUGACAAUUGAUUAAU
.((((.......)))).--((((...----------------..).)))(((--(.....)))).......((..(((((((.....)))))))..))..... ( -15.90)
>consensus
CGCAGCAACAUCCUGCU__CGCCUG_____CUUCCACU_UGGGACUGCUGCU__CCAAAUGAGUUAUAAAUUCAGCUGUCAAGUAUUUUGACAAUUGAUUAAU
.((((((...(((...........................)))..))))))....................((((.((((((.....)))))).))))..... (-12.90 = -14.23 +   1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:27 2006