Locus 1723

Sequence ID	2R_DroMel_CAF1
Location	6,486,062 – 6,486,182
Length	120
Max. P	0.755170

overview

Window 7

Location	6,486,062 – 6,486,156
Length	94
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	84.87
Mean single sequence MFE	-35.53
Consensus MFE	-25.07
Energy contribution	-26.90
Covariance contribution	1.83
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.71
SVM decision value	0.07
SVM RNA-class probability	0.567455
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6486062 94 + 20766785
AGGCUGCGAAGGCUGGGAAGCCAGG--AUCUGCGUCCUGCAGACAAACUUCCGCUGGAGGAAAUUUUAUGCAGGGCACGGCAAAAGGAUGCGCAGC
..((((((..((((....))))...--..(((.((((((((...(((.((((......)))).)))..)))))))).)))..........)))))) ( -38.90)
>DroSec_CAF1 53941 94 + 1
AGGUUGCGCAGGCUGGGAAGCCAGG--AUCUGCGUCCUGCAGACAAACUUCCGCUGGAGGAAAUUUUAUGCAGGGCACGGCAAAAGGAUGCGCAGC
..((((((((((((....))))...--..(((.((((((((...(((.((((......)))).)))..)))))))).)))........)))))))) ( -41.30)
>DroSim_CAF1 41495 94 + 1
AGGUUGCGCAGGCUGGGAAGCCAGG--AUCUGCGUCCUGCAGACAAACUUCCGCUGGAGGAAAUUUUAUGCAGGGCACGGCAAAAGGAUGCGCAGC
..((((((((((((....))))...--..(((.((((((((...(((.((((......)))).)))..)))))))).)))........)))))))) ( -41.30)
>DroEre_CAF1 52196 81 + 1
-------------UGGGAAGCCAGG--AUCUGCGUCCUGCAGACAAACUUCCGCUGCUGGAAAUUUUAUGCAGGGCACGGCAAAAGGAUGCGCAGC
-------------(((....)))..--..((((((((((((...(((.(((((....))))).)))..))))))))...(((......))))))). ( -29.70)
>DroAna_CAF1 53265 84 + 1
-------GAGGGCUC---UGCCAGG--AUCUGCGUCCUGCAGACAAACUUCCGCUGGAGGAAAUUUUAUGCAGGGCACGGCAAAAGGAUGCGCAGC
-------...(((..---.)))...--..((((((((((((...(((.((((......)))).)))..))))))))...(((......))))))). ( -30.20)
>DroPer_CAF1 50912 92 + 1
AGG--GGGCAGG--GGGCGGCGAGGGGUACCCCGGGCUGCAGACAAACUUCCGCUAAAGGAAAUUUUAUGCAGGGCACGGCCAAAGGAUGCGCAGC
...--(.(((..--((.((((..(((....)))...(((((...(((.((((......)))).)))..))))).)).)).))......))).)... ( -31.80)
>consensus
AGG__GCGCAGGCUGGGAAGCCAGG__AUCUGCGUCCUGCAGACAAACUUCCGCUGGAGGAAAUUUUAUGCAGGGCACGGCAAAAGGAUGCGCAGC
............((((....)))).....((((((((((((...(((.((((......)))).)))..))))))))...(((......))))))). (-25.07 = -26.90 +   1.83)

alignment

secondary structure

dotplot

Window 8

Location	6,486,062 – 6,486,156
Length	94
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	84.87
Mean single sequence MFE	-33.30
Consensus MFE	-24.16
Energy contribution	-24.52
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-2.93
Structure conservation index	0.73
SVM decision value	0.49
SVM RNA-class probability	0.755170
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6486062 94 - 20766785
GCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUCCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGCUUCCCAGCCUUCGCAGCCU
((((((((......))).(((.((((((..((((((((......))))))))...)))))).))).((.--...((((....)))).))))))).. ( -38.40)
>DroSec_CAF1 53941 94 - 1
GCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUCCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGCUUCCCAGCCUGCGCAACCU
..((((((..........(((.((((((..((((((((......))))))))...)))))).)))....--...((((....)))))))))).... ( -36.20)
>DroSim_CAF1 41495 94 - 1
GCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUCCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGCUUCCCAGCCUGCGCAACCU
..((((((..........(((.((((((..((((((((......))))))))...)))))).)))....--...((((....)))))))))).... ( -36.20)
>DroEre_CAF1 52196 81 - 1
GCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCAGCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGCUUCCCA-------------
((((((((......))).((((...))))..........)))))(((((((.((((((.....))))))--...)))))))..------------- ( -30.70)
>DroAna_CAF1 53265 84 - 1
GCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUCCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGCA---GAGCCCUC-------
.(((((((......))).(((.((((((..((((((((......))))))))...)))))).)))....--....)))---).......------- ( -30.60)
>DroPer_CAF1 50912 92 - 1
GCUGCGCAUCCUUUGGCCGUGCCCUGCAUAAAAUUUCCUUUAGCGGAAGUUUGUCUGCAGCCCGGGGUACCCCUCGCCGCCC--CCUGCCC--CCU
.....(((......(((.(((..(((((..((((((((......))))))))...)))))...(((....))).))).))).--..)))..--... ( -27.70)
>consensus
GCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUCCAGCGGAAGUUUGUCUGCAGGACGCAGAU__CCUGGCUUCCCAGCCUGCGC__CCU
.(((((((......)))...(.((((((..((((((((......))))))))...)))))).)))))............................. (-24.16 = -24.52 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	6,486,080 – 6,486,182
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.91
Mean single sequence MFE	-32.35
Consensus MFE	-25.72
Energy contribution	-24.89
Covariance contribution	-0.83
Combinations/Pair	1.24
Mean z-score	-1.84
Structure conservation index	0.80
SVM decision value	0.33
SVM RNA-class probability	0.690470
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6486080 102 - 20766785
---ACAUGG-C----------AUCCAUGUAUUAUUUAAGCGCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUCCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGC--U
---((((((-.----------..))))))...........((((.(((......))))(((.((((((..((((((((......))))))))...)))))).)))....--...)))--. ( -32.80)
>DroPse_CAF1 51245 104 - 1
---ACAUGG-C----------AUCCAUGUAUUAUUUAAGCGCUGCGCAUCCUUUGGCCGUGCCCUGCAUAAAAUUUCCUUUAGCGGAAGUUUGUCUGCAGCCCGGGGUACCCCUCGC--C
---((((((-.----------..)))))).........((((.((.((.....)))).)))).(((((..((((((((......))))))))...)))))...(((....)))....--. ( -33.30)
>DroEre_CAF1 52201 102 - 1
---ACAUGG-C----------AUCCAUGUAUUAUUUAAGCGCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCAGCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGC--U
---((((((-.----------..))))))...........((((.(((......))))(((.((((((..((((((((......))))))))...)))))).)))....--...)))--. ( -32.90)
>DroWil_CAF1 68095 118 - 1
AGGAUAUGGGCAACUGUCCGGCUCCAUGUAUUAUUUAAGCAUUGCGCAUCCUUUUGCCGUGCCUUGCAUAAAAUUUCAUUCUGCGGAAGUUUGUCUGCAGCUCCGUCAC--CGUCACCAU
.(((..(((((....)))))..)))........((((.(((..((((...........))))..))).))))........(((((((......))))))).........--......... ( -28.50)
>DroAna_CAF1 53273 102 - 1
---ACAUGG-C----------AUCCAUGUAUUAUUUAAGCGCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUCCAGCGGAAGUUUGUCUGCAGGACGCAGAU--CCUGGC--A
---((((((-.----------..))))))...........((((.(((......))))(((.((((((..((((((((......))))))))...)))))).)))....--...)))--. ( -33.30)
>DroPer_CAF1 50926 104 - 1
---ACAUGG-C----------AUCCAUGUAUUAUUUAAGCGCUGCGCAUCCUUUGGCCGUGCCCUGCAUAAAAUUUCCUUUAGCGGAAGUUUGUCUGCAGCCCGGGGUACCCCUCGC--C
---((((((-.----------..)))))).........((((.((.((.....)))).)))).(((((..((((((((......))))))))...)))))...(((....)))....--. ( -33.30)
>consensus
___ACAUGG_C__________AUCCAUGUAUUAUUUAAGCGCUGCGCAUCCUUUUGCCGUGCCCUGCAUAAAAUUUCCUUCAGCGGAAGUUUGUCUGCAGCACGCAGAU__CCUCGC__U
...((((((..............)))))).........((((.(((........))).)))).(((((..((((((((......))))))))...)))))....(((.....)))..... (-25.72 = -24.89 +  -0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:42 2006