Locus 1775

Sequence ID	2L_DroMel_CAF1
Location	4,855,874 – 4,856,004
Length	130
Max. P	0.829875

overview

Window 2

Location	4,855,874 – 4,855,972
Length	98
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	80.61
Mean single sequence MFE	-23.72
Consensus MFE	-19.52
Energy contribution	-19.85
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.82
SVM decision value	0.71
SVM RNA-class probability	0.829875
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4855874 98 + 22407834
---UCAAUUCC------CAUGACUCC----AG-ACCAUAUAUCAUCGGCUCCUGCGACUUCCGGUUGUCGCUUUUGGCAC-------CCGCCAUUCCCACUGUCUAUUUAUAGGCGCCG
---........------.........----..-............((((.((((((((........)))))...((((..-------..))))..................))).)))) ( -23.40)
>DroPse_CAF1 7580 116 + 1
---CACACUCUUUUUGACAUAAUUUCCUACACAUCCAUAUAUCAUCGGCUACUCCGACUUCCGGUUGUCGCUUUUGGCAUUUGCUAUUCGCCAUUCCCACUGUCUAUUUAUAGGCGCCG
---..........................................((((.............((..((.((...((((....))))...)).))..))...(((((....))))))))) ( -19.60)
>DroEre_CAF1 6639 96 + 1
-----CACUCC------CAUGGCUCC----AG-ACCAUAUAUCAUCGGCUCCUGCGACUUCCGGUUGUCGCUUUUGGCAG-------CCGCCAUUCCCACUGUCUAUUUAUAGGCGCCG
-----......------...(((...----..-............(((((((.(((((........)))))....)).))-------)))...........(((((....)))))))). ( -27.60)
>DroYak_CAF1 6441 96 + 1
-----CACUCC------CAUGGCUCC----AG-ACCAUAUAUCAUCGGCUCCUGCGACUUCCGGUUGUCGCUUUUGGCAC-------CCGCCAUUCCCACUGUCUAUUUAUAGGCGCCG
-----......------.(((((...----.)-.)))).......((((.((((((((........)))))...((((..-------..))))..................))).)))) ( -26.10)
>DroAna_CAF1 10949 101 + 1
UGCCCACACCC------CAUAGUGCC----AG-ACUAUAUAUCAUCGGCUCCUGCGACUUCCGGUUGUCGCUUUUGGCAU-------UUGCCAUUCCCACUGUCUAUUUAUAGGCGCCG
...........------.(((((...----..-))))).......((((.((((((((........)))))...((((..-------..))))..................))).)))) ( -26.00)
>DroPer_CAF1 7471 116 + 1
---CACACUCUUUUUGACAUAAUUUCCUACACAUCCAUAUAUCAUCGGCUACUCCGACUUCCGGUUGUCGCUUUUGGCAUUUGCUAUUCGCCAUUCCCACUGUCUAUUUAUAGGCGCCG
---..........................................((((.............((..((.((...((((....))))...)).))..))...(((((....))))))))) ( -19.60)
>consensus
___C_CACUCC______CAUAACUCC____AG_ACCAUAUAUCAUCGGCUCCUGCGACUUCCGGUUGUCGCUUUUGGCAU_______CCGCCAUUCCCACUGUCUAUUUAUAGGCGCCG
.............................................((((....(((((........)))))...((((...........))))........(((((....))))))))) (-19.52 = -19.85 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	4,855,900 – 4,856,004
Length	104
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	80.66
Mean single sequence MFE	-35.04
Consensus MFE	-24.35
Energy contribution	-24.55
Covariance contribution	0.20
Combinations/Pair	1.05
Mean z-score	-1.38
Structure conservation index	0.70
SVM decision value	0.19
SVM RNA-class probability	0.624750
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4855900 104 - 22407834
CGG--------CGGUUUUCAUGUGCGGUUGUCUGCGUGAGCGGCGCCUAUAAAUAGACAGUGGGAAUGGCGG-------GUGCCAAAAGCGACAACCGGAAGUCGCAGGAGCCGAUGAU
((.--------((((((...((((((((((((.((....))(((((((......................))-------)))))......)))))))).....)))).)))))).)).. ( -38.55)
>DroPse_CAF1 7617 108 - 1
AGG--------AGGCAGUC--GUG-ACGUGUCUGCGUGAGCGGCGCCUAUAAAUAGACAGUGGGAAUGGCGAAUAGCAAAUGCCAAAAGCGACAACCGGAAGUCGGAGUAGCCGAUGAU
...--------.(((.(((--((.-..(((.((((....)))))))..............(((.(...((.....))...).)))...)))))..(((.....)))....)))...... ( -32.50)
>DroEre_CAF1 6663 112 - 1
GCGUGGCGUAGUGGUUUCCAUGUGAAGAUGUAUGCGUGAGCGGCGCCUAUAAAUAGACAGUGGGAAUGGCGG-------CUGCCAAAAGCGACAACCGGAAGUCGCAGGAGCCGAUGAU
((.((((((.((.((((((((((..(..((((.((((.....)))).))))..)..))).))))))).)).)-------).))))...(((((........)))))....))....... ( -36.00)
>DroYak_CAF1 6465 101 - 1
GCGUGG-----------CCAUGUGAGGGUGUCUGCGUGAGCGGCGCCUAUAAAUAGACAGUGGGAAUGGCGG-------GUGCCAAAAGCGACAACCGGAAGUCGCAGGAGCCGAUGAU
.(((((-----------((......(((((.((((....)))))))))..................((((..-------..))))...(((((........)))))..).))).))).. ( -34.30)
>DroAna_CAF1 10978 101 - 1
GAG--------UGGC---UGGGCGGUAGUGGCUGCGUGAGCGGCGCCUAUAAAUAGACAGUGGGAAUGGCAA-------AUGCCAAAAGCGACAACCGGAAGUCGCAGGAGCCGAUGAU
...--------((((---(.((((...((.(((((....))))).(((((.........)))))....))..-------.))))....(((((........)))))...)))))..... ( -36.40)
>DroPer_CAF1 7508 108 - 1
AGG--------AGGCAGUC--GUG-ACGUGUCUGCGUGAGCGGCGCCUAUAAAUAGACAGUGGGAAUGGCGAAUAGCAAAUGCCAAAAGCGACAACCGGAAGUCGGAGUAGCCGAUGAU
...--------.(((.(((--((.-..(((.((((....)))))))..............(((.(...((.....))...).)))...)))))..(((.....)))....)))...... ( -32.50)
>consensus
GGG________AGGC__UCAUGUG_AGGUGUCUGCGUGAGCGGCGCCUAUAAAUAGACAGUGGGAAUGGCGA_______AUGCCAAAAGCGACAACCGGAAGUCGCAGGAGCCGAUGAU
.................................((....))(((.(((((.........)))))..(((((.........)))))...(((((........)))))....)))...... (-24.35 = -24.55 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:53 2006