Locus 6628

Sequence ID	3L_DroMel_CAF1
Location	17,627,172 – 17,627,308
Length	136
Max. P	0.978815

overview

Window 3

Location	17,627,172 – 17,627,274
Length	102
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	67.37
Mean single sequence MFE	-29.32
Consensus MFE	-17.18
Energy contribution	-16.06
Covariance contribution	-1.12
Combinations/Pair	1.39
Mean z-score	-1.98
Structure conservation index	0.59
SVM decision value	1.82
SVM RNA-class probability	0.978815
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17627172 102 - 23771897
GGUGUUAUGGAUGACCUGGUGGACUCCAGUGACCUGGACGAGGAAGUGCGCAAUUUCUUUUUUUAGGCAGCC---AG-CAAGUCAUUUUU------GUCGUUAACACAACUG
.((((((.(((((((.((.(((((....))(.((((((.((((((((.....)))))))).)))))))..))---).-)).)))))))..------.....))))))..... ( -30.60)
>DroPse_CAF1 15313 81 - 1
GGGGUGAUGGAUGAUCUGGUUGACUCCAGCGACCUGGACGAGGAGGUGCGAAAUUUCUUCCUCUAGGUAUAU---CGCCAUGU-----U-----------------------
..(((((((......((((......))))..(((((((.((((((((.....)))))))).))))))).)))---))))....-----.----------------------- ( -31.90)
>DroYak_CAF1 8749 108 - 1
GGGGUAAUGGAUGACUUGGUGGACUCCAGUGACCUGGACGAGGAAGUGCGCAAUUUCUUUUUUUAGGCAGGC---AG-CAUGUAAUUAUUGUCAUUGUCGUUAACACAAGUG
.............(((((((.(((..((((((((((((.((((((((.....)))))))).)))))((....---.)-)...........)))))))..))).)).))))). ( -29.10)
>DroMoj_CAF1 5511 84 - 1
AGUGUUAUAGAUGAACUUGUUGACUCCAGCGAUUUGGAUGAGGAAGUGCGCAAGUUUUUCUUCUAAGUCAAAUCAAGCCAAGU-----U-----------------------
.............(((((((((....))))(((((((..(((((((.((....)).)))))))....))))))).....))))-----)----------------------- ( -23.10)
>DroPer_CAF1 6821 81 - 1
GGGGUGAUGGAUGAUCUGGUUGACUCCAGCGACCUGGACGAGGAGGUGCGAAAUUUCUUCCUCUAGGUAUAU---CGCCAUGU-----U-----------------------
..(((((((......((((......))))..(((((((.((((((((.....)))))))).))))))).)))---))))....-----.----------------------- ( -31.90)
>consensus
GGGGUGAUGGAUGACCUGGUUGACUCCAGCGACCUGGACGAGGAAGUGCGCAAUUUCUUCUUCUAGGUAGAC___AGCCAUGU_____U_______________________
...............((((......))))...((((((.((((((((.....)))))))).))))))............................................. (-17.18 = -16.06 +  -1.12)

alignment

secondary structure

dotplot

Window 4

Location	17,627,202 – 17,627,308
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.50
Mean single sequence MFE	-36.03
Consensus MFE	-17.12
Energy contribution	-14.18
Covariance contribution	-2.94
Combinations/Pair	1.58
Mean z-score	-2.10
Structure conservation index	0.48
SVM decision value	1.19
SVM RNA-class probability	0.928695
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17627202 106 - 23771897
AAAAGAU------UUGGAAGUUGUGGAACUUCUGGUGUCCGGUGUUAUGGAUGACCUGGUGGACUCCAGUGACCUGGACGAGGAAGUGCGCAAUUUCUUUUUUUAGGCAGCC--------
.(((((.------..((((((((((..((((((..(((((((.((((((((.(.((....)).))))).))))))))))).)))))).)))))))))).)))))........-------- ( -41.10)
>DroVir_CAF1 5246 103 - 1
GAAGGAC------UUGGAGGUGGUUGAGCUACUUGUGCCGGGUGUCAUAGAUGAUCUUGUCGACUCCGCCGACUUGGAUGAGGAGGUACGCAAGUUUUUCUUCUAAGUC-----------
(((((((------(((.((((((.....))))))(((((.((((.....(((......))).....))))..(((....)))..))))).)))))))))).........----------- ( -31.20)
>DroGri_CAF1 5069 114 - 1
AAAGGAU------UUGGAGGUGAUUGAGCUGCUUGUGCCUGGUGUUAUGGAUGAUCUGGUCGAAUCCACCGACUUGGAUGAGGAAGUGCGCAAGUUUUUCUACUAAGUCUAAGUCUAAGU
...((((------((((((((.(((.(((.(((.......))))))...))).))))..))))))))...(((((((((..(((((.((....)).))))).....)))))))))..... ( -33.40)
>DroYak_CAF1 8785 106 - 1
AAAAGAU------UUGGAAGUUGUGGAACUUCUGGUGUCCGGGGUAAUGGAUGACUUGGUGGACUCCAGUGACCUGGACGAGGAAGUGCGCAAUUUCUUUUUUUAGGCAGGC--------
.(((((.------..((((((((((..((((((..((((((((....((((.(.((....)).)))))....)))))))).)))))).)))))))))).)))))........-------- ( -39.90)
>DroMoj_CAF1 5522 107 - 1
AAAGGAU------UUGGAGGUGAUUGAGCUGCUUGUGCCGAGUGUUAUAGAUGAACUUGUUGACUCCAGCGAUUUGGAUGAGGAAGUGCGCAAGUUUUUCUUCUAAGUCAAA-------U
....(((------(((((((.((.......(((((((((...(.((((...((((.((((((....)))))))))).)))).)..).)))))))).)).))))))))))...-------. ( -28.60)
>DroPer_CAF1 6830 112 - 1
GAAGGAGCUGGAGCUGGAGGCGGUGGAACUGCUCGUACCUGGGGUGAUGGAUGAUCUGGUUGACUCCAGCGACCUGGACGAGGAGGUGCGAAAUUUCUUCCUCUAGGUAUAU--------
......((((((((..((.((((.....))))((((.((.........))))))))..)....))))))).(((((((.((((((((.....)))))))).)))))))....-------- ( -42.00)
>consensus
AAAGGAU______UUGGAGGUGGUGGAACUGCUUGUGCCCGGUGUUAUGGAUGAUCUGGUCGACUCCAGCGACCUGGACGAGGAAGUGCGCAAGUUCUUCUUCUAAGUAGAA________
..............((((..(((....((.....))..((((.((((....)))))))))))..))))...(((((((.((((((.(.....).)))))).)))))))............ (-17.12 = -14.18 +  -2.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:02 2006