Locus 6794

Sequence ID	2L_DroMel_CAF1
Location	19,004,213 – 19,004,491
Length	278
Max. P	0.998406

overview

Window 2

Location	19,004,213 – 19,004,331
Length	118
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	96.79
Mean single sequence MFE	-25.52
Consensus MFE	-23.22
Energy contribution	-23.62
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.27
Structure conservation index	0.91
SVM decision value	3.09
SVM RNA-class probability	0.998406
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19004213 118 - 22407834
CAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUUAAUCGAACAAGACGACACAAUAAAGUUUUGUAUGAGCAGAGAUAAAGUUUAAAAUAAAAACACUAUUGUU-UUGGUAAA
......((....((((....)))).(((((.(((((((((..(((.(((((((...........))))))).)))..)))))))))))))).....((((((....))))-)))).... ( -28.10)
>DroSec_CAF1 7209 118 - 1
CAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUUAAUCGAACAAGACGACACAAUAAAGUUUUGUAUGAGCAGAGAUAAAGUUUAAAAUAAAAACACUAUUAUU-UUGGUAAA
............((((....)))).(((((.(((((((((..(((.(((((((...........))))))).)))..))))))))))))))..........((((.....-.))))... ( -26.80)
>DroSim_CAF1 5567 119 - 1
CAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUUAAUCGAACAAGACGACACAAUAAAGUUUUGUAUGAGCAGAGAUAAAGUUUAAAAUAAAAACACUAUUAUUUUUGGUAAA
.((((.......((((....)))).(((((.(((((((((..(((.(((((((...........))))))).)))..)))))))))))))).....................))))... ( -26.50)
>DroEre_CAF1 7315 116 - 1
CAUCAUCCGUUCGCUGGAGUCGGCCUAAAC--UUAUUUUUAAUCGAACAAGACGACACAAUAAAGUUUUGUAUGAGCAGAGAUAAAGUUUAAAAUAAAAACCCUAUUAUU-UUGGUAAA
.....((((.....))))....(((.((((--((((((((..(((.(((((((...........))))))).)))..)))))).))))))(((((((........)))))-)))))... ( -21.80)
>DroYak_CAF1 4355 116 - 1
CAUCAUCCGCUCGCUGGAGUCGGCCUAAAC--UUAUUUUUAAUCGAACAAGACGACCCAAUAAAGUUUUGUAUGAGCAGAGAUAAAGUUUAAAAUAAAAACACUAUUAUU-UUGGUAAA
......((((((....))).)))..(((((--((((((((..(((.(((((((...........))))))).)))..)))))).)))))))..........((((.....-.))))... ( -24.40)
>consensus
CAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUUAAUCGAACAAGACGACACAAUAAAGUUUUGUAUGAGCAGAGAUAAAGUUUAAAAUAAAAACACUAUUAUU_UUGGUAAA
.((((.......((((....)))).(((((.(((((((((..(((.(((((((...........))))))).)))..)))))))))))))).....................))))... (-23.22 = -23.62 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	19,004,291 – 19,004,411
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.16
Mean single sequence MFE	-36.62
Consensus MFE	-35.82
Energy contribution	-35.50
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-1.46
Structure conservation index	0.98
SVM decision value	1.50
SVM RNA-class probability	0.958986
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19004291 120 - 22407834
ACCAACAUCGAGCUGGGCACCGCCUGUGGUAAAUACUUCCGCGUGUGCACCCUGUCCAUCACCGAUCCUGGAGAUUCGGACAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUU
.........((((.(((((((((....(((....)))...))).)))).)).((((((((.(((....))).)))..)))))......))))((((....))))................ ( -37.30)
>DroSec_CAF1 7287 120 - 1
ACCAACAUCGAGCUGGGCACCGCCUGCGGUAAAUACUUCCGCGUGUGCACCCUGUCCAUCACCGAUCCUGGAGAUUCGGACAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUU
.........((((.(((...(((.(((((.........))))).)))..)))((((((((.(((....))).)))..)))))......))))((((....))))................ ( -38.10)
>DroSim_CAF1 5646 120 - 1
ACCAACAUCGAGCUGGGCACCGCCUGCGGUAAAUACUUCCGCGUGUGCACCCUGUCCAUCACCGAUCCUGGAGAUUCGGACAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUU
.........((((.(((...(((.(((((.........))))).)))..)))((((((((.(((....))).)))..)))))......))))((((....))))................ ( -38.10)
>DroEre_CAF1 7393 118 - 1
ACCAACAUCGAGCUGGGCACCGCCUGCGGUAAAUAUUUCCGCGUGUGCACCCUGUCCAUCACCGAUCCUGGAGAUUCGGACAUCAUCCGUUCGCUGGAGUCGGCCUAAAC--UUAUUUUU
.........(..(.(((...(((.(((((.........))))).)))..))).)..)....((((..(..(.((..((((.....)))).)).)..)..)))).......--........ ( -33.20)
>DroYak_CAF1 4433 118 - 1
ACCAACAUUGAGCUGGGCACCGCCUGCGGUAAAUACUUCCGCGUGUGCACCCUGUCCAUCACCGAUCCUGGAGAUUCGGACAUCAUCCGCUCGCUGGAGUCGGCCUAAAC--UUAUUUUU
........((((.(((((((((....))))....(((((.(((.(((.....((((((((.(((....))).)))..))))).....))).))).)))))..)))))..)--)))..... ( -36.40)
>consensus
ACCAACAUCGAGCUGGGCACCGCCUGCGGUAAAUACUUCCGCGUGUGCACCCUGUCCAUCACCGAUCCUGGAGAUUCGGACAUCAUCCGCUCGCUGGAGACGGCCUAAACAUUUAUUUUU
.........((((.(((...(((.(((((.........))))).)))..)))((((((((.(((....))).)))..)))))......))))((((....))))................ (-35.82 = -35.50 +  -0.32)

alignment

secondary structure

dotplot

Window 4

Location	19,004,371 – 19,004,491
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-44.60
Consensus MFE	-42.04
Energy contribution	-41.92
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.12
Structure conservation index	0.94
SVM decision value	0.10
SVM RNA-class probability	0.583737
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19004371 120 + 22407834
GGAAGUAUUUACCACAGGCGGUGCCCAGCUCGAUGUUGGUGCCGCUGUAGUGCUGGACUUCAGUCUUGGCCAGCAUAGCGUAGUACUCGAUCUCGGACUUCCUGCAAUGUGAAGAGCACA
((((((...(((.((.(((((..((.(((.....)))))..)))))((.(((((((.((........))))))))).)))).))).(((....))))))))).....((((.....)))) ( -44.50)
>DroSec_CAF1 7367 120 + 1
GGAAGUAUUUACCGCAGGCGGUGCCCAGCUCGAUGUUGGUGCCGCUGUAGUGCUGGACUUCAGUCUUGGCCAGCAUGGCGUAGUACUCGAUCUCGGACUUCCUGCAAUGGGAAGAGCACA
.((.(((((...(((.(((((..((.(((.....)))))..)))))...(((((((.((........))))))))).))).))))))).........((((((.....))))))...... ( -45.10)
>DroSim_CAF1 5726 120 + 1
GGAAGUAUUUACCGCAGGCGGUGCCCAGCUCGAUGUUGGUGCCGCUGUAGUGCUGGACUUCAGUCUUGGCCAGCAUGGCGUAGUACUCGAUCUCGGACUUCCUGCAAUGGGAAGAGCACA
.((.(((((...(((.(((((..((.(((.....)))))..)))))...(((((((.((........))))))))).))).))))))).........((((((.....))))))...... ( -45.10)
>DroEre_CAF1 7471 120 + 1
GGAAAUAUUUACCGCAGGCGGUGCCCAGCUCGAUGUUGGUGCCGCUGUAGUGCUGGACUUCAGUCUUGGCCAGCAUGGCGUAGUACUCGAUCUCGGACUUCCUGCAAUGGGAAGAGCGCA
.............((((.(((..((.(((.....)))))..))))))).(((((((.((........))))))))).((((.....(((....))).((((((.....)))))).)))). ( -44.50)
>DroYak_CAF1 4511 120 + 1
GGAAGUAUUUACCGCAGGCGGUGCCCAGCUCAAUGUUGGUGCCGCUGUAAUGCUGGACUUCAGUCUUGGCCAGCAUGGCGUAGUACUCGAUCUCGGACUUCCUGCAAUGGGAAAAACGGA
.((.(((((...(((.(((((..((.(((.....)))))..)))))...(((((((.((........))))))))).))).)))))))....(((...(((((.....)))))...))). ( -43.80)
>consensus
GGAAGUAUUUACCGCAGGCGGUGCCCAGCUCGAUGUUGGUGCCGCUGUAGUGCUGGACUUCAGUCUUGGCCAGCAUGGCGUAGUACUCGAUCUCGGACUUCCUGCAAUGGGAAGAGCACA
((((((...(((.((.(((((..((.(((.....)))))..)))))((.(((((((.((........))))))))).)))).))).(((....))))))))).................. (-42.04 = -41.92 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:05 2006