Locus 1244

Sequence ID	3L_DroMel_CAF1
Location	3,537,761 – 3,537,928
Length	167
Max. P	0.840161

overview

Window 0

Location	3,537,761 – 3,537,859
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	94.39
Mean single sequence MFE	-24.12
Consensus MFE	-18.66
Energy contribution	-19.06
Covariance contribution	0.40
Combinations/Pair	1.14
Mean z-score	-2.06
Structure conservation index	0.77
SVM decision value	0.63
SVM RNA-class probability	0.806782
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3537761 98 + 23771897
CCAUAUUUGGCUUAAGUAUUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGCCUUAAUUGGGAUCAUGUGUUGGUAAAU
........(((..((((.......((((((...))))))..))))..)))......((((((.((((((((((.....))).)))))))))))))... ( -21.90)
>DroSec_CAF1 67926 97 + 1
CCAUAUUUGGCUUGAGUAUUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGCCUUAAUUGGGCUCAUAUG-UGGUAAAU
((((((.(((((((.((((((....(((((...)))))..(((....)))...)))))))))))....(((((.....))))))).)))-)))..... ( -25.40)
>DroSim_CAF1 69057 98 + 1
CCAUAUUUGGCCUGAGUAUUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGACUUAAUUGGGCUCAUAUGCUGGUAAAU
..(((...((((............((((((...)))))).))))..))).......((((.((((((((..(((....)))..))))))))))))... ( -22.92)
>DroEre_CAF1 85960 98 + 1
CCGUAUUUGGCUUGAGUAUUUAAUUGACAUUUUGUGUCGGGGCUUUUGUUUUGAAAUACCCAAUAUAUGGCCUUAAUUGGACUCAUAUGUUGGUAAAU
..(((((((((..((((......(((((((...))))))).))))..)))...))))))(((((((((((((......)).).))))))))))..... ( -26.00)
>DroYak_CAF1 70931 98 + 1
CCAUAUUUGGCUUGAGUAUUUAAUUGACAUUUUGUGUCGGGGCUUUUGUUUUGAAAUACCGAAUAUAUAGCCUUAAUUGGGCUCAUAUGUUGGUAAAU
........(((..((((......(((((((...))))))).))))..)))......((((.((((((((((((.....))))).)))))))))))... ( -24.40)
>consensus
CCAUAUUUGGCUUGAGUAUUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGCCUUAAUUGGGCUCAUAUGUUGGUAAAU
........(((..((((.......((((((...))))))..))))..)))......((((.((((((((((((.....)))).))))))))))))... (-18.66 = -19.06 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	3,537,779 – 3,537,888
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.57
Mean single sequence MFE	-27.51
Consensus MFE	-18.54
Energy contribution	-18.78
Covariance contribution	0.24
Combinations/Pair	1.16
Mean z-score	-1.92
Structure conservation index	0.67
SVM decision value	0.01
SVM RNA-class probability	0.539543
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3537779 109 + 23771897
UUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGCCUUAAUUGGGAUCAUGUGUUGGUAAAUAAGUCGUUUCAAAUUUCUUGGAAAAG-----------AGA
.......(((........(((..((....))..)))..((((((.((((((((((.....))).))))))))))))).....)))........((((((....)))-----------))) ( -25.60)
>DroSec_CAF1 67944 108 + 1
UUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGCCUUAAUUGGGCUCAUAUG-UGGUAAAUAAGUCAUUUCAGAUUUCUUGGAAAAG-----------AGA
.......(((((...)))))(((((((...........(((((..((((((((((.....)))).))))))-)))))...)))))))......((((((....)))-----------))) ( -26.34)
>DroSim_CAF1 69075 109 + 1
UUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGACUUAAUUGGGCUCAUAUGCUGGUAAAUAAGUCGUUUCAGAUUUCUUGGAAAAG-----------AGA
.......(((........(((..((....))..)))..((((.((((((((..(((....)))..)))))))))))).....)))........((((((....)))-----------))) ( -26.40)
>DroEre_CAF1 85978 120 + 1
UUUAAUUGACAUUUUGUGUCGGGGCUUUUGUUUUGAAAUACCCAAUAUAUGGCCUUAAUUGGACUCAUAUGUUGGUAAAUAAAUCGUUUCAGAUUUCGUGGAAAAGUAGACUUACACAAA
............(((((((.((.((((((.(..(((((...(((((((((((((......)).).))))))))))........((......))))))).).))))))...)).))))))) ( -29.50)
>DroYak_CAF1 70949 120 + 1
UUUAAUUGACAUUUUGUGUCGGGGCUUUUGUUUUGAAAUACCGAAUAUAUAGCCUUAAUUGGGCUCAUAUGUUGGUAAAUAAGUCGUUUCAGAUUUCGUAGAAAUGUAGAUGUACGGAAA
.......(((........(((((((....)))))))..((((.((((((((((((.....))))).))))))))))).....)))........(((((((.(........).))))))). ( -29.70)
>consensus
UUUAAUUGACAUUUUGUGUCGUGGCUUUUGUUUUGAAAUACCGAGUAUAUGGCCUUAAUUGGGCUCAUAUGUUGGUAAAUAAGUCGUUUCAGAUUUCUUGGAAAAG___________AGA
......((((((...)))))).((..((((...(((..((((.((((((((((((.....)))).))))))))))))......)))...))))..))....................... (-18.54 = -18.78 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	3,537,819 – 3,537,928
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.78
Mean single sequence MFE	-25.45
Consensus MFE	-13.14
Energy contribution	-14.14
Covariance contribution	1.00
Combinations/Pair	1.17
Mean z-score	-2.01
Structure conservation index	0.52
SVM decision value	0.75
SVM RNA-class probability	0.840161
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3537819 109 + 23771897
CCGAGUAUAUGGCCUUAAUUGGGAUCAUGUGUUGGUAAAUAAGUCGUUUCAAAUUUCUUGGAAAAG-----------AGAAAAAUUUGGUGACCAGGAAAUAGUUAAAUUCAGACUACAA
((((.((((((((((.....))).)))))))))))......(((((((((...((((((....)))-----------))).....((((...))))))))).(.......).)))).... ( -22.80)
>DroSec_CAF1 67984 107 + 1
CCGAGUAUAUGGCCUUAAUUGGGCUCAUAUG-UGGUAAAUAAGUCAUUUCAGAUUUCUUGGAAAAG-----------AGAA-AAUUGGGUGGCCAGGAAAUACUUAAAUUUAAACUACCA
(((..((((((((((.....)))).))))))-)))....(((((.(((((...((((((....)))-----------))).-..((((....)))))))))))))).............. ( -26.20)
>DroSim_CAF1 69115 109 + 1
CCGAGUAUAUGGACUUAAUUGGGCUCAUAUGCUGGUAAAUAAGUCGUUUCAGAUUUCUUGGAAAAG-----------AGAAAAAUUGGGCGACCAGGAAAUAGUUAAAUUCAAACUACCA
...((((((((..(((....)))..))))))))((((........(((((...((((((....)))-----------)))....((((....))))))))).(((.......))))))). ( -27.50)
>DroEre_CAF1 86018 120 + 1
CCCAAUAUAUGGCCUUAAUUGGACUCAUAUGUUGGUAAAUAAAUCGUUUCAGAUUUCGUGGAAAAGUAGACUUACACAAAAUAAUUGCUGAACCAGGAAAUAGUGAAAUUUAAACAACCA
.(((((((((((((......)).).))))))))))..........((((((.(((((.(((...(((((...............)))))...))).)))))..))))))........... ( -28.66)
>DroYak_CAF1 70989 104 + 1
CCGAAUAUAUAGCCUUAAUUGGGCUCAUAUGUUGGUAAAUAAGUCGUUUCAGAUUUCGUAGAAAUGUAGAUGUACGGAAAAUAAUUAAAUGACCAGGAAGUAGU----------------
((.((((((((((((.....))))).))))))).........(((((((....(((((((.(........).))))))).......)))))))..)).......---------------- ( -22.10)
>consensus
CCGAGUAUAUGGCCUUAAUUGGGCUCAUAUGUUGGUAAAUAAGUCGUUUCAGAUUUCUUGGAAAAG___________AGAAAAAUUGGGUGACCAGGAAAUAGUUAAAUUCAAACUACCA
((.((((((((((((.....)))).)))))))))).................(((((((((...............................)))))))))................... (-13.14 = -14.14 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:58 2006