Locus 2286

Sequence ID	3R_DroMel_CAF1
Location	6,499,505 – 6,499,599
Length	94
Max. P	0.943258

overview

Window 6

Location	6,499,505 – 6,499,599
Length	94
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	72.93
Mean single sequence MFE	-29.32
Consensus MFE	-9.92
Energy contribution	-9.64
Covariance contribution	-0.28
Combinations/Pair	1.46
Mean z-score	-2.08
Structure conservation index	0.34
SVM decision value	1.33
SVM RNA-class probability	0.943258
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6499505 94 + 27905053
--------ACUUUUCUAGGACCAUUUGAUUGUUGAUUAGGUGGACUUUGAGCCCCCCAAAAAGUACCCCUUCCUUCAGGGGGACACCCCUGACAAGCGUCUC
--------........((((((((((((((...))))))))))(((((...........)))))......))))(((((((....))))))).......... ( -26.20)
>DroSec_CAF1 262980 97 + 1
CAUAGGGACCUUGUCUAGGACCAUUCGAUUCAUACAUAGGAGGGCUUUGAGCCCCCCAAAAAGUACCCUUUCC-----GGGGACACCCCUGACAAGCGUCUC
....(((((((((((.(((...................((.((((.....)))).)).....((.((((....-----))))))...))))))))).))))) ( -35.00)
>DroSim_CAF1 292371 97 + 1
CAUAGGGACCUUUUCUAAGACCAUUCAAUUAAUACAUAGAAGGGCUUUGAGCCCCCCAAAAAGUACCCCUUCA-----GGGGACACCCCUGACAAGCGUCUC
....((((((((.((.......................((((((((((...........))))...))))))(-----((((...))))))).))).))))) ( -24.40)
>DroEre_CAF1 276093 92 + 1
AGCAAUGACCCUCCCUAGGACCACUGGUUUCAGGCUUGGGGGGACCCUG--CCCC-C-AAAAGGACCCCUCCA-----AG-GACACCCCUGACAAGCGUCUC
......(((.((.(((..((((...))))..)))(((((((((..(((.--....-.-...)))..)))))))-----))-.............)).))).. ( -29.50)
>DroYak_CAF1 271940 96 + 1
AAUAGGGUCUUUCUCUAGGACUACUUGUUUCAGGUUUAGGG-UACUUUGGGCCCCCCAUUAAGGACCCCUCCA-----AGGGGCUCCCCUGACAAGCGUCUC
..(((((.....)))))((((..((((..(((((....(((-(.......))))........(((((((....-----.)))).)))))))))))).)))). ( -31.50)
>consensus
AAUAGGGACCUUCUCUAGGACCAUUCGAUUCAUGCUUAGGAGGACUUUGAGCCCCCCAAAAAGUACCCCUUCA_____GGGGACACCCCUGACAAGCGUCUC
.................((((.................(((((........................)))))......((((....)))).......)))). ( -9.92 =  -9.64 +  -0.28)

alignment

secondary structure

dotplot

Window 7

Location	6,499,505 – 6,499,599
Length	94
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	72.93
Mean single sequence MFE	-34.32
Consensus MFE	-17.06
Energy contribution	-18.70
Covariance contribution	1.64
Combinations/Pair	1.27
Mean z-score	-1.83
Structure conservation index	0.50
SVM decision value	0.61
SVM RNA-class probability	0.797588
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6499505 94 - 27905053
GAGACGCUUGUCAGGGGUGUCCCCCUGAAGGAAGGGGUACUUUUUGGGGGGCUCAAAGUCCACCUAAUCAACAAUCAAAUGGUCCUAGAAAAGU--------
...((.(((.(((((((....)))))))....))).))..((((((((((((.....))))(((................)))))))))))...-------- ( -29.39)
>DroSec_CAF1 262980 97 - 1
GAGACGCUUGUCAGGGGUGUCCCC-----GGAAAGGGUACUUUUUGGGGGGCUCAAAGCCCUCCUAUGUAUGAAUCGAAUGGUCCUAGACAAGGUCCCUAUG
..(((.((((((((((.(((.(((-----((((((....)))))))))((((.....)))).................))).)))).)))))))))...... ( -36.20)
>DroSim_CAF1 292371 97 - 1
GAGACGCUUGUCAGGGGUGUCCCC-----UGAAGGGGUACUUUUUGGGGGGCUCAAAGCCCUUCUAUGUAUUAAUUGAAUGGUCUUAGAAAAGGUCCCUAUG
..........(((((((...))))-----))).((((.((((((((((((((.....)))))))..........((((......)))))))))))))))... ( -32.70)
>DroEre_CAF1 276093 92 - 1
GAGACGCUUGUCAGGGGUGUC-CU-----UGGAGGGGUCCUUUU-G-GGGG--CAGGGUCCCCCCAAGCCUGAAACCAGUGGUCCUAGGGAGGGUCAUUGCU
.....(((((...((((((((-((-----..((((....)))).-.-))))--))....)))).))))).......(((((..(((....)))..))))).. ( -39.80)
>DroYak_CAF1 271940 96 - 1
GAGACGCUUGUCAGGGGAGCCCCU-----UGGAGGGGUCCUUAAUGGGGGGCCCAAAGUA-CCCUAAACCUGAAACAAGUAGUCCUAGAGAAAGACCCUAUU
..((((((((((((((((.((((.-----....)))))))....(((((..(.....)..-)))))..)))))..))))).))).................. ( -33.50)
>consensus
GAGACGCUUGUCAGGGGUGUCCCC_____UGAAGGGGUACUUUUUGGGGGGCUCAAAGUCCCCCUAAGCAUGAAUCAAAUGGUCCUAGAAAAGGUCCCUAUG
..(((.(((.(((((((((((((..........))))))))....(((((((.....)))))))...................))).)).))))))...... (-17.06 = -18.70 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:38 2006