Locus 5518

Sequence ID	3R_DroMel_CAF1
Location	14,522,565 – 14,522,703
Length	138
Max. P	0.915539

overview

Window 5

Location	14,522,565 – 14,522,666
Length	101
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	80.31
Mean single sequence MFE	-35.40
Consensus MFE	-26.23
Energy contribution	-25.79
Covariance contribution	-0.44
Combinations/Pair	1.07
Mean z-score	-2.03
Structure conservation index	0.74
SVM decision value	1.10
SVM RNA-class probability	0.915539
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14522565 101 - 27905053
UGGCCAUUACCAUUACCAAUGGCAUCGCUAUUGCCAUUACCAUUA---CCAUUACCUUUGUCAUGGCCAAGGGGAAUGGGAGUAA-----------GGAGUGGGAGUGGGACUGG
...(((((.(((((.(((((((((.......))))))).......---(((((.((((((.......)))))).)))))......-----------))))))).)))))...... ( -35.20)
>DroEre_CAF1 19101 94 - 1
UGGCCAUUACCAUUACCAAUGGCAUUGCCAUUACCAUUACCACUA---CCAUUACCUUUGUCAUGGCCAAAGGGAGUG------------------GGAGUGGGAGUGGGACUGG
..((((((.........))))))....(((...(((((.(((((.---(((((.((((((.......)))))).))))------------------).))))).)))))...))) ( -36.00)
>DroYak_CAF1 25673 109 - 1
GGGCCAUUACCAUUACCAAUGGCAUUGCCAUUACCAUUACCACCAUUCCCAUUACCUUUGUCAUGGCCACCGGGAGUG------CGAGUUUGAGUUGGAGUGGGAGUGGGAGUGG
((.......))......((((((...)))))).(((((....(((((((((((.((....(((...((((.....)))------.)....)))...))))))))))))).))))) ( -35.00)
>consensus
UGGCCAUUACCAUUACCAAUGGCAUUGCCAUUACCAUUACCACUA___CCAUUACCUUUGUCAUGGCCAAAGGGAGUG__________________GGAGUGGGAGUGGGACUGG
...(((((.(((((.((((((((...))))))..((((.((.......((((.((....)).))))......))))))..................))))))).)))))...... (-26.23 = -25.79 +  -0.44)

alignment

secondary structure

dotplot

Window 6

Location	14,522,594 – 14,522,703
Length	109
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.02
Mean single sequence MFE	-34.15
Consensus MFE	-15.36
Energy contribution	-17.00
Covariance contribution	1.64
Combinations/Pair	1.26
Mean z-score	-2.48
Structure conservation index	0.45
SVM decision value	0.53
SVM RNA-class probability	0.772198
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14522594 109 + 27905053
UCCCCUUGGCCAUGACAAAGGUAAUGG---UAAUGGUAAUGGCAAUAGCGAUGCCAUUGGUAAUGGU-AAUG----GCCAUGCCAACUAGACACUCAUAUACUGCUCCUAUUGGAGC
...((...(((((.((....)).))))---)...)).(((((((.......)))))))((((.((((-....----))))))))...................(((((....))))) ( -32.60)
>DroSec_CAF1 19338 109 + 1
UCCCGUUGGCCAUGACAAAGGUAAUGG---UAAUGGUAAUGGCAAUAGCAGUGCCAUUGGUAAUGGU-AAUG----GCAUUGCCAACUAGACACUCAUAUACUGCUCCUAUUGGAGC
..((((((.((((.((....)).))))---))))))...(((((((.((..((((((.....)))))-)...----)))))))))..................(((((....))))) ( -37.10)
>DroSim_CAF1 19290 109 + 1
UCCCGUUGGCCAUGACAAAGGUAAUGG---UAAUGGUAAUGGCAAUAGCAAUGCCAUUGGUAAUGGU-AAUG----GCCAUGCCAACUAGACACUCAUAUACUGCUCCUAUUGGAGC
..((((((.((((.((....)).))))---)))))).(((((((.......)))))))((((.((((-....----))))))))...................(((((....))))) ( -34.40)
>DroEre_CAF1 19123 107 + 1
UCCCUUUGGCCAUGACAAAGGUAAUGG---UAGUGGUAAUGGUAAUGGCAAUGCCAUUGGUAAUGGU-AAUG----GCCAUGCCAACUAGACACUCAU--ACUGCUCCUAUUAGGGC
..((((((.......))))))((((((---.((..(((.(((((.((((..((((((.....)))))-)...----)))))))))....(.....).)--))..)).)))))).... ( -35.30)
>DroYak_CAF1 25707 112 + 1
UCCCGGUGGCCAUGACAAAGGUAAUGGGAAUGGUGGUAAUGGUAAUGGCAAUGCCAUUGGUAAUGGU-AAUG----GCCCUGCCAACUAGACACUCAUGUACUACUCCUAUUAAGGC
(((((...(((........)))..)))))((((((....((((..(((((..(((((((.......)-))))----))..)))))))))..))).)))........(((....))). ( -34.40)
>DroAna_CAF1 18429 94 + 1
-ACUAAUGGCAAUGACAAUGGUAAUGG---UAGCAGUAAUGGUAAUGGUAAUGGGUUAGGCUAUAGCCCAUGCCAUGCCAUGCCAGCUAGAUAUGUAU-------------------
-.(((.((((........((.((....---)).))...((((((.(((((.(((((((.....))))))))))))))))))))))..)))........------------------- ( -31.10)
>consensus
UCCCGUUGGCCAUGACAAAGGUAAUGG___UAAUGGUAAUGGCAAUAGCAAUGCCAUUGGUAAUGGU_AAUG____GCCAUGCCAACUAGACACUCAUAUACUGCUCCUAUUGGAGC
..((((((.((........))))))))......(((((((((((.......)))))))(((.(((((.........)))))))).))))..............((((......)))) (-15.36 = -17.00 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:10 2006