Locus 6224

Sequence ID	2L_DroMel_CAF1
Location	17,313,806 – 17,313,912
Length	106
Max. P	0.858776

overview

Window 5

Location	17,313,806 – 17,313,912
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.61
Mean single sequence MFE	-36.78
Consensus MFE	-28.40
Energy contribution	-28.88
Covariance contribution	0.48
Combinations/Pair	1.12
Mean z-score	-1.89
Structure conservation index	0.77
SVM decision value	0.73
SVM RNA-class probability	0.834324
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17313806 106 + 22407834
UUUGCGUGUGU---G-UUU----------GGGACUUGCAACUUGUCGCCGCAAAAUGAAUUGAACUUUUAUGGCUAAUGACGUUGCACGUUGCAAGCGGCAUGCUGCAUGGCACACGUGU
...((((((((---.-.((----------(.(((.((((((..((((..((...(((((.......))))).))...)))))))))).))).)))((((....))))...)))))))).. ( -37.50)
>DroSec_CAF1 11438 106 + 1
UUUGCGUGUGU---G-UUU----------GGGACUUGCAACUUGUCGCCGCAAAAUGAAUUGAACUUUUAUGGCUAAUGACGUUGCACGUUGCAAGCGGCAUGCUGCAUGGCACACGUGU
...((((((((---.-.((----------(.(((.((((((..((((..((...(((((.......))))).))...)))))))))).))).)))((((....))))...)))))))).. ( -37.50)
>DroSim_CAF1 12914 106 + 1
UUUGCGUGUGU---G-UUU----------GGGACUUGCAACUUGUCGCCGCAAAAUGAAUUGAACUUUUAUGGCUAAUGACGUUGCACGUUGCAAGCGGCAUGCUGCAUGGCACACGUGU
...((((((((---.-.((----------(.(((.((((((..((((..((...(((((.......))))).))...)))))))))).))).)))((((....))))...)))))))).. ( -37.50)
>DroEre_CAF1 13685 104 + 1
UUUGCGUG--U---G-UUU----------GGGACUUGCAACUUGUCGCCGCAAAAUGAAUUGAACUUUUAUGGCUAAUGACGUUGCACGUUGCAAGCGGCAUGUUGCAUGGCACACGUGU
...(((((--(---(-((.----------......((((((.((((((.((...(((((.......))))).))........((((.....)))))))))).)))))).))))))))).. ( -35.80)
>DroAna_CAF1 21539 120 + 1
UGCGAGUGGCCGAAGCUUUAAGGGACGAGGGGACCUGCAACUUGUCGCCACAAAAUGAAUUGAACUUUUAUGGCUAAUGACGUUGCACGUUGCAUACGGCAUGUUGCGUGGCGCACGUGU
.(((.(((((((........(((..(....)..)))(((((.((((((((.((((..........)))).)))).......(((((.....))).)))))).))))).)))).))).))) ( -35.60)
>consensus
UUUGCGUGUGU___G_UUU__________GGGACUUGCAACUUGUCGCCGCAAAAUGAAUUGAACUUUUAUGGCUAAUGACGUUGCACGUUGCAAGCGGCAUGCUGCAUGGCACACGUGU
..(((((((((..................(.(((.((((((..(((((((.((((..........)))).))))....))))))))).))).)..((((....))))...))))))))). (-28.40 = -28.88 +   0.48)

alignment

secondary structure

dotplot

Window 6

Location	17,313,806 – 17,313,912
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.61
Mean single sequence MFE	-29.40
Consensus MFE	-22.26
Energy contribution	-22.82
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.76
SVM decision value	0.82
SVM RNA-class probability	0.858776
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17313806 106 - 22407834
ACACGUGUGCCAUGCAGCAUGCCGCUUGCAACGUGCAACGUCAUUAGCCAUAAAAGUUCAAUUCAUUUUGCGGCGACAAGUUGCAAGUCCC----------AAA-C---ACACACGCAAA
...((((((...((((((.....)).))))((.((((((.......(((.(((((..........))))).))).....)))))).))...----------...-.---.)))))).... ( -28.10)
>DroSec_CAF1 11438 106 - 1
ACACGUGUGCCAUGCAGCAUGCCGCUUGCAACGUGCAACGUCAUUAGCCAUAAAAGUUCAAUUCAUUUUGCGGCGACAAGUUGCAAGUCCC----------AAA-C---ACACACGCAAA
...((((((...((((((.....)).))))((.((((((.......(((.(((((..........))))).))).....)))))).))...----------...-.---.)))))).... ( -28.10)
>DroSim_CAF1 12914 106 - 1
ACACGUGUGCCAUGCAGCAUGCCGCUUGCAACGUGCAACGUCAUUAGCCAUAAAAGUUCAAUUCAUUUUGCGGCGACAAGUUGCAAGUCCC----------AAA-C---ACACACGCAAA
...((((((...((((((.....)).))))((.((((((.......(((.(((((..........))))).))).....)))))).))...----------...-.---.)))))).... ( -28.10)
>DroEre_CAF1 13685 104 - 1
ACACGUGUGCCAUGCAACAUGCCGCUUGCAACGUGCAACGUCAUUAGCCAUAAAAGUUCAAUUCAUUUUGCGGCGACAAGUUGCAAGUCCC----------AAA-C---A--CACGCAAA
...((((((....((.....)).((((((((((.....)(((....(((.(((((..........))))).))))))..)))))))))...----------...-)---)--)))).... ( -27.20)
>DroAna_CAF1 21539 120 - 1
ACACGUGCGCCACGCAACAUGCCGUAUGCAACGUGCAACGUCAUUAGCCAUAAAAGUUCAAUUCAUUUUGUGGCGACAAGUUGCAGGUCCCCUCGUCCCUUAAAGCUUCGGCCACUCGCA
....(((.(((..(((((.((((((.....))).)))..(((....(((((((((..........))))))))))))..)))))(((..(....)..))).........))))))..... ( -35.50)
>consensus
ACACGUGUGCCAUGCAGCAUGCCGCUUGCAACGUGCAACGUCAUUAGCCAUAAAAGUUCAAUUCAUUUUGCGGCGACAAGUUGCAAGUCCC__________AAA_C___ACACACGCAAA
....(((((...((((((.....)).))))((.((((((.......(((.(((((..........))))).))).....)))))).))........................)))))... (-22.26 = -22.82 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:41 2006