Locus 5822

Sequence ID	2R_DroMel_CAF1
Location	18,454,456 – 18,454,547
Length	91
Max. P	0.988681

overview

Window 4

Location	18,454,456 – 18,454,547
Length	91
Sequences	6
Columns	91
Reading direction	forward
Mean pairwise identity	77.05
Mean single sequence MFE	-33.60
Consensus MFE	-20.48
Energy contribution	-21.05
Covariance contribution	0.57
Combinations/Pair	1.17
Mean z-score	-2.53
Structure conservation index	0.61
SVM decision value	1.93
SVM RNA-class probability	0.983023
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18454456 91 + 20766785
GGCUGUGACCAUAGCCAGCAUGGCCAAAGCGCUGUGCUUAAGUGGUCCAAGCGACCGAAAGCACUUUGACCAUGCGGUGGUGGCCAAAUCC
((((((....))))))....((((((.(.(((.((((((...(((((.....))))).)))))).........))).)..))))))..... ( -36.40)
>DroVir_CAF1 15888 77 + 1
-----UGCCC-AGUU-A-CAAUGCAAAAGCAUUGUGCUUAAGUGGUC-AACUGACCAAAAGCACUUUGACCAUGCGGUG---CACG--CGG
-----...((-.(((-(-.(((((....)))))((((((...(((((-....))))).))))))..))))...(((...---..))--))) ( -25.40)
>DroSec_CAF1 16865 91 + 1
GGCUGUGACCAUAGCCAGCAUGGCCAAAGCGCUGUGCUUAAGUGGUCCAAGCGACCGAAAGCACUUUGACCAUGCGGUGGUGGCCAAAUCC
((((((....))))))....((((((.(.(((.((((((...(((((.....))))).)))))).........))).)..))))))..... ( -36.40)
>DroEre_CAF1 16289 86 + 1
GGCUGUGACCAUAGCCAGCAUGGCCA--GCAUGGUGCUUAAGUGGUCCAAGCGACCGAAAGCACUUUGACCAUGCGG---UGGCCAAAUCC
((((((....))))))....((((((--(((((((((((...(((((.....))))).))))......)))))))..---))))))..... ( -37.30)
>DroYak_CAF1 16990 86 + 1
GGCGGCGACCAUAGCCAGCAUGGCCA--GCAUGGUGCUUAAGUGGUCCAGGCGACCGAAAGCACUUUGACCAUGCGG---UGGCCAAAUCC
((((((.......))).((((((...--.((.(((((((...(((((.....))))).))))))).)).))))))..---..)))...... ( -37.00)
>DroAna_CAF1 15340 87 + 1
UGAUAUGGGAGGUCGCUCCAUUGCCAAAGCGCUGUGCUUAAGUGGUCCAAGCGACCAAAAGCACUUUGACCAUGCGG---UGGGAUAA-CC
..........(((.(..(((((((.....((..((((((...(((((.....))))).))))))..)).....))))---)))..).)-)) ( -29.10)
>consensus
GGCUGUGACCAUAGCCAGCAUGGCCAAAGCACUGUGCUUAAGUGGUCCAAGCGACCGAAAGCACUUUGACCAUGCGG___UGGCCAAAUCC
.............((((((((((......((..((((((...(((((.....))))).))))))..)).)))))).....))))....... (-20.48 = -21.05 +   0.57)

alignment

secondary structure

dotplot

Window 5

Location	18,454,456 – 18,454,547
Length	91
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	77.05
Mean single sequence MFE	-35.78
Consensus MFE	-25.85
Energy contribution	-27.45
Covariance contribution	1.60
Combinations/Pair	1.21
Mean z-score	-3.25
Structure conservation index	0.72
SVM decision value	2.13
SVM RNA-class probability	0.988681
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18454456 91 - 20766785
GGAUUUGGCCACCACCGCAUGGUCAAAGUGCUUUCGGUCGCUUGGACCACUUAAGCACAGCGCUUUGGCCAUGCUGGCUAUGGUCACAGCC
((...((((((...((((((((((((((((((....((.((((((.....)))))))))))))))))))))))).))...))))))...)) ( -43.00)
>DroVir_CAF1 15888 77 - 1
CCG--CGUG---CACCGCAUGGUCAAAGUGCUUUUGGUCAGUU-GACCACUUAAGCACAAUGCUUUUGCAUUG-U-AACU-GGGCA-----
...--((((---(...)))))(((..(((((((.(((((....-)))))...))))(((((((....))))))-)-.)))-.))).----- ( -27.10)
>DroSec_CAF1 16865 91 - 1
GGAUUUGGCCACCACCGCAUGGUCAAAGUGCUUUCGGUCGCUUGGACCACUUAAGCACAGCGCUUUGGCCAUGCUGGCUAUGGUCACAGCC
((...((((((...((((((((((((((((((....((.((((((.....)))))))))))))))))))))))).))...))))))...)) ( -43.00)
>DroEre_CAF1 16289 86 - 1
GGAUUUGGCCA---CCGCAUGGUCAAAGUGCUUUCGGUCGCUUGGACCACUUAAGCACCAUGC--UGGCCAUGCUGGCUAUGGUCACAGCC
.((((((((((---..(((((((((..((((((..((((.....))))....)))))).....--))))))))))))))).))))...... ( -36.70)
>DroYak_CAF1 16990 86 - 1
GGAUUUGGCCA---CCGCAUGGUCAAAGUGCUUUCGGUCGCCUGGACCACUUAAGCACCAUGC--UGGCCAUGCUGGCUAUGGUCGCCGCC
.((((((((((---..(((((((((..((((((..((((.....))))....)))))).....--))))))))))))))).))))...... ( -36.70)
>DroAna_CAF1 15340 87 - 1
GG-UUAUCCCA---CCGCAUGGUCAAAGUGCUUUUGGUCGCUUGGACCACUUAAGCACAGCGCUUUGGCAAUGGAGCGACCUCCCAUAUCA
((-(......)---))....((((...((((((.(((((.....)))))...))))))...(((((......))))))))).......... ( -28.20)
>consensus
GGAUUUGGCCA___CCGCAUGGUCAAAGUGCUUUCGGUCGCUUGGACCACUUAAGCACAACGCUUUGGCCAUGCUGGCUAUGGUCACAGCC
((...((((((.....(((((((((((((((((..((((.....))))....)))))).....)))))))))))))))))...))...... (-25.85 = -27.45 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:18 2006