Locus 9804

Sequence ID	3R_DroMel_CAF1
Location	26,048,990 – 26,049,128
Length	138
Max. P	0.685633

overview

Window 6

Location	26,048,990 – 26,049,092
Length	102
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-40.55
Consensus MFE	-19.90
Energy contribution	-19.10
Covariance contribution	-0.80
Combinations/Pair	1.26
Mean z-score	-2.11
Structure conservation index	0.49
SVM decision value	-0.04
SVM RNA-class probability	0.513176
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26048990 102 - 27905053
CAUCGCACUGGUGGCAACCCUGGUCAGCGG--GGAGGCCCGGCAAUCCAGGCAGCUGGUCAACCUGUUUAAGGUUGCAUACUCAUGCGACAAAUGUGCCAAGCA
....((..(((((((...(((((...((.(--((...))).))...)))))..))).((((((((.....)))))((((....)))))))......)))).)). ( -36.40)
>DroPse_CAF1 46236 101 - 1
CGUGGAGCUGGUGGCAGCUCCGGUCGGCGCCAGAAUG---GAGAAUGCCGCCAGCUGGGCAACCUGUUUGAUGUUGCAUGUUCAUGUGACAAAUGUUGCACGCA
.(((.(((((((((((.(((((.((.......)).))---)))..)))))))))))..(((((..(((...(((..(((....)))..))))))))))).))). ( -45.20)
>DroSim_CAF1 42907 102 - 1
CAUCGCACUGGUGGCAACCCUGGUCAGCGG--GGAAGCCCGGCAAUCCAGGCAGCUGGUCAACCUGUUUGAGGUUGCAUACUCAUGCGACAAAUGUGCCACGCA
....((....((((((......(((..(((--(....))))(((((((((((((.(.....).))))))).))))))..........))).....)))))))). ( -38.20)
>DroEre_CAF1 46190 101 - 1
CGUCGCACUGGUGGCAACCCUGGCCAGCGG--GCAUGC-AGGCUAUCCAGGCAGCUGGUCAACCUGUUUGAGGUUGCAUACUCAUGCGACAAAUGUGCCACGCA
.((((((..((((((((((...(((....)--))..((-(((....((((....))))....)))))....)))))).))))..))))))...((((...)))) ( -40.00)
>DroYak_CAF1 43031 97 - 1
CGUCGCACUGGUGGCAACCCUGGCAACC------CUGG-CAGCUAUUCGGGCAGCUGGCCAACCUGUUUGAGGUUGCAUACUCAUGCGACAAAUGUGCCACGCA
.((((((..(((((((((((..(((...------.(((-(((((........)))).))))...)))..).)))))).))))..))))))...((((...)))) ( -37.10)
>DroPer_CAF1 48886 101 - 1
CGUGGAGCUGGUGGCAGCUCCGGUCGGCGCCAGAAUG---GAGAAUGCCGCCAGCAGGGCAACCUGUUUGAUGUUGCAUGUUCAUGUGACAAAUGUUGCACGCA
((((.(((((((((((.(((((.((.......)).))---)))..))))))))(((((....)))))....(((..(((....)))..)))...))).)))).. ( -46.40)
>consensus
CGUCGCACUGGUGGCAACCCUGGUCAGCGG__GAAUGC_CGGCAAUCCAGGCAGCUGGUCAACCUGUUUGAGGUUGCAUACUCAUGCGACAAAUGUGCCACGCA
(((.((((.((((((.......)))........................(((.....))).)))........(((((((....)))))))....)))).))).. (-19.90 = -19.10 +  -0.80)

alignment

secondary structure

dotplot

Window 7

Location	26,049,014 – 26,049,128
Length	114
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.15
Mean single sequence MFE	-44.98
Consensus MFE	-20.94
Energy contribution	-20.33
Covariance contribution	-0.61
Combinations/Pair	1.20
Mean z-score	-2.76
Structure conservation index	0.47
SVM decision value	0.32
SVM RNA-class probability	0.685633
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26049014 114 + 27905053
UAUGCAACCUUAAACAGGUUGACCAGCUGCCUGGAUUGCCGGGCCUCC--CCGCUGACCAGGGUUGCCACCAGUGCGAUGGCAACUGUCAAAUUUGACAAAUGACUG---GUCAAGCGG
....((((((.....)))))).......((((((....))))))....--(((((((((((((((((((.(.....).))))))))((((....))))......)))---))).))))) ( -50.10)
>DroPse_CAF1 46260 113 + 1
CAUGCAACAUCAAACAGGUUGCCCAGCUGGCGGCAUUCUC---CAUUCUGGCGCCGACCGGAGCUGCCACCAGCUCCACGAGAGCUGUCAGAUUUGACAAACGACUG---GUCAAGCGG
...(((((.........)))))((.(((((((.((.....---.....)).))))(((((((((((....)))))))........((((......)))).......)---))).))))) ( -39.80)
>DroSim_CAF1 42931 114 + 1
UAUGCAACCUCAAACAGGUUGACCAGCUGCCUGGAUUGCCGGGCUUCC--CCGCUGACCAGGGUUGCCACCAGUGCGAUGGCAACUGUCAAAUUUGACAAAUGACUG---GUCAAGCGG
....((((((.....)))))).......((((((....))))))....--(((((((((((((((((((.(.....).))))))))((((....))))......)))---))).))))) ( -50.50)
>DroEre_CAF1 46214 113 + 1
UAUGCAACCUCAAACAGGUUGACCAGCUGCCUGGAUAGCCU-GCAUGC--CCGCUGGCCAGGGUUGCCACCAGUGCGACGGCAACUGUCAAAUUUGACAAAUGACUG---GUCAAGCGG
..............(((((((.((((....)))).))))))-).....--((((((((((((((((((...........)))))))((((....))))......)))---))).))))) ( -45.10)
>DroYak_CAF1 43055 112 + 1
UAUGCAACCUCAAACAGGUUGGCCAGCUGCCCGAAUAGCUG-CCAG------GGUUGCCAGGGUUGCCACCAGUGCGACGGCAACUGUCAAAUUUGACAAAUGACUGGUGGUCAAGCGG
...(((((((.........((((.(((((......))))))-))))------))))))...(.(((((((((((((....))...(((((....)))))....)))))))).))).).. ( -43.00)
>DroPer_CAF1 48910 113 + 1
CAUGCAACAUCAAACAGGUUGCCCUGCUGGCGGCAUUCUC---CAUUCUGGCGCCGACCGGAGCUGCCACCAGCUCCACGAGAGCUGUCAGAUUUGACAAACGACUG---GUCAAGCGG
...(((((.........))))).(((((((((.((.....---.....)).))))(((((((((((....)))))))........((((......)))).......)---))).))))) ( -41.40)
>consensus
UAUGCAACCUCAAACAGGUUGACCAGCUGCCUGGAUUGCCG_GCAUCC__CCGCUGACCAGGGUUGCCACCAGUGCGACGGCAACUGUCAAAUUUGACAAAUGACUG___GUCAAGCGG
....((((((.....)))))).((.(((((.......))................(((((((((((((...........)))))))((((....))))......)))...))).))))) (-20.94 = -20.33 +  -0.61)

alignment

secondary structure

dotplot

Window 8

Location	26,049,014 – 26,049,128
Length	114
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.15
Mean single sequence MFE	-46.10
Consensus MFE	-22.97
Energy contribution	-23.87
Covariance contribution	0.89
Combinations/Pair	1.22
Mean z-score	-2.41
Structure conservation index	0.50
SVM decision value	0.11
SVM RNA-class probability	0.587570
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26049014 114 - 27905053
CCGCUUGAC---CAGUCAUUUGUCAAAUUUGACAGUUGCCAUCGCACUGGUGGCAACCCUGGUCAGCGG--GGAGGCCCGGCAAUCCAGGCAGCUGGUCAACCUGUUUAAGGUUGCAUA
(((((.(((---(((.....(((((....)))))(((((((((.....))))))))).)))))))))))--((..(((.((....)).)))..)).(.((((((.....)))))))... ( -52.20)
>DroPse_CAF1 46260 113 - 1
CCGCUUGAC---CAGUCGUUUGUCAAAUCUGACAGCUCUCGUGGAGCUGGUGGCAGCUCCGGUCGGCGCCAGAAUG---GAGAAUGCCGCCAGCUGGGCAACCUGUUUGAUGUUGCAUG
((((..((.---...))..((((((....)))))).....))))(((((((((((.(((((.((.......)).))---)))..)))))))))))..(((((.........)))))... ( -44.40)
>DroSim_CAF1 42931 114 - 1
CCGCUUGAC---CAGUCAUUUGUCAAAUUUGACAGUUGCCAUCGCACUGGUGGCAACCCUGGUCAGCGG--GGAAGCCCGGCAAUCCAGGCAGCUGGUCAACCUGUUUGAGGUUGCAUA
(((((.(((---(((.....(((((....)))))(((((((((.....))))))))).)))))))))))--((....)).(((((((((((((.(.....).))))))).))))))... ( -52.60)
>DroEre_CAF1 46214 113 - 1
CCGCUUGAC---CAGUCAUUUGUCAAAUUUGACAGUUGCCGUCGCACUGGUGGCAACCCUGGCCAGCGG--GCAUGC-AGGCUAUCCAGGCAGCUGGUCAACCUGUUUGAGGUUGCAUA
..((..(((---((((....(((((....)))))((((((..(.....)..))))))(((((..(((..--(....)-..)))..)))))..)))))))(((((.....)))))))... ( -44.00)
>DroYak_CAF1 43055 112 - 1
CCGCUUGACCACCAGUCAUUUGUCAAAUUUGACAGUUGCCGUCGCACUGGUGGCAACCCUGGCAACC------CUGG-CAGCUAUUCGGGCAGCUGGCCAACCUGUUUGAGGUUGCAUA
....(((.((((((((...((((((....))))))..((....))))))))))))).....((((((------(..(-(((.......(((.....)))...))))..).))))))... ( -38.80)
>DroPer_CAF1 48910 113 - 1
CCGCUUGAC---CAGUCGUUUGUCAAAUCUGACAGCUCUCGUGGAGCUGGUGGCAGCUCCGGUCGGCGCCAGAAUG---GAGAAUGCCGCCAGCAGGGCAACCUGUUUGAUGUUGCAUG
..((((.((---.((..(((.((((....))))))).)).)).))))((((((((.(((((.((.......)).))---)))..))))))))(((((....)))))............. ( -44.60)
>consensus
CCGCUUGAC___CAGUCAUUUGUCAAAUUUGACAGUUGCCGUCGCACUGGUGGCAACCCUGGUCAGCGG__GAAUGC_CGGCAAUCCAGGCAGCUGGUCAACCUGUUUGAGGUUGCAUA
.((((((((.....))))..(((((....)))))(((((((((.....))))))))).......))))............((((((((((((...((....)))))))).))))))... (-22.97 = -23.87 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:42:34 2006