Locus 8928

Sequence ID	3R_DroMel_CAF1
Location	23,943,240 – 23,943,338
Length	98
Max. P	0.736254

overview

Window 5

Location	23,943,240 – 23,943,338
Length	98
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	79.85
Mean single sequence MFE	-38.82
Consensus MFE	-23.84
Energy contribution	-23.48
Covariance contribution	-0.36
Combinations/Pair	1.17
Mean z-score	-1.79
Structure conservation index	0.61
SVM decision value	0.41
SVM RNA-class probability	0.725582
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23943240 98 + 27905053
GGUGUGAGUCUGCCUU-GGGUCGUGUUGCU----------UGGUGUCGAUGUCGCUGCCAGUGUUUGACUAAGCGCCACGGAGACGCAGUCGAUGAAACUGACACUUUU
(((((.(((((((.((-...(((((.((((----------((..(((((...(((.....))).))))))))))).))))).)).))))........))).)))))... ( -31.50)
>DroPse_CAF1 156367 103 + 1
------CAGGGGCCUAGGGGUCGUAUAGCCGCUUGGGCUCCGGUGUCGAUGUCGCUACCAGUGUUUGACUAAGCGUCAGGGAGGCGCAGUCAAUGAAAUCGACACUUUU
------..(((((((((((((......))).))))))))))(((((((((.((((.....))..((((((..(((((.....))))))))))).)).)))))))))... ( -47.50)
>DroSec_CAF1 144791 98 + 1
GGUGUGAGUCUGCCUU-GGGUCGUGUUGCU----------CGGUGUCGAUGUCGUUGCCAGUGUUUGACUAAGCGCCACGAAGGCGCAGUCGAUGAAACUGACACUUUU
(((((.(((...(.((-((((((...((((----------.((((.((....)).))))))))..)))))..(((((.....)))))...))).)..))).)))))... ( -32.00)
>DroEre_CAF1 150293 98 + 1
GGUGUGAGUGUGCCUU-GGGUCGUGUUGCU----------UGGUGUCGAUGUCGCUGGCAGUGUUUGACUAAGCGCCACGGAGGCGCAGUCGAUGAAACCGACACUUUU
(((.(((.((((((((-....((((.((((----------((..(((((...(((.....))).))))))))))).)))))))))))).))).....)))......... ( -36.60)
>DroAna_CAF1 153297 103 + 1
UGUGUGAGUGCGCCUU-GGGUCGUAUUGCCG-----GCGAUGGUGUCGAUGUCGCUGCCAGUGUUGGACUAAGCGCCAUGGAGGCGCAGUCAAUGAAAUCGACACUUUC
.((((((.((((((((-.((.(((...((((-----(((.(((((.((....)).))))).)))))).)...)))))...)))))))).))..((....)))))).... ( -40.60)
>DroPer_CAF1 156889 103 + 1
------CAGGGGCCUAGGGGUCGUAUAGCCGUUUGGGCUCCGGUGUCGAUGUCGCUACCAGUGUUUGACUAAGCGUCAGGGAGGCGCAGUCAAUGAAAUCGACACUUUU
------..(((((((((((((......))).))))))))))(((((((((.((((.....))..((((((..(((((.....))))))))))).)).)))))))))... ( -44.70)
>consensus
GGUGUGAGUGUGCCUU_GGGUCGUAUUGCC__________CGGUGUCGAUGUCGCUGCCAGUGUUUGACUAAGCGCCACGGAGGCGCAGUCAAUGAAACCGACACUUUU
...........(((....)))....................(((((((....(((.....))).((((((..(((((.....)))))))))))......)))))))... (-23.84 = -23.48 +  -0.36)

alignment

secondary structure

dotplot

Window 6

Location	23,943,240 – 23,943,338
Length	98
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.85
Mean single sequence MFE	-27.72
Consensus MFE	-21.53
Energy contribution	-21.87
Covariance contribution	0.33
Combinations/Pair	1.10
Mean z-score	-1.33
Structure conservation index	0.78
SVM decision value	0.44
SVM RNA-class probability	0.736254
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23943240 98 - 27905053
AAAAGUGUCAGUUUCAUCGACUGCGUCUCCGUGGCGCUUAGUCAAACACUGGCAGCGACAUCGACACCA----------AGCAACACGACCC-AAGGCAGACUCACACC
....((((.((((((...(((((((((.....)))))..))))......(((...((....))...)))----------.............-...).))))).)))). ( -23.10)
>DroPse_CAF1 156367 103 - 1
AAAAGUGUCGAUUUCAUUGACUGCGCCUCCCUGACGCUUAGUCAAACACUGGUAGCGACAUCGACACCGGAGCCCAAGCGGCUAUACGACCCCUAGGCCCCUG------
....((((((((.((.(((((((.((.((...)).)).)))))))((....))...)).)))))))).((.(((..((.((........)).)).))).))..------ ( -30.30)
>DroSec_CAF1 144791 98 - 1
AAAAGUGUCAGUUUCAUCGACUGCGCCUUCGUGGCGCUUAGUCAAACACUGGCAACGACAUCGACACCG----------AGCAACACGACCC-AAGGCAGACUCACACC
....(((((((((.....))))).(((((((((..((((.((((.....))))..((....)).....)----------)))..)))))...-.))))......)))). ( -26.80)
>DroEre_CAF1 150293 98 - 1
AAAAGUGUCGGUUUCAUCGACUGCGCCUCCGUGGCGCUUAGUCAAACACUGCCAGCGACAUCGACACCA----------AGCAACACGACCC-AAGGCACACUCACACC
....((((((((.((...(((((((((.....)))))..)))).......(....))).))))))))..----------.............-................ ( -26.10)
>DroAna_CAF1 153297 103 - 1
GAAAGUGUCGAUUUCAUUGACUGCGCCUCCAUGGCGCUUAGUCCAACACUGGCAGCGACAUCGACACCAUCGC-----CGGCAAUACGACCC-AAGGCGCACUCACACA
((..((((((((.((.......(((((.....)))))...(.(((....))))...)).))))))))..))((-----(((........)).-..)))........... ( -31.30)
>DroPer_CAF1 156889 103 - 1
AAAAGUGUCGAUUUCAUUGACUGCGCCUCCCUGACGCUUAGUCAAACACUGGUAGCGACAUCGACACCGGAGCCCAAACGGCUAUACGACCCCUAGGCCCCUG------
....((((((((.((.(((((((.((.((...)).)).)))))))((....))...)).)))))))).((.(((.....((........))....))).))..------ ( -28.70)
>consensus
AAAAGUGUCGAUUUCAUCGACUGCGCCUCCGUGGCGCUUAGUCAAACACUGGCAGCGACAUCGACACCA__________AGCAACACGACCC_AAGGCACACUCACACC
....((((((((.((...(((((((((.....)))))..)))).......(....))).)))))))).......................................... (-21.53 = -21.87 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:54 2006