Locus 5101

Sequence ID	3L_DroMel_CAF1
Location	13,989,581 – 13,989,779
Length	198
Max. P	0.942238

overview

Window 1

Location	13,989,581 – 13,989,686
Length	105
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	89.78
Mean single sequence MFE	-42.98
Consensus MFE	-39.03
Energy contribution	-38.87
Covariance contribution	-0.16
Combinations/Pair	1.24
Mean z-score	-1.78
Structure conservation index	0.91
SVM decision value	1.32
SVM RNA-class probability	0.942238
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13989581 105 + 23771897
GCGGCAGCACGAUCUGUUGCUGUUGUUGAGUGGGUUGAGGCUGUUGCUGUUGAGGCUGGCCGGGCCAAGAGGUUUGCGGCCGCAAUCCACGCGGAACAAAUUGCU
(((((((((.....)))))))))((((..((((((((.((((((.(((.....((((.....))))....)))..)))))).))))))))....))))....... ( -43.20)
>DroPse_CAF1 3157 102 + 1
GCGGCAACACAAGUUGCUGUUGUUGCUGCGGAGCUUGAGGCUGCUGAUGUUG---CUGUCCUGGCCAAGAUGUUUGCGGCCGCAGUCCACGCGGUGCAAACUGCU
(((((((((((......)).)))))))))(((..(((.((((((.((((((.---..((....))...)))))).)))))).))))))..(((((....))))). ( -42.60)
>DroSec_CAF1 3094 105 + 1
GCGGCAGCACGAUCUGUUGCUGUUGUUGAGUGGGUUGAGGCUGUUGCUGUUGAGGCUGACCGGGCCAAGAGGUUUGCGGCCGCAAUCCACGCGGAACAAAUUGCU
(((((((((.....)))))))))((((..((((((((.((((((.(((.....((((.....))))....)))..)))))).))))))))....))))....... ( -43.20)
>DroSim_CAF1 3377 105 + 1
GCGGCAGCACGAUCUGUUGCUGUUGUUGAGUGGGUUGAGGCUGUUGCUGUUGAGGCUGGCCGGGCCAAGAGGUUUGCGGCCGCAAUCCACGCGGAACAAAUUGCU
(((((((((.....)))))))))((((..((((((((.((((((.(((.....((((.....))))....)))..)))))).))))))))....))))....... ( -43.20)
>DroEre_CAF1 3126 105 + 1
GCGGCAGCACGAUCUGUUGCUGUUGCUGGGUGGGUUGCGGUUGUUGCUGUUGAGGUUGGCCAGGCCAAGAGGUUUGCGGCCGCAAACCACGCGGAACAAAUUGCU
(((((((((.....)))))))(((.(((.((((.((((((((((.(((.....((((.....))))....)))..)))))))))).)))).)))))).....)). ( -44.60)
>DroYak_CAF1 3130 105 + 1
GCGGCAGCACGAUCUGUUGCUGUUGCUGAGUGGGUUGAGGUUGUUGCUGUUGAGGUUGGCCGGGCCAAGAAGUUUGCGGCCGCAAUCCACGCGGAACAAAUUGCU
(((((((((.....)))))))(((.(((.((((((((.((((((.(((.......(((((...)))))..)))..)))))).)))))))).)))))).....)). ( -41.10)
>consensus
GCGGCAGCACGAUCUGUUGCUGUUGCUGAGUGGGUUGAGGCUGUUGCUGUUGAGGCUGGCCGGGCCAAGAGGUUUGCGGCCGCAAUCCACGCGGAACAAAUUGCU
(((((((((........)))))))))...((((((((.((((((.(((.....((((.....))))....)))..)))))).))))))))((((......)))). (-39.03 = -38.87 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	13,989,686 – 13,989,779
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	90.32
Mean single sequence MFE	-40.80
Consensus MFE	-33.42
Energy contribution	-33.74
Covariance contribution	0.32
Combinations/Pair	1.16
Mean z-score	-1.54
Structure conservation index	0.82
SVM decision value	0.48
SVM RNA-class probability	0.751768
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13989686 93 + 23771897
GCUGAGGCUGCGGCUGCGGCGUUGUUGGUCCACCGGGCAGGGGUGAUUGCAUCCCAACACUGGUGGGUGUGCCUGGAGUGCUGGACGCCAUUU
((((......))))...(((((..(..(..(.((((((.((((((....)))))).(((((....))))))))))).)..)..)))))).... ( -42.10)
>DroSec_CAF1 3199 93 + 1
GCUGAGGUUGCGGCUGCGGCGUUGUUGGUCCACCAGGCAGGGGUGAUUGCAUCCCAACACUGGUGGGUGUGCCUGGAGUGCUGGGCGCAAGCU
(((((.(((((....))))).)).....(((((((((..((((((....))))))..).))))))))((((((..(....)..))))))))). ( -43.90)
>DroSim_CAF1 3482 93 + 1
GCUGAGGUUGCGGCUGCGGCGUUGUUGGUCCACCGGGCAGGGGUGAUUGCAUCCCAACACUGGUGGGUGUGCCUGGAGUGCUGGGCGCAAGCU
(((((.(((((....))))).)).....(((((((((..((((((....))))))..).))))))))((((((..(....)..))))))))). ( -43.20)
>DroEre_CAF1 3231 87 + 1
GCUGAG------GCUGCGGCGUUGUUGGUCCACCGGGUAGGGGUGAUUGCAUCCCAACACUAGUUGGUGUGCCCGGAGUGCUGGGCGCAAUCU
((((..------....))))...(((((((((((((((.((((((....)))))).(((((....))))))))))).....))))).)))).. ( -36.90)
>DroYak_CAF1 3235 93 + 1
GCUGAGGUUGCGGCUGCGGCGUUGUCGGUCCACCGGGCAAGGGGGAUUGCAUCCCAACACUAGUGGGUGUGCCAGGAGUGCUGGGAGCCAUUU
((((......))))...(((..((.((((((.((......)).))))))))(((((.((((..(((.....)))..)))).)))))))).... ( -37.90)
>consensus
GCUGAGGUUGCGGCUGCGGCGUUGUUGGUCCACCGGGCAGGGGUGAUUGCAUCCCAACACUGGUGGGUGUGCCUGGAGUGCUGGGCGCAAUCU
((((.(((....))).))))((..((((..(.((((((.((((((....)))))).(((((....))))))))))).)..))))..))..... (-33.42 = -33.74 +   0.32)

alignment

secondary structure

dotplot

Window 3

Location	13,989,686 – 13,989,779
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	90.32
Mean single sequence MFE	-31.14
Consensus MFE	-25.20
Energy contribution	-26.48
Covariance contribution	1.28
Combinations/Pair	1.08
Mean z-score	-1.96
Structure conservation index	0.81
SVM decision value	1.28
SVM RNA-class probability	0.939820
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13989686 93 - 23771897
AAAUGGCGUCCAGCACUCCAGGCACACCCACCAGUGUUGGGAUGCAAUCACCCCUGCCCGGUGGACCAACAACGCCGCAGCCGCAGCCUCAGC
....(((((...(((..((((.(((........)))))))..)))..(((((.......))))).......)))))((....))......... ( -27.50)
>DroSec_CAF1 3199 93 - 1
AGCUUGCGCCCAGCACUCCAGGCACACCCACCAGUGUUGGGAUGCAAUCACCCCUGCCUGGUGGACCAACAACGCCGCAGCCGCAACCUCAGC
.((((((((((((((((...((.....))...))))))))).)))))......((((..((((.........))))))))..))......... ( -31.50)
>DroSim_CAF1 3482 93 - 1
AGCUUGCGCCCAGCACUCCAGGCACACCCACCAGUGUUGGGAUGCAAUCACCCCUGCCCGGUGGACCAACAACGCCGCAGCCGCAACCUCAGC
.((((((((((((((((...((.....))...))))))))).)))))......((((..((((.........))))))))..))......... ( -31.50)
>DroEre_CAF1 3231 87 - 1
AGAUUGCGCCCAGCACUCCGGGCACACCAACUAGUGUUGGGAUGCAAUCACCCCUACCCGGUGGACCAACAACGCCGCAGC------CUCAGC
.((((((((((((((((...((....))....))))))))).))))))).........(((((.........)))))....------...... ( -32.90)
>DroYak_CAF1 3235 93 - 1
AAAUGGCUCCCAGCACUCCUGGCACACCCACUAGUGUUGGGAUGCAAUCCCCCUUGCCCGGUGGACCGACAACGCCGCAGCCGCAACCUCAGC
....(((((((((((((..(((.....)))..)))))))))).((((......)))).(((((.........)))))..)))........... ( -32.30)
>consensus
AGAUUGCGCCCAGCACUCCAGGCACACCCACCAGUGUUGGGAUGCAAUCACCCCUGCCCGGUGGACCAACAACGCCGCAGCCGCAACCUCAGC
.((((((((((((((((...((....))....))))))))).)))))))....((((..((((.........))))))))............. (-25.20 = -26.48 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:01 2006