Locus 4484

Sequence ID	3R_DroMel_CAF1
Location	11,866,176 – 11,866,328
Length	152
Max. P	0.891581

overview

Window 5

Location	11,866,176 – 11,866,293
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.25
Mean single sequence MFE	-29.00
Consensus MFE	-16.54
Energy contribution	-18.23
Covariance contribution	1.69
Combinations/Pair	1.15
Mean z-score	-2.42
Structure conservation index	0.57
SVM decision value	0.97
SVM RNA-class probability	0.891581
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11866176 117 + 27905053
UAAUUAAGUUUAGCUAAUUGUGUGA-CUUUCUGAAACGUAUUUUCGGAAUA-GCUUAGUUCUAGCUAACUAUCAUGAAUUAGCUAUGUUUAAUUGAAUUUUGGGUCGCAAAUGGGG-UUU
((((((((..(((((((((.(((((-..((((((((.....))))))))((-(((.......)))))....))))))))))))))..))))))))......((..(.(....).).-.)) ( -28.30)
>DroSec_CAF1 22549 118 + 1
UAAUUAAGUUUAGCUAAUUGUGUGC-CUUUCUGAAACGUAUUUUCGGAAUA-GCUUAAUUCUAGCUAAGUACCAUGAAUUAGCUUAGUUUAAUUGAAUUUCGGGUCGCAAGUGGGACUUU
(((((((..(.((((((((((((((-..((((((((.....))))))))((-(((.......))))).))).))).)))))))).)..)))))))......(((((.(....).))))). ( -30.80)
>DroEre_CAF1 23040 116 + 1
UAAUUAAGUUUAGCUAAUUAUGUAUAUUUUCAGAAGCGUUUUUUAGGACUAGGCGCGAUUC----UAAGUACCAUAAAUUGGCUAAAUUUAAUUGAAUUUCGAGUCGCAAAUGUGGUCUU
((((((((((((((((((((((..(((((..(((.((((((.........))))))...))----)))))).))).)))))))))))))))))))......(((((((....)))).))) ( -30.30)
>DroYak_CAF1 23653 116 + 1
UAAUUAAGUUUAGCUAAUUGUGUUCCCUAUCUGCAACGUAUUUUGGGAAUAAGAUUGAUUC----UAAGUACCAUUAACUAGCUAAAUUUAAUUGAAUUCCGAGUCGCAAAUAGGCCCUU
((((((((((((((((.((((((((((....(((...)))....)))))))(((.....))----).........))).))))))))))))))))......(.(((.......))).).. ( -26.60)
>consensus
UAAUUAAGUUUAGCUAAUUGUGUGC_CUUUCUGAAACGUAUUUUCGGAAUA_GCUUAAUUC____UAAGUACCAUGAAUUAGCUAAAUUUAAUUGAAUUUCGAGUCGCAAAUGGGGCCUU
((((((((((((((((((((((.......(((((((.....)))))))....(((((........)))))..))).)))))))))))))))))))......................... (-16.54 = -18.23 +   1.69)

alignment

secondary structure

dotplot

Window 6

Location	11,866,215 – 11,866,328
Length	113
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	81.90
Mean single sequence MFE	-21.82
Consensus MFE	-12.02
Energy contribution	-12.84
Covariance contribution	0.81
Combinations/Pair	1.06
Mean z-score	-2.11
Structure conservation index	0.55
SVM decision value	-0.03
SVM RNA-class probability	0.520131
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11866215 113 - 27905053
AAACUAAGUGCCAUUCAGGCAGCUCUUAAACUAAAAAA-CCCCAUUUGCGACCCAAAAUUCAAUUAAACAUAGCUAAUUCAUGAUAGUUAGCUAGAACUAAGC-UAUUCCGAAAA
.........(((.....)))((((..............-.....((((.....)))).............(((((((((......)))))))))......)))-).......... ( -15.60)
>DroSec_CAF1 22588 114 - 1
AAACUAAGUGCCAUUCAGGCAGCUCUUAAACUAGAAAAGUCCCACUUGCGACCCGAAAUUCAAUUAAACUAAGCUAAUUCAUGGUACUUAGCUAGAAUUAAGC-UAUUCCGAAAA
...(((((((((((((.((..(((((......))).(((.....)))))..)).)))....(((((........)))))..))))))))))...((((.....-.))))...... ( -21.30)
>DroEre_CAF1 23080 111 - 1
AAACUAAGUGCCAUUCAGGCAGCUCUUAACCAAUAAAGACCACAUUUGCGACUCGAAAUUCAAUUAAAUUUAGCCAAUUUAUGGUACUUA----GAAUCGCGCCUAGUCCUAAAA
...(((((((((((...(((.(.((((........)))).)..............(((((......))))).))).....))))))))))----).................... ( -21.20)
>DroYak_CAF1 23693 111 - 1
AAACUAAGUGCCAUUCUGGCAGCUCUUAACUAAGAAAGGGCCUAUUUGCGACUCGGAAUUCAAUUAAAUUUAGCUAGUUAAUGGUACUUA----GAAUCAAUCUUAUUCCCAAAA
...(((((((((((((((((.((((((........))))))..............(((((......))))).)))))..)))))))))))----).................... ( -29.20)
>consensus
AAACUAAGUGCCAUUCAGGCAGCUCUUAAACAAGAAAAGCCCCAUUUGCGACCCGAAAUUCAAUUAAACUUAGCUAAUUCAUGGUACUUA____GAAUCAAGC_UAUUCCGAAAA
...(((((((((((...(((.((........................))((........))...........))).....)))))))))))........................ (-12.02 = -12.84 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:35 2006