Locus 8249

Sequence ID	3R_DroMel_CAF1
Location	22,074,987 – 22,075,146
Length	159
Max. P	0.979877

overview

Window 7

Location	22,074,987 – 22,075,106
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.41
Mean single sequence MFE	-35.76
Consensus MFE	-31.56
Energy contribution	-31.20
Covariance contribution	-0.36
Combinations/Pair	1.09
Mean z-score	-1.40
Structure conservation index	0.88
SVM decision value	0.69
SVM RNA-class probability	0.822413
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22074987 119 + 27905053
AACACGUUGUCCUUGAGGGACAGGGUUAAUUAUGCCAAAAUAUUUUGUCAGCUUCACGUGGCAAGAG-AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAA
..((((.(((((((....((((((((.......))).((((.((((((((........)))))))).-.))))....)))))..)))))))..((((.(((....)))..)))))))).. ( -35.70)
>DroSec_CAF1 67020 119 + 1
GCCACGUUGUCCUUGAGGGACAGGGUUAAUUAUGCCAAAAUAUUUUGUCAGCUUCACGUGGCAAGAG-AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAA
..((((.(((((((....((((((((.......))).((((.((((((((........)))))))).-.))))....)))))..)))))))..((((.(((....)))..)))))))).. ( -35.50)
>DroSim_CAF1 60459 119 + 1
GCCACGUUGUCCUUGAGGGACAGGGUUAAUUAUGCCAAAAUAUUUUGUCAGCUUCACGUGGCAAGAG-AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAA
..((((.(((((((....((((((((.......))).((((.((((((((........)))))))).-.))))....)))))..)))))))..((((.(((....)))..)))))))).. ( -35.50)
>DroEre_CAF1 61640 119 + 1
ACCACUUUGUUCUUGAG-GACAGGGUUAAUUAUGCCAAAAUAUUUUGUCAGCUUCACGUGGCAAGGGGAAUUUGUCGUUGACAAAAGGACAUUAGCCGGCAUUGUAGCGAGGCUUGUGAA
.(((((((((((....)-))))))))................((((((((((.......((((((.....)))))))))))))))))).(((.((((.((......))..)))).))).. ( -35.11)
>DroYak_CAF1 69509 120 + 1
ACCAUUUUGUCCUUGAGGGACAGGGUUAAUUAUGCCAAAAUAUUUUGUCAGCUUCACGUGGCAAGGGAAGUUUGUCGUUGACAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAA
.((.(((((((..(((.((((..(((.......)))......((((((((........))))))))...)))).)))..))))))))).(((.((((.(((....)))..)))).))).. ( -37.00)
>consensus
ACCACGUUGUCCUUGAGGGACAGGGUUAAUUAUGCCAAAAUAUUUUGUCAGCUUCACGUGGCAAGAG_AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAA
..(((..(((((((.((.((((((((.......)))......((((((((........)))))))).....))))).)).....)))))))..((((.(((....)))..)))).))).. (-31.56 = -31.20 +  -0.36)

alignment

secondary structure

dotplot

Window 8

Location	22,074,987 – 22,075,106
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.41
Mean single sequence MFE	-26.42
Consensus MFE	-22.20
Energy contribution	-23.16
Covariance contribution	0.96
Combinations/Pair	1.04
Mean z-score	-1.41
Structure conservation index	0.84
SVM decision value	0.20
SVM RNA-class probability	0.632064
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22074987 119 - 27905053
UUCACAAGCCUCGCUACAAAGCCGGCUAAUGUCCUUUUGACAACGACAAACU-CUCUUGCCACGUGAAGCUGACAAAAUAUUUUGGCAUAAUUAACCCUGUCCCUCAAGGACAACGUGUU
..(((.((((..(((....))).))))..(((((((..(((((((.(((...-...)))...)))...((..(.........)..))...........))))....)))))))..))).. ( -25.70)
>DroSec_CAF1 67020 119 - 1
UUCACAAGCCUCGCUACAAAGCCGGCUAAUGUCCUUUUGACAACGACAAACU-CUCUUGCCACGUGAAGCUGACAAAAUAUUUUGGCAUAAUUAACCCUGUCCCUCAAGGACAACGUGGC
......((((..(((....))).))))..((((.....))))..........-.....(((((((...((..(.........)..))...........(((((.....)))))))))))) ( -30.20)
>DroSim_CAF1 60459 119 - 1
UUCACAAGCCUCGCUACAAAGCCGGCUAAUGUCCUUUUGACAACGACAAACU-CUCUUGCCACGUGAAGCUGACAAAAUAUUUUGGCAUAAUUAACCCUGUCCCUCAAGGACAACGUGGC
......((((..(((....))).))))..((((.....))))..........-.....(((((((...((..(.........)..))...........(((((.....)))))))))))) ( -30.20)
>DroEre_CAF1 61640 119 - 1
UUCACAAGCCUCGCUACAAUGCCGGCUAAUGUCCUUUUGUCAACGACAAAUUCCCCUUGCCACGUGAAGCUGACAAAAUAUUUUGGCAUAAUUAACCCUGUC-CUCAAGAACAAAGUGGU
(((((.((((..((......)).))))........((((((...)))))).............)))))((..(.........)..)).......(((((.((-.....))....)).))) ( -20.60)
>DroYak_CAF1 69509 120 - 1
UUCACAAGCCUCGCUACAAAGCCGGCUAAUGUCCUUUUGUCAACGACAAACUUCCCUUGCCACGUGAAGCUGACAAAAUAUUUUGGCAUAAUUAACCCUGUCCCUCAAGGACAAAAUGGU
(((((.((((..(((....))).))))........((((((...)))))).............)))))((..(.........)..)).......(((.(((((.....)))))....))) ( -25.40)
>consensus
UUCACAAGCCUCGCUACAAAGCCGGCUAAUGUCCUUUUGACAACGACAAACU_CUCUUGCCACGUGAAGCUGACAAAAUAUUUUGGCAUAAUUAACCCUGUCCCUCAAGGACAACGUGGU
......((((..((......)).))))..((((...........))))..........(((((((...((..(.........)..))...........(((((.....)))))))))))) (-22.20 = -23.16 +   0.96)

alignment

secondary structure

dotplot

Window 9

Location	22,075,027 – 22,075,146
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.41
Mean single sequence MFE	-39.17
Consensus MFE	-36.41
Energy contribution	-36.41
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.93
SVM decision value	1.85
SVM RNA-class probability	0.979877
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22075027 119 + 27905053
UAUUUUGUCAGCUUCACGUGGCAAGAG-AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAAAUCAGAACUUCCUUUGGCCGCCGGCUUUGUCCUUGAUCCU
....(((.((((.......((((((..-..)))))))))).)))(((((((..(((((((.....((.((((.((.((....)).))))))))......))))))).)))))))...... ( -37.71)
>DroSec_CAF1 67060 119 + 1
UAUUUUGUCAGCUUCACGUGGCAAGAG-AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAAAUCAGAACUUCCUUUGGCCGCCGGCUUUGUCCUUGAUCCU
....(((.((((.......((((((..-..)))))))))).)))(((((((..(((((((.....((.((((.((.((....)).))))))))......))))))).)))))))...... ( -37.71)
>DroSim_CAF1 60499 119 + 1
UAUUUUGUCAGCUUCACGUGGCAAGAG-AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAAAUCAGAACUUCCUUUGGCCGCCGGCUUUGUCCUUGAUCCU
....(((.((((.......((((((..-..)))))))))).)))(((((((..(((((((.....((.((((.((.((....)).))))))))......))))))).)))))))...... ( -37.71)
>DroEre_CAF1 61679 120 + 1
UAUUUUGUCAGCUUCACGUGGCAAGGGGAAUUUGUCGUUGACAAAAGGACAUUAGCCGGCAUUGUAGCGAGGCUUGUGAAAUCAGAACUUCCUUUGGCCGCCGGCUUUGUCCUUGAUCCU
....((((((((.......((((((.....))))))))))))))(((((((..(((((((.....((.((((.((.((....)).))))))))......))))))).)))))))...... ( -42.21)
>DroYak_CAF1 69549 120 + 1
UAUUUUGUCAGCUUCACGUGGCAAGGGAAGUUUGUCGUUGACAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAAAUCUGAACUUCCUUUGGCCGCCGGCUUUGUCCUUGAUCCU
....((((((((.......((((((.....))))))))))))))(((((((..(((((((.(((...)))((((.(.(((........))))...))))))))))).)))))))...... ( -40.51)
>consensus
UAUUUUGUCAGCUUCACGUGGCAAGAG_AGUUUGUCGUUGUCAAAAGGACAUUAGCCGGCUUUGUAGCGAGGCUUGUGAAAUCAGAACUUCCUUUGGCCGCCGGCUUUGUCCUUGAUCCU
....(((.((((.......((((((.....)))))))))).)))(((((((..(((((((.(((...)))((((.(.(((........))))...))))))))))).)))))))...... (-36.41 = -36.41 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:06:46 2006