Locus 1019

Sequence ID	2R_DroMel_CAF1
Location	4,222,296 – 4,222,496
Length	200
Max. P	0.988029

overview

Window 7

Location	4,222,296 – 4,222,416
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-33.46
Consensus MFE	-27.80
Energy contribution	-29.16
Covariance contribution	1.36
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	0.83
SVM decision value	0.61
SVM RNA-class probability	0.798493
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4222296 120 - 20766785
AUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGUGCCUCACCUUCAACUUUGUUGCCCGCCGAUCCGCUGGGCUGUUCAUGUGGUCCCUAUUCG
....(((.(..(((((..(((.......(((((..((((((((((.....))))))))))...)))))............((((((......)).)))))))....)))))..)...))) ( -36.90)
>DroSec_CAF1 34012 120 - 1
AUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGAGCCUCACCUUCAACUUUGUUGCCCGCCGAUCCGCUGGGCUGUUCAUGUGGUCCCUAUUCG
....(((.(..(((((..(((.......(((((...(((((((((.....)))))))))....)))))............((((((......)).)))))))....)))))..)...))) ( -33.90)
>DroSim_CAF1 61733 120 - 1
AUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGAGCCUCACCUUCAACUUUGUUGCCCGCCGAUCCGCUGGGCUGUUCAUGUGGUCCCUAUUCG
....(((.(..(((((..(((.......(((((...(((((((((.....)))))))))....)))))............((((((......)).)))))))....)))))..)...))) ( -33.90)
>DroEre_CAF1 35319 120 - 1
AUGAAGGCGUAACCAUCUACAUAUUCCUCGUGAUAACCAUCACCACCACCUUGUGGUGGUGCCUCACCUUCAACUUUGUUGCCCGCCGAUCCGCUGGCUUGUUCAUGUGGUCCAUAUUCA
.((((((((((((................(((((....)))))(((((((....)))))))................)))))..)))((.(((((((.....))).))))))....)))) ( -31.30)
>DroYak_CAF1 36549 120 - 1
ACGAAGGCGUUACCAUCUACAUAUUCCUGAUAAUAACCAUCACAACCACCUUGUGGUGGUGCCUCACAUUCAACUUCGUUGCCCGCCGAUCCGCUGGGUUGUUCAUGUGGAGCAUAUUCA
((((((..((........)).......(((.....((((((((((.....))))))))))...))).......))))))(((((((((((((...)))))).....)))).)))...... ( -31.30)
>consensus
AUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGUGCCUCACCUUCAACUUUGUUGCCCGCCGAUCCGCUGGGCUGUUCAUGUGGUCCCUAUUCG
.....((.....))..((((((......(((((..((((((((((.....))))))))))...)))))............((((((......)).)))).....)))))).......... (-27.80 = -29.16 +   1.36)

alignment

secondary structure

dotplot

Window 8

Location	4,222,336 – 4,222,456
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.50
Mean single sequence MFE	-31.24
Consensus MFE	-24.42
Energy contribution	-26.22
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.78
SVM decision value	0.24
SVM RNA-class probability	0.649352
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4222336 120 - 20766785
AAGAAACUCAACUCCCGCGGUCAAGUAGUCUUGUAUGGAGAUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGUGCCUCACCUUCAACUUUGUU
..(((..(((.((((......((((....))))...)))).)))..(((((......)))))......(((((..((((((((((.....))))))))))...))))))))......... ( -33.40)
>DroSec_CAF1 34052 120 - 1
AAGAAAAUCAACUCCCACGGUCAAGUAGUCUUGUAUGGAGAUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGAGCCUCACCUUCAACUUUGUU
..(((..(((.((((......((((....))))...)))).)))..(((((......)))))......(((((...(((((((((.....)))))))))....))))))))......... ( -30.60)
>DroSim_CAF1 61773 120 - 1
AAGAAAAUCAACUCCCACGGUCAAGUAGUCUUGUAUGGAGAUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGAGCCUCACCUUCAACUUUGUU
..(((..(((.((((......((((....))))...)))).)))..(((((......)))))......(((((...(((((((((.....)))))))))....))))))))......... ( -30.60)
>DroEre_CAF1 35359 120 - 1
AAGAAGCUCAACGCCCGCGGUCAAGUAACCUUGUAUGGGGAUGAAGGCGUAACCAUCUACAUAUUCCUCGUGAUAACCAUCACCACCACCUUGUGGUGGUGCCUCACCUUCAACUUUGUU
..((((.......(((.((..((((....))))..))))).((((((.(....................(((((....)))))(((((((....)))))))...).)))))).))))... ( -32.50)
>DroYak_CAF1 36589 120 - 1
AAGAAACUCAACUCCCGUGGUCAAGUAGUCUUGUACGGAGACGAAGGCGUUACCAUCUACAUAUUCCUGAUAAUAACCAUCACAACCACCUUGUGGUGGUGCCUCACAUUCAACUUCGUU
..............(((((..((((....))))))))).(((((((..((........)).......(((.....((((((((((.....))))))))))...))).......))))))) ( -29.10)
>consensus
AAGAAACUCAACUCCCGCGGUCAAGUAGUCUUGUAUGGAGAUGACGGUGUAACCAUCUACAUAUUCCUGGUGAUAACCAUCACAACCACCUUGUGGUGGUGCCUCACCUUCAACUUUGUU
.(((...(((.((((......((((....))))...)))).))).((.....)).)))..........(((((..((((((((((.....))))))))))...)))))............ (-24.42 = -26.22 +   1.80)

alignment

secondary structure

dotplot

Window 9

Location	4,222,376 – 4,222,496
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.83
Mean single sequence MFE	-31.79
Consensus MFE	-26.74
Energy contribution	-26.74
Covariance contribution	0.00
Combinations/Pair	1.15
Mean z-score	-2.18
Structure conservation index	0.84
SVM decision value	2.10
SVM RNA-class probability	0.988029
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4222376 120 + 20766785
AUGGUUAUCACCAGGAAUAUGUAGAUGGUUACACCGUCAUCUCCAUACAAGACUACUUGACCGCGGGAGUUGAGUUUCUUCUGUAAGACCAAUUCGAUGCCCACAUUGACUGCCAAACCU
.((((..(((...((..((((.((((((........)))))).))))((((....)))).))(.(((.((((((((((((....))))..)))))))).))).)..)))..))))..... ( -32.30)
>DroSec_CAF1 34092 120 + 1
AUGGUUAUCACCAGGAAUAUGUAGAUGGUUACACCGUCAUCUCCAUACAAGACUACUUGACCGUGGGAGUUGAUUUUCUUCUGCAACACCAAUUCAAUGCCCACGUUGACCACCAAACCU
.((((((.(....((..((((.((((((........)))))).))))((((....)))).))(((((.(((((....................))))).)))))).))))))........ ( -31.15)
>DroSim_CAF1 61813 120 + 1
AUGGUUAUCACCAGGAAUAUGUAGAUGGUUACACCGUCAUCUCCAUACAAGACUACUUGACCGUGGGAGUUGAUUUUCUUCUGCAACACCAAUUCAAUGCCCACGUUGACCACCAAACCU
.((((((.(....((..((((.((((((........)))))).))))((((....)))).))(((((.(((((....................))))).)))))).))))))........ ( -31.15)
>DroEre_CAF1 35399 120 + 1
AUGGUUAUCACGAGGAAUAUGUAGAUGGUUACGCCUUCAUCCCCAUACAAGGUUACUUGACCGCGGGCGUUGAGCUUCUUUUCCAAUACAAAUUCAAUGCCCACGUUGACCACCAAACCU
.((((((..(((.((..((((..(((((........)))))..))))((((....)))).))..((((((((((..................)))))))))).)))))))))........ ( -34.87)
>DroYak_CAF1 36629 120 + 1
AUGGUUAUUAUCAGGAAUAUGUAGAUGGUAACGCCUUCGUCUCCGUACAAGACUACUUGACCACGGGAGUUGAGUUUCUUUUCCAAUACAAAUUCAAUGCCCACGUUGACCACCAAGCCU
.((((((......((..((((.((((((........)))))).))))((((....)))).))..(((.(((((((((.(........).))))))))).)))....))))))........ ( -29.50)
>consensus
AUGGUUAUCACCAGGAAUAUGUAGAUGGUUACACCGUCAUCUCCAUACAAGACUACUUGACCGCGGGAGUUGAGUUUCUUCUGCAACACCAAUUCAAUGCCCACGUUGACCACCAAACCU
.((((..(((...((..((((.((((((........)))))).))))((((....)))).))..(((.((((((((..............)))))))).)))....)))..))))..... (-26.74 = -26.74 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:22 2006