Locus 7828

Sequence ID	3R_DroMel_CAF1
Location	20,975,658 – 20,975,753
Length	95
Max. P	0.998784

overview

Window 9

Location	20,975,658 – 20,975,753
Length	95
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	71.65
Mean single sequence MFE	-45.60
Consensus MFE	-24.69
Energy contribution	-25.93
Covariance contribution	1.24
Combinations/Pair	1.17
Mean z-score	-3.18
Structure conservation index	0.54
SVM decision value	3.22
SVM RNA-class probability	0.998784
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20975658 95 + 27905053
GCGUGGCA--AAGUGGUGGGAUCGGU-------A---UACUCCUCCAUUGGAG--GAGGACCAAGU-----CAG-----GCCAUCGUUUGCCAUGCGAUACUGUCGCCGAUUAGGCGGC
((((((((--(((((((..(((.(((-------.---..(((((((...))))--))).)))..))-----)..-----)))))..))))))))))......((((((.....)))))) ( -50.30)
>DroSec_CAF1 15700 97 + 1
GCGUGGCA--AAGUGGUGGGAUCGGC-AU----A---UACUCCUCCAUUGGAG--GAGGACCCAGC-----CAG-----GCCAUCGUUUGCCAUGCGAUACUGUCGCCGAUUAGGCGGC
((((((((--((.((((((..(.(((-..----.---..(((((((...))))--)))......))-----)).-----.))))))))))))))))......((((((.....)))))) ( -50.00)
>DroSim_CAF1 15763 97 + 1
GCGUGGCA--AAGUGGUGGGAUCGGU-AU----A---UACUCCUCCAUUGGAG--GAGGACCCAGC-----CAG-----GCCAUCGUUUGCCAUGCGAUACUGUCGCCGAUUAGGCGGC
((((((((--(((((((.((...(((-..----.---..(((((((...))))--))).)))...)-----)..-----)))))..))))))))))......((((((.....)))))) ( -49.50)
>DroEre_CAF1 17900 99 + 1
GCGUGGCA--AAGUGGCGGAAUCGGGC----------UCCUCCUCCG-UGGAG--AAGGACCAGGCCAGACCAG-----GCCAUCCUUUGCCAUGCGAUACUGUCACCGAUUAGGCGGC
((((((((--(((.((........((.----------((((.(((..-..)))--.)))))).((((......)-----))).)))))))))))))....(((((........))))). ( -43.60)
>DroYak_CAF1 16643 118 + 1
GCGUGGUAAAAAGUGAAGGAAUCGGGCAUAGGGAUUCUCCUCCUGCA-UGGAGCCAUGUGCCAGUCCAGUCCAGGACAUGCCAUCGUUUGCCAUGCGAUACUGUCGCCGAUUAGGCGGC
((((((((((..(((.........((((((.((...((((.......-.)))))).)))))).((((......))))....)))..))))))))))......((((((.....)))))) ( -49.50)
>DroAna_CAF1 15642 92 + 1
GCGUAGGAC------CAGGAUCCUGGCCCUGGAUCCUUGCUUCAGCU-UGGGG--AAGGAGGAA--------AU-----GCCA-----UGCGAUGCGAUACUGUCGCCGAUUAGGCGUC
...((((.(------(((....)))).))))..(((((.((((....-....)--)))))))).--------((-----(((.-----..((..(((((...)))))))....))))). ( -30.70)
>consensus
GCGUGGCA__AAGUGGUGGAAUCGGG_AU____A___UACUCCUCCA_UGGAG__AAGGACCAAGC_____CAG_____GCCAUCGUUUGCCAUGCGAUACUGUCGCCGAUUAGGCGGC
((((((((....((((((....)................((((......))))..........................)))))....))))))))......((((((.....)))))) (-24.69 = -25.93 +   1.24)

alignment

secondary structure

dotplot

Window 0

Location	20,975,658 – 20,975,753
Length	95
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	71.65
Mean single sequence MFE	-36.40
Consensus MFE	-13.88
Energy contribution	-14.97
Covariance contribution	1.08
Combinations/Pair	1.11
Mean z-score	-1.81
Structure conservation index	0.38
SVM decision value	-0.05
SVM RNA-class probability	0.505793
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20975658 95 - 27905053
GCCGCCUAAUCGGCGACAGUAUCGCAUGGCAAACGAUGGC-----CUG-----ACUUGGUCCUC--CUCCAAUGGAGGAGUA---U-------ACCGAUCCCACCACUU--UGCCACGC
..((((.....))))........((.(((((((.(.(((.-----..(-----(.(((((.(((--((((...)))))))..---.-------)))))))...))))))--))))).)) ( -36.10)
>DroSec_CAF1 15700 97 - 1
GCCGCCUAAUCGGCGACAGUAUCGCAUGGCAAACGAUGGC-----CUG-----GCUGGGUCCUC--CUCCAAUGGAGGAGUA---U----AU-GCCGAUCCCACCACUU--UGCCACGC
..((((.....))))........((.(((((((.(.(((.-----.((-----((...((.(((--((((...))))))).)---)----..-))))...))).)..))--))))).)) ( -37.00)
>DroSim_CAF1 15763 97 - 1
GCCGCCUAAUCGGCGACAGUAUCGCAUGGCAAACGAUGGC-----CUG-----GCUGGGUCCUC--CUCCAAUGGAGGAGUA---U----AU-ACCGAUCCCACCACUU--UGCCACGC
..((((.....))))........((.(((((((.(.(((.-----..(-----(.(.(((.(((--((((...)))))))..---.----..-))).).))..))))))--))))).)) ( -35.30)
>DroEre_CAF1 17900 99 - 1
GCCGCCUAAUCGGUGACAGUAUCGCAUGGCAAAGGAUGGC-----CUGGUCUGGCCUGGUCCUU--CUCCA-CGGAGGAGGA----------GCCCGAUUCCGCCACUU--UGCCACGC
..((((.....))))........((.((((((((..((((-----..((((.(((....(((((--(((..-..))))))))----------))).))))..)))))))--))))).)) ( -44.30)
>DroYak_CAF1 16643 118 - 1
GCCGCCUAAUCGGCGACAGUAUCGCAUGGCAAACGAUGGCAUGUCCUGGACUGGACUGGCACAUGGCUCCA-UGCAGGAGGAGAAUCCCUAUGCCCGAUUCCUUCACUUUUUACCACGC
..((((.....))))...(((..((((((....(.(((((..((((......))))..)).))).)..)))-)))..((((.(((((.........)))))))))......)))..... ( -35.40)
>DroAna_CAF1 15642 92 - 1
GACGCCUAAUCGGCGACAGUAUCGCAUCGCA-----UGGC-----AU--------UUCCUCCUU--CCCCA-AGCUGAAGCAAGGAUCCAGGGCCAGGAUCCUG------GUCCUACGC
...(((......((((.....))))......-----.)))-----..--------.((((.(((--(....-....))))..))))...((((((((....)))------))))).... ( -30.32)
>consensus
GCCGCCUAAUCGGCGACAGUAUCGCAUGGCAAACGAUGGC_____CUG_____GCUUGGUCCUC__CUCCA_UGGAGGAGUA___U____AU_CCCGAUCCCACCACUU__UGCCACGC
..((((.....))))........((.(((((.....(((...........................((((......))))................(....).))).....))))).)) (-13.88 = -14.97 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:42 2006