Locus 4429

Sequence ID	3L_DroMel_CAF1
Location	12,926,922 – 12,927,061
Length	139
Max. P	0.999854

overview

Window 6

Location	12,926,922 – 12,927,021
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	70.91
Mean single sequence MFE	-30.16
Consensus MFE	-10.92
Energy contribution	-10.20
Covariance contribution	-0.72
Combinations/Pair	1.28
Mean z-score	-2.21
Structure conservation index	0.36
SVM decision value	1.74
SVM RNA-class probability	0.975089
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12926922 99 + 23771897
AC------CAGAUCCGUUUUUGCAAUCCGUAAAGGAAUCUAUUGAUGUGGUUGUAGAGGA----------GGAU--UCAGAAGAAUCCAAAUCGGAAUCAAAAACG---GAAUGGUUUUU
((------((..((((((((((...((((........(((((..........)))))...----------((((--((....))))))....))))..))))))))---)).)))).... ( -31.90)
>DroSec_CAF1 47648 102 + 1
AACAUAAACAGUUCCGUUUUUGCAAUCCGUCAGAGAAUCUAUUGAUGUGGUUGUAGA-------------GGAU--UCAGAAGAAUCCAAAUCGGAAUCAAAAAAG---GAAUUGUUUUU
.....((((((((((...(((((((((((((((........)))))).)))))))))-------------((((--((....)))))).................)---))))))))).. ( -33.10)
>DroSim_CAF1 51442 102 + 1
AACAUAAACAGAUCCGUUUUUGCUAUCCGUUAGAGAAUCUAUUGAUGUGGUUGUAGA-------------GGAU--UCAGAAGAAUCCAAAUCGGAAUCAAUAAAG---GAAUAGUUUUU
..........((((((..(((((.(((((((((........)))))).))).)))))-------------((((--((....))))))....))).))).......---........... ( -20.80)
>DroEre_CAF1 53204 120 + 1
ACUGUGAACAGACCCUUCGUCGCAAUCCGUGAAGGAAUCCGUUGUGGAGGUUGUAGAGGAUUCCUGAGAUGGAUCAUCAGAAGAAUCCGAAUCGGAAUCAGUAUUCCACUUAACAGGCUU
.((((.(((.((.((((((.((.....))))))))..)).)))((((((.........((((((.((..(((((..((....)))))))..))))))))....))))))...)))).... ( -33.32)
>DroYak_CAF1 50771 111 + 1
ACUGUGCACAGACCCUUUGUCGCUGUCCGAAAGGGAAUCUGUUGAGGAGGUUGUAG------CCUGGGAUGGAUCACCAGAAGAAUCCGAAUCGGAAUCAGAAUCG---AUAUUGGGCUU
.(((....))).(((..(((((((((((((...(((.(((.......((((....)------)))((((....)).))...))).)))...)))))..)))...))---)))..)))... ( -31.70)
>consensus
ACCAUAAACAGAUCCGUUUUUGCAAUCCGUAAGGGAAUCUAUUGAUGUGGUUGUAGA_____________GGAU__UCAGAAGAAUCCAAAUCGGAAUCAAAAAAG___GAAUUGUUUUU
..........((((((((..((...(((.....)))...))..)))).))))..............................((.(((.....))).))..................... (-10.92 = -10.20 +  -0.72)

alignment

secondary structure

dotplot

Window 7

Location	12,926,922 – 12,927,021
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	70.91
Mean single sequence MFE	-28.64
Consensus MFE	-9.74
Energy contribution	-9.18
Covariance contribution	-0.56
Combinations/Pair	1.27
Mean z-score	-3.42
Structure conservation index	0.34
SVM decision value	4.26
SVM RNA-class probability	0.999854
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12926922 99 - 23771897
AAAAACCAUUC---CGUUUUUGAUUCCGAUUUGGAUUCUUCUGA--AUCC----------UCCUCUACAACCACAUCAAUAGAUUCCUUUACGGAUUGCAAAAACGGAUCUG------GU
....((((.((---((((((((..((((....((((((....))--))))----------...((((............))))........))))...))))))))))..))------)) ( -31.20)
>DroSec_CAF1 47648 102 - 1
AAAAACAAUUC---CUUUUUUGAUUCCGAUUUGGAUUCUUCUGA--AUCC-------------UCUACAACCACAUCAAUAGAUUCUCUGACGGAUUGCAAAAACGGAACUGUUUAUGUU
..(((((.(((---(.((((((..((((....((((((....))--))))-------------................(((.....))).))))...)))))).)))).)))))..... ( -27.90)
>DroSim_CAF1 51442 102 - 1
AAAAACUAUUC---CUUUAUUGAUUCCGAUUUGGAUUCUUCUGA--AUCC-------------UCUACAACCACAUCAAUAGAUUCUCUAACGGAUAGCAAAAACGGAUCUGUUUAUGUU
..((((...((---(.((.(((..((((....((((((....))--))))-------------................(((.....))).))))...))).)).)))...))))..... ( -22.10)
>DroEre_CAF1 53204 120 - 1
AAGCCUGUUAAGUGGAAUACUGAUUCCGAUUCGGAUUCUUCUGAUGAUCCAUCUCAGGAAUCCUCUACAACCUCCACAACGGAUUCCUUCACGGAUUGCGACGAAGGGUCUGUUCACAGU
....((((...(((((.....((.......))((((((((..((((...))))..)))))))).........)))))(((((((.(((((.((.....))..)))))))))))).)))). ( -35.30)
>DroYak_CAF1 50771 111 - 1
AAGCCCAAUAU---CGAUUCUGAUUCCGAUUCGGAUUCUUCUGGUGAUCCAUCCCAGG------CUACAACCUCCUCAACAGAUUCCCUUUCGGACAGCGACAAAGGGUCUGUGCACAGU
.((((......---.((.(((((.......))))).))...(((.((....)))))))------))............(((((..((((((((.....)))..))))))))))....... ( -26.70)
>consensus
AAAAACAAUUC___CGUUUUUGAUUCCGAUUUGGAUUCUUCUGA__AUCC_____________UCUACAACCACAUCAAUAGAUUCCCUUACGGAUUGCAAAAACGGAUCUGUUCACAGU
....................((..((((....(((.(((..(((...............................)))..))).)))....))))...)).................... ( -9.74 =  -9.18 +  -0.56)

alignment

secondary structure

dotplot

Window 8

Location	12,926,956 – 12,927,061
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	68.48
Mean single sequence MFE	-23.38
Consensus MFE	-7.28
Energy contribution	-8.00
Covariance contribution	0.72
Combinations/Pair	1.26
Mean z-score	-2.66
Structure conservation index	0.31
SVM decision value	2.49
SVM RNA-class probability	0.994586
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12926956 105 - 23771897
UUAUACUUCGGCAGUCGAGUUGGAUUUGGAUUUGCUUGCUAAAAACCAUUC---CGUUUUUGAUUCCGAUUUGGAUUCUUCUGA--AUCC----------UCCUCUACAACCACAUCAAU
.......((((.(((((((.((((..(((.(((........))).))).))---))..)))))))))))...((((((....))--))))----------.................... ( -26.00)
>DroSec_CAF1 47688 99 - 1
UUAUAGAUCGGCAGUCGAU---AGUUUAUAUUUGCUUUAUAAAAACAAUUC---CUUUUUUGAUUCCGAUUUGGAUUCUUCUGA--AUCC-------------UCUACAACCACAUCAAU
....(((((((.((((((.---..((((((.......))))))........---.....)))))))))))))((((((....))--))))-------------................. ( -19.99)
>DroSim_CAF1 51482 99 - 1
UUAUAGAUCGGCAGUCGAU---AGUUUAUAUUUGCUUUAUAAAAACUAUUC---CUUUAUUGAUUCCGAUUUGGAUUCUUCUGA--AUCC-------------UCUACAACCACAUCAAU
....(((((((.(((((((---((((((((.......))))))........---..))))))))))))))))((((((....))--))))-------------................. ( -22.70)
>DroEre_CAF1 53244 108 - 1
UUAUAGAUCGUCUGUCAGU---AG-----AAUUGCU----AAGCCUGUUAAGUGGAAUACUGAUUCCGAUUCGGAUUCUUCUGAUGAUCCAUCUCAGGAAUCCUCUACAACCUCCACAAC
.....(((((...((((((---(.-----..(..((----.((....)).))..)..)))))))..))))).((((((((..((((...))))..))))))))................. ( -27.50)
>DroYak_CAF1 50811 99 - 1
UUAUAAAUUGUCUGCCGGU---GG-----AAUUGCU----AAGCCCAAUAU---CGAUUCUGAUUCCGAUUCGGAUUCUUCUGGUGAUCCAUCCCAGG------CUACAACCUCCUCAAC
.........(((((..(((---((-----(.(..((----(.(........---)((.(((((.......))))).))...)))..))))))).))))------)............... ( -20.70)
>consensus
UUAUAGAUCGGCAGUCGAU___AGUUU__AUUUGCUU__UAAAAACAAUUC___CGUUUUUGAUUCCGAUUUGGAUUCUUCUGA__AUCC_____________UCUACAACCACAUCAAU
....(((((((.((((((.........................................)))))))))))))((((((....))..)))).............................. ( -7.28 =  -8.00 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:25 2006