Locus 1084

Sequence ID	3L_DroMel_CAF1
Location	3,172,483 – 3,172,612
Length	129
Max. P	0.998814

overview

Window 8

Location	3,172,483 – 3,172,584
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	71.74
Mean single sequence MFE	-20.20
Consensus MFE	-9.05
Energy contribution	-8.50
Covariance contribution	-0.55
Combinations/Pair	1.20
Mean z-score	-2.06
Structure conservation index	0.45
SVM decision value	1.16
SVM RNA-class probability	0.924180
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3172483 101 - 23771897
CUGAAAUUAGUACCGAAUCGAGUACAGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACAGAUUCU------ACUACUUCUGAAAUUAGUACCGAAUCGAGU-------------
.........(((((((.(((.((((.(((((..........).)))).))))))).))).)))).((((((------((((.((....)).)))))..)))))....------------- ( -22.60)
>DroPse_CAF1 11367 111 - 1
CAACUGUUACCACGGAUUCAUCUACUGAAUCAACUGU---------AACCACGGAUUCAUCCACUGAAUCUUCCCCUGCCACUACAGAUACUUCAACAGAAUCAUCCACUUUAACCACAG
...((((.......((((((.....))))))..((((---------......(((((((.....)))))))....(((......)))........)))).................)))) ( -18.30)
>DroSec_CAF1 9618 101 - 1
CUGAAAUUAGUACCGAAUCGAGUACCGAUUCUACUACAUCUGAGCUAACUACCGAAUCGAGUACAGAUUCU------ACUACUUCUGAAAUUAGUACCGAAUCGAGU-------------
.......(((((..((((((.....)))))))))))................(((.(((.((((.(((((.------.........).)))).))))))).)))...------------- ( -19.70)
>DroSim_CAF1 9915 101 - 1
CUGAAAUUAGUACCGAAUCGAGUACAGAUUCUACUACAUCUGAGCUAACUACCGAAUCGAGUACAGAUUCU------ACUACUUCUGAAAUUAGUACCGAAUCGAGU-------------
.........(((((((.((((((.(((((........))))).)))......))).))).)))).((((((------((((.((....)).)))))..)))))....------------- ( -21.90)
>DroEre_CAF1 9537 101 - 1
CUGAAAUUAGUACCGAAUCCACUACAGAUUCUACUACUUCUGAAAUUAGUACCGAAUCUAGUACAGAUUCU------ACUACUUCUGAAAUUAGUACCGAAUCUAGU-------------
.........................(((((((((((.(((.(((..(((((..((((((.....)))))))------)))).))).)))..)))))..))))))...------------- ( -19.00)
>DroYak_CAF1 9847 101 - 1
CUGAGCUGACUACCGAAUCCACUUCAGAUUCUACUACUUCUGAAACUAGUACCGAAUCAAGUACAGAUUCA------ACUACAUCUGAACUUACAACUGAUUCGAGU-------------
.............((((((.......((((((((((.((....)).)))))..)))))((((.(((((...------.....))))).))))......))))))...------------- ( -19.70)
>consensus
CUGAAAUUAGUACCGAAUCGACUACAGAUUCUACUACUUCUGAAAUAACUACCGAAUCGAGUACAGAUUCU______ACUACUUCUGAAAUUAGUACCGAAUCGAGU_____________
..............(((((.......)))))......................(((((.......))))).................................................. ( -9.05 =  -8.50 +  -0.55)

alignment

secondary structure

dotplot

Window 9

Location	3,172,510 – 3,172,612
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	73.40
Mean single sequence MFE	-29.16
Consensus MFE	-9.71
Energy contribution	-9.22
Covariance contribution	-0.50
Combinations/Pair	1.36
Mean z-score	-2.35
Structure conservation index	0.33
SVM decision value	0.85
SVM RNA-class probability	0.865228
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3172510 102 + 23771897
AGU------AGAAUCUGUACUCGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCUGUACUCGAUUCGGUACUAAUUUCAGA---AGUAGUAGAAUCUGUACUCG---------AUUCGGU
...------.(((((.((((..(((((..(((((.((((.((((((((((((((.......)))))..)))).))))).))---)))))))))))).))))..)---------))))... ( -29.20)
>DroPse_CAF1 11407 111 + 1
GGCAGGGGAAGAUUCAGUGGAUGAAUCCGUGGUU---------ACAGUUGAUUCAGUAGAUGAAUCCGUGGUAACAGUUGAUUCAGUGGAUGAAUCUGUAGUGGAAGGUGAAGAUUCACU
.........(((((((.....((((((....(((---------((....((((((.....))))))....)))))....)))))).....))))))).........(((((....))))) ( -30.60)
>DroSec_CAF1 9645 102 + 1
AGU------AGAAUCUGUACUCGAUUCGGUAGUUAGCUCAGAUGUAGUAGAAUCGGUACUCGAUUCGGUACUAAUUUCAGA---UGUAGUAGAAUCGGUACUCG---------AUUCCGU
...------.(((((.((((.((((((.........((.((((.(((((((((((.....))))))..))))))))).)).---.......))))))))))..)---------))))... ( -28.03)
>DroSim_CAF1 9942 102 + 1
AGU------AGAAUCUGUACUCGAUUCGGUAGUUAGCUCAGAUGUAGUAGAAUCUGUACUCGAUUCGGUACUAAUUUCAGA---UGUAGUAGAAUCGGUACUCG---------AUUCCGU
...------.(((((.((((.((((((.........((.((((.((((((((((.......)))))..))))))))).)).---.......))))))))))..)---------))))... ( -25.53)
>DroEre_CAF1 9564 102 + 1
AGU------AGAAUCUGUACUAGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCUGUAGUGGAUUCGGUACUAAUUUCAGA---AGUAGUAGAAUCUGUACUGG---------AUUCGGU
...------.((((((((((.((((((..(((((.((((.(((((((((((((((.....))))))..)))).))))).))---))))))))))))))))).))---------))))... ( -34.40)
>DroYak_CAF1 9874 102 + 1
AGU------UGAAUCUGUACUUGAUUCGGUACUAGUUUCAGAAGUAGUAGAAUCUGAAGUGGAUUCGGUAGUCAGCUCAGA---UGUAGUAGAAUCUGAAGUGG---------AUUCGGU
..(------((((((((((((......)))))...(((((((..((.((..((((((.((.(((......))).)))))))---).)).))...))))))).))---------)))))). ( -27.20)
>consensus
AGU______AGAAUCUGUACUCGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCUGUACUCGAUUCGGUACUAAUUUCAGA___AGUAGUAGAAUCUGUACUCG_________AUUCGGU
..........(((((.......)))))......................((((((.....))))))...................................................... ( -9.71 =  -9.22 +  -0.50)

alignment

secondary structure

dotplot

Window 0

Location	3,172,510 – 3,172,612
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.40
Mean single sequence MFE	-26.07
Consensus MFE	-9.05
Energy contribution	-8.50
Covariance contribution	-0.55
Combinations/Pair	1.20
Mean z-score	-4.34
Structure conservation index	0.35
SVM decision value	3.24
SVM RNA-class probability	0.998814
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3172510 102 - 23771897
ACCGAAU---------CGAGUACAGAUUCUACUACU---UCUGAAAUUAGUACCGAAUCGAGUACAGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACAGAUUCU------ACU
...((((---------(..((((.((((((((((.(---((.(((..(((((..(((((.......)))))))))).))).)))..)))))..)))))..)))).))))).------... ( -27.90)
>DroPse_CAF1 11407 111 - 1
AGUGAAUCUUCACCUUCCACUACAGAUUCAUCCACUGAAUCAACUGUUACCACGGAUUCAUCUACUGAAUCAACUGU---------AACCACGGAUUCAUCCACUGAAUCUUCCCCUGCC
.((((....))))..........(((((((.....((((((....(((((....((((((.....))))))....))---------)))....)))))).....)))))))......... ( -26.10)
>DroSec_CAF1 9645 102 - 1
ACGGAAU---------CGAGUACCGAUUCUACUACA---UCUGAAAUUAGUACCGAAUCGAGUACCGAUUCUACUACAUCUGAGCUAACUACCGAAUCGAGUACAGAUUCU------ACU
..(((((---------(..((((((((((.......---((.((...(((((..((((((.....)))))))))))..)).))..........)))))).)))).))))))------... ( -28.03)
>DroSim_CAF1 9942 102 - 1
ACGGAAU---------CGAGUACCGAUUCUACUACA---UCUGAAAUUAGUACCGAAUCGAGUACAGAUUCUACUACAUCUGAGCUAACUACCGAAUCGAGUACAGAUUCU------ACU
..(((((---------(..(((((((((((((((..---........)))))........(((.(((((........))))).))).......)))))).)))).))))))------... ( -26.70)
>DroEre_CAF1 9564 102 - 1
ACCGAAU---------CCAGUACAGAUUCUACUACU---UCUGAAAUUAGUACCGAAUCCACUACAGAUUCUACUACUUCUGAAAUUAGUACCGAAUCUAGUACAGAUUCU------ACU
...((((---------(..(((((((((((((((.(---((.(((..(((((..(((((.......)))))))))).))).)))..)))))..)))))).)))).))))).------... ( -27.00)
>DroYak_CAF1 9874 102 - 1
ACCGAAU---------CCACUUCAGAUUCUACUACA---UCUGAGCUGACUACCGAAUCCACUUCAGAUUCUACUACUUCUGAAACUAGUACCGAAUCAAGUACAGAUUCA------ACU
...((((---------(...((((((.........(---((((((.((...........)).))))))).........))))))....((((........)))).))))).------... ( -20.67)
>consensus
ACCGAAU_________CCAGUACAGAUUCUACUACA___UCUGAAAUUAGUACCGAAUCGACUACAGAUUCUACUACUUCUGAAAUAACUACCGAAUCGAGUACAGAUUCU______ACU
......................................................(((((.......)))))......................(((((.......))))).......... ( -9.05 =  -8.50 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:39 2006