Locus 2540

Sequence ID 2R_DroMel_CAF1
Location 9,033,450 – 9,033,541
Length 91
Max. P 0.895392
window4181 window4182

overview

Window 1

Location 9,033,450 – 9,033,541
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 63.14
Mean single sequence MFE -20.95
Consensus MFE -8.71
Energy contribution -8.93
Covariance contribution 0.22
Combinations/Pair 1.08
Mean z-score -1.60
Structure conservation index 0.42
SVM decision value 0.37
SVM RNA-class probability 0.710134
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9033450 91 + 20766785
GAGUAGAGUCUUCCAAAGAAGGACUCUCACAAGCUCAUUAAGCUC-UUCGU----ACAGUCACAU------------CAUGCUAUAUCUGUACUUAAAA-----AAAA-------AAUAC
((((((((((((.......)))))))).....)))).........-...((----((((......------------..........))))))......-----....-------..... ( -17.79)
>DroPse_CAF1 10054 111 + 1
GAGUAGUGUUUUGGA---UAGAACUCCUAAAAGCUCAGCAAACUU-UACAUACAUACAGUUGCAUCUGUUUGUGUUCGAUGCAACGACUGUACCUUGUA-----ACGAAACUCUAAAAUC
((((.(.((((((((---......)))..))))).)......(.(-((((....((((((((((((...........))))))...))))))...))))-----).)..))))....... ( -23.40)
>DroSec_CAF1 9735 88 + 1
GAGUAGAGUCUUCCAAGGAAGGACUCUCACAAGCUCAUUAAGCUC-UUCGU----AAAGUCGAUA------------UAUGAUAUAUCUGUACUUCCAA-----ACAA----------AA
(((((((((((((....))).)))))).....)))).........-.....----.(((((((((------------((...)))))).).))))....-----....----------.. ( -17.10)
>DroSim_CAF1 9124 89 + 1
GAGUAGAGUCUUCCAAGGAAGGACUCUCACAAGCUCAUUAAGCUC-UUCGU----ACAGUCGAUA------------UAUGAUAUAUCUGUACUUCCAA-----AAAA---------UAA
(((((((((((((....))).)))))).....)))).........-...((----((((...(((------------(...))))..))))))......-----....---------... ( -21.30)
>DroYak_CAF1 9774 106 + 1
GAGUAGAGUCUUCGGAGGAAGGACUCUCACAAGCUCAUUAAGCUCAUUCGU----ACAGUCACAUCUGCUUUAUCUGCAUGUCAUAUCUGUACUUCCAAUAUCCAAAA----------AA
(((((((((((((....))).))))))....((((.....)))).))))((----((((......((((.......))).)......))))))...............----------.. ( -22.70)
>DroPer_CAF1 6813 111 + 1
GAGUAGUGUUUUGGA---UAGAACUCCUAAAAGCUCAGCAAACUU-UACAUACAUACAGUUGCAUCUGUUUGUGUUCGAUGCAACGACUGUACCUUGUA-----AUGAAACUCUAAUAUC
((((.(.((((((((---......)))..))))).)......(.(-((((....((((((((((((...........))))))...))))))...))))-----).)..))))....... ( -23.40)
>consensus
GAGUAGAGUCUUCCAAGGAAGGACUCUCACAAGCUCAUUAAGCUC_UUCGU____ACAGUCGCAU____________CAUGCUAUAUCUGUACUUCCAA_____AAAA__________AA
((((((((((((.......)))))))).....)))).................................................................................... ( -8.71 =  -8.93 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 9,033,450 – 9,033,541
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 63.14
Mean single sequence MFE -25.60
Consensus MFE -9.51
Energy contribution -8.73
Covariance contribution -0.77
Combinations/Pair 1.30
Mean z-score -2.01
Structure conservation index 0.37
SVM decision value 0.99
SVM RNA-class probability 0.895392
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9033450 91 - 20766785
GUAUU-------UUUU-----UUUUAAGUACAGAUAUAGCAUG------------AUGUGACUGU----ACGAA-GAGCUUAAUGAGCUUGUGAGAGUCCUUCUUUGGAAGACUCUACUC
.....-------....-----......((((((.((((.....------------.)))).))))----))...-((((((...))))))((.((((((.(((....))))))))))).. ( -24.20)
>DroPse_CAF1 10054 111 - 1
GAUUUUAGAGUUUCGU-----UACAAGGUACAGUCGUUGCAUCGAACACAAACAGAUGCAACUGUAUGUAUGUA-AAGUUUGCUGAGCUUUUAGGAGUUCUA---UCCAAAACACUACUC
.......((((....(-----(((((.(((((((...((((((...........))))))))))))).).))))-).((((...((((((....))))))..---....))))...)))) ( -27.40)
>DroSec_CAF1 9735 88 - 1
UU----------UUGU-----UUGGAAGUACAGAUAUAUCAUA------------UAUCGACUUU----ACGAA-GAGCUUAAUGAGCUUGUGAGAGUCCUUCCUUGGAAGACUCUACUC
.(----------((((-----...(((((...((((((...))------------)))).)))))----)))))-((((((...))))))((.((((((.(((....))))))))))).. ( -23.90)
>DroSim_CAF1 9124 89 - 1
UUA---------UUUU-----UUGGAAGUACAGAUAUAUCAUA------------UAUCGACUGU----ACGAA-GAGCUUAAUGAGCUUGUGAGAGUCCUUCCUUGGAAGACUCUACUC
...---------...(-----(((..(((...((((((...))------------)))).)))..----.))))-((((((...))))))((.((((((.(((....))))))))))).. ( -22.90)
>DroYak_CAF1 9774 106 - 1
UU----------UUUUGGAUAUUGGAAGUACAGAUAUGACAUGCAGAUAAAGCAGAUGUGACUGU----ACGAAUGAGCUUAAUGAGCUUGUGAGAGUCCUUCCUCCGAAGACUCUACUC
.(----------(((((((....(((.((((((.((((...(((.......)))..)))).))))----))..(..(((((...)))))..).....)))....))))))))........ ( -27.70)
>DroPer_CAF1 6813 111 - 1
GAUAUUAGAGUUUCAU-----UACAAGGUACAGUCGUUGCAUCGAACACAAACAGAUGCAACUGUAUGUAUGUA-AAGUUUGCUGAGCUUUUAGGAGUUCUA---UCCAAAACACUACUC
.......((((....(-----(((((.(((((((...((((((...........))))))))))))).).))))-).((((...((((((....))))))..---....))))...)))) ( -27.50)
>consensus
GU__________UUUU_____UUGGAAGUACAGAUAUAGCAUA____________AUGCGACUGU____ACGAA_GAGCUUAAUGAGCUUGUGAGAGUCCUUCCUUCGAAGACUCUACUC
..........................(((.........................................((...((((((...)))))).))((((((.(((....)))))))))))). ( -9.51 =  -8.73 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:31 2006