Locus 7347

Sequence ID 3L_DroMel_CAF1
Location 19,713,854 – 19,713,946
Length 92
Max. P 0.867325
window11933 window11934

overview

Window 3

Location 19,713,854 – 19,713,946
Length 92
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 70.35
Mean single sequence MFE -20.83
Consensus MFE -15.27
Energy contribution -16.40
Covariance contribution 1.13
Combinations/Pair 1.09
Mean z-score -1.20
Structure conservation index 0.73
SVM decision value 0.54
SVM RNA-class probability 0.775998
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19713854 92 + 23771897
--------------------------ACAUAAUUA-AAAA-AACAUCCAUACUUACGCGAUAUGUUUGUUGUAUAGUGUGUAAGUAUGUGCUGCAAUUGUUGGUGUAGUCGCAGCCACAG
--------------------------.........-....-......((((((((((((.((((.......)))).)))))))))))).(((((.((((......)))).)))))..... ( -24.30)
>DroSec_CAF1 23098 93 + 1
--------------------------AAAUAAUUU-AAAAUAUCAUUCAUACUUACGCGAUAUGUUUGUUGUAUAGUGUGUAAGUAUGUGCUGCAAUUGUUGGUGUAGUCACAACCACGG
--------------------------.........-............(((((((((((.((((.......)))).)))))))))))((((((((........))))).)))........ ( -21.10)
>DroEre_CAF1 25808 118 + 1
UUAUCUACUAAAUAUGCCCUAUUUAUAAACAUUAUAUAAC-UAAAUCCACACUUACGCGAUAUGUUUGUGGUAUAGUUUGUAAGUAUGUGCUGCAAUUGUUGGUGUAGUCACAA-CACGG
.................(((((((((((((.(((......-)))..(((((...(((.....))).)))))....)))))))))))(((((((((........))))).)))).-...)) ( -21.70)
>DroYak_CAF1 23909 118 + 1
-UUUAUAAUGUAAAUCCCCUAAAUAUAAACAAUAUAUAAC-AAAAUCCAUACUUACGCGAUAUGUUUGUUGUAUAGUUCGUAAAUAUGUGCUGUAAUUAUUUGCCUAGUCACAACCACAA
-.......(((............((..(((..((((((((-(((...(((((......).))))))))))))))))))..))....((((((((((....))))..)).))))...))). ( -16.20)
>consensus
__________________________AAACAAUAU_AAAA_AAAAUCCAUACUUACGCGAUAUGUUUGUUGUAUAGUGUGUAAGUAUGUGCUGCAAUUGUUGGUGUAGUCACAACCACAG
................................................(((((((((((.((((.......)))).)))))))))))((((((((........))))).)))........ (-15.27 = -16.40 +   1.13)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 19,713,854 – 19,713,946
Length 92
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 70.35
Mean single sequence MFE -19.86
Consensus MFE -13.41
Energy contribution -12.72
Covariance contribution -0.69
Combinations/Pair 1.31
Mean z-score -1.46
Structure conservation index 0.68
SVM decision value 0.85
SVM RNA-class probability 0.867325
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19713854 92 - 23771897
CUGUGGCUGCGACUACACCAACAAUUGCAGCACAUACUUACACACUAUACAACAAACAUAUCGCGUAAGUAUGGAUGUU-UUUU-UAAUUAUGU--------------------------
.....(((((((............))))))).(((((((((.(...................).)))))))))......-....-.........-------------------------- ( -18.51)
>DroSec_CAF1 23098 93 - 1
CCGUGGUUGUGACUACACCAACAAUUGCAGCACAUACUUACACACUAUACAACAAACAUAUCGCGUAAGUAUGAAUGAUAUUUU-AAAUUAUUU--------------------------
..(..(((((..........)))))..)....(((((((((.(...................).)))))))))...........-.........-------------------------- ( -16.91)
>DroEre_CAF1 25808 118 - 1
CCGUG-UUGUGACUACACCAACAAUUGCAGCACAUACUUACAAACUAUACCACAAACAUAUCGCGUAAGUGUGGAUUUA-GUUAUAUAAUGUUUAUAAAUAGGGCAUAUUUAGUAGAUAA
..(((-(((..(............)..)))))).........(((((..(((((.((.......))...)))))...))-)))......((((((((((((.....))))).))))))). ( -22.50)
>DroYak_CAF1 23909 118 - 1
UUGUGGUUGUGACUAGGCAAAUAAUUACAGCACAUAUUUACGAACUAUACAACAAACAUAUCGCGUAAGUAUGGAUUUU-GUUAUAUAUUGUUUAUAUUUAGGGGAUUUACAUUAUAAA-
.(((((((((((.((......)).))))))).)))).......................(((.(.(((((((((((..(-((...)))..))))))))))).).)))............- ( -21.50)
>consensus
CCGUGGUUGUGACUACACCAACAAUUGCAGCACAUACUUACAAACUAUACAACAAACAUAUCGCGUAAGUAUGGAUGUU_GUUA_AAAUUAUUU__________________________
.....(((((((............))))))).(((((((((.......................)))))))))............................................... (-13.41 = -12.72 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:37 2006