Locus 1712

Sequence ID X_DroMel_CAF1
Location 4,777,341 – 4,777,440
Length 99
Max. P 0.923799
window2809 window2810

overview

Window 9

Location 4,777,341 – 4,777,440
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 58.91
Mean single sequence MFE -22.96
Consensus MFE -10.40
Energy contribution -12.30
Covariance contribution 1.90
Combinations/Pair 1.32
Mean z-score -1.53
Structure conservation index 0.45
SVM decision value -0.01
SVM RNA-class probability 0.529904
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4777341 99 + 22224390
GGACUAGAGGUGGU-GGAGA---------AACAUCGAUGCCAAACAUCGAUAUUUUCGAAAAAUCACAUAAAUUGGUGUUUUUUGAUGAAUCAUUUUAU-----------UCAAAUUUUU
......((((((((-.....---------...(((((((.....)))))))....((((((((.(((........)))))))))))...))))))))..-----------.......... ( -20.20)
>DroSec_CAF1 14165 119 + 1
CGACUAGAGGUGGA-GAAAAAUUGAUGCCAACAUCGAUGUCAAACAUCGAUAUUUUCGAAGAAUCACAAACAUCGGUGUUUUUCGAGGAAUCAUCGUAUAAAUUGUAAGUACAAAUUAAU
(((.....((((..-((...(((((((....))))))).))...))))(((.(((((((((((.(((........))))))))))))))))).)))..(((.((((....)))).))).. ( -27.80)
>DroWil_CAF1 12799 103 + 1
AAAGUAGCGGUGGAAGAAACAACAAGGGCACUAUCGAU-----ACAUCGAUAAUUUUGCAAGUUUUCGAUAAAUACUAUUUGUGCCUGAAUUACAGUUU-----------CCAAAUUA-U
..........((((((.........((((((((((((.-----...))))))........(((...........)))....)))))).........)))-----------))).....-. ( -20.87)
>consensus
AGACUAGAGGUGGA_GAAAAA___A_G_CAACAUCGAUG_CAAACAUCGAUAUUUUCGAAAAAUCACAAAAAUUGGUGUUUUUCGAUGAAUCAUAGUAU___________ACAAAUUA_U
......(((((((...................(((((((.....)))))))....((((((((.(((........)))))))))))....)))))))....................... (-10.40 = -12.30 +   1.90)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 4,777,341 – 4,777,440
Length 99
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 58.91
Mean single sequence MFE -20.17
Consensus MFE -10.46
Energy contribution -10.13
Covariance contribution -0.33
Combinations/Pair 1.20
Mean z-score -1.52
Structure conservation index 0.52
SVM decision value 1.16
SVM RNA-class probability 0.923799
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4777341 99 - 22224390
AAAAAUUUGA-----------AUAAAAUGAUUCAUCAAAAAACACCAAUUUAUGUGAUUUUUCGAAAAUAUCGAUGUUUGGCAUCGAUGUU---------UCUCC-ACCACCUCUAGUCC
.......(((-----------((......)))))((.((((((((........))).))))).))(((((((((((.....))))))))))---------)....-.............. ( -17.60)
>DroSec_CAF1 14165 119 - 1
AUUAAUUUGUACUUACAAUUUAUACGAUGAUUCCUCGAAAAACACCGAUGUUUGUGAUUCUUCGAAAAUAUCGAUGUUUGACAUCGAUGUUGGCAUCAAUUUUUC-UCCACCUCUAGUCG
..(((.((((....)))).))).....((((.(((((((.(((((........))).)).))))).((((((((((.....)))))))))))).)))).......-.............. ( -23.60)
>DroWil_CAF1 12799 103 - 1
A-UAAUUUGG-----------AAACUGUAAUUCAGGCACAAAUAGUAUUUAUCGAAAACUUGCAAAAUUAUCGAUGU-----AUCGAUAGUGCCCUUGUUGUUUCUUCCACCGCUACUUU
.-.....(((-----------((....((((...(((((.....(((.............))).....((((((...-----.)))))))))))...))))....))))).......... ( -19.32)
>consensus
A_UAAUUUGA___________AUACAAUGAUUCAUCAAAAAACACCAAUUUUUGUGAUUUUUCGAAAAUAUCGAUGUUUG_CAUCGAUGUUG_C_U___UUUUUC_UCCACCUCUAGUCC
..................................................................((((((((((.....))))))))))............................. (-10.46 = -10.13 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:14 2006