Locus 8687

Sequence ID	3R_DroMel_CAF1
Location	23,194,836 – 23,194,940
Length	104
Max. P	0.835670

overview

Window 1

Location	23,194,836 – 23,194,940
Length	104
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	76.17
Mean single sequence MFE	-28.61
Consensus MFE	-17.00
Energy contribution	-17.50
Covariance contribution	0.50
Combinations/Pair	1.21
Mean z-score	-1.72
Structure conservation index	0.59
SVM decision value	0.73
SVM RNA-class probability	0.835670
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23194836 104 + 27905053
CU--------UUCAAUCUC-------CUUCAUUCGCAGAUAUUACAUGGAGCGCAAGAUCUUCCAGCAUCUCCUGGAGCUCAAGUCGCUGCAGAUUCGCUCCAGUAAGCUGAACGAGGC
..--------........(-------(((......(((...((((.(((((((...((((((((((......)))))((..........)))))))))))))))))).)))...)))). ( -30.10)
>DroVir_CAF1 10353 107 + 1
UU--------UGCAUGCUCUU----AUACUCUUUGCAGAUACUACAUGGAGCGCAAGAUCUUCCAGCAUCUGCUGGAGCUCAAGUCGCUACAAAUACGCUCAAACAAGCUGAACGAAGC
((--------((((.......----........)))))).........(((((........((((((....))))))((.......))........)))))......(((......))) ( -24.06)
>DroGri_CAF1 11050 100 + 1
CU--------GCCAU-----------CCCUAUUUGCAGAUACUACAUGGAGCGCAAGAUCUUUCAGCAUCUGCUUGAGCUCAAGUCGCUGCAGAUACGCUCCAACAAGCUGAACGAGGC
..--------.....-----------.(((.....(((........(((((((....((((..((((....(((((....))))).)))).)))).))))))).....)))....))). ( -28.12)
>DroWil_CAF1 38448 113 + 1
CC------UCUUGAAAUUUAUGUUUGUUUCAUUUGCAGAUAUUACAUGGAGCGCAAGAUCUUUCAGCAUUUGCUGGAGCUGAAAUCCCUACAGAUACGUUCCAGUAAACUGAAUGAGUC
..------(((((...(((((((.((((((....).)))))..)))))))...)))))((.(((((..(((((((((((....(((......)))..)))))))))))))))).))... ( -31.60)
>DroMoj_CAF1 10849 107 + 1
CU--------GGCACACUUCA----CUUCUAUUUGCAGAUACUACAUGGAGCGCAAGAUCUUCCAGCAUCUGCUGGAGCUCAAGUCGCUGCAAAUACGCUCCAACAAGCUGAACGAGGU
..--------.....(((((.----....(((((((((..(((....(((.(....).)))((((((....)))))).....)))..))))))))).(((......))).....))))) ( -31.90)
>DroAna_CAF1 8546 114 + 1
CCUACUUUG-UUUAAUUUCUC----GUUUCAUUUGCAGAUACUACAUGGAACGAAAGAUCUUCCAGCAUCUUCUCGAGCUUAAAUCUCUGCAGAUCCGCUCCAGCAAGCUCAACGAGGC
.........-.......((((----(((..(((((((((.......((((((....)...)))))((.((.....)))).......)))))))))..(((......)))..))))))). ( -25.90)
>consensus
CU________UUCAAACUC_______UUCCAUUUGCAGAUACUACAUGGAGCGCAAGAUCUUCCAGCAUCUGCUGGAGCUCAAGUCGCUGCAGAUACGCUCCAACAAGCUGAACGAGGC
..............................((((((((..(((....(((.(....).)))((((((....)))))).....)))..))))))))..(((......))).......... (-17.00 = -17.50 +   0.50)

alignment

secondary structure

dotplot

Window 2

Location	23,194,836 – 23,194,940
Length	104
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	76.17
Mean single sequence MFE	-32.68
Consensus MFE	-17.49
Energy contribution	-17.38
Covariance contribution	-0.11
Combinations/Pair	1.28
Mean z-score	-1.63
Structure conservation index	0.54
SVM decision value	0.02
SVM RNA-class probability	0.543232
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23194836 104 - 27905053
GCCUCGUUCAGCUUACUGGAGCGAAUCUGCAGCGACUUGAGCUCCAGGAGAUGCUGGAAGAUCUUGCGCUCCAUGUAAUAUCUGCGAAUGAAG-------GAGAUUGAA--------AG
.((((((((.(((((((((((((.((((.(((((.((((.....))))...)))))..))))....))))))).)))).....))))))).))-------)........--------.. ( -34.70)
>DroVir_CAF1 10353 107 - 1
GCUUCGUUCAGCUUGUUUGAGCGUAUUUGUAGCGACUUGAGCUCCAGCAGAUGCUGGAAGAUCUUGCGCUCCAUGUAGUAUCUGCAAAGAGUAU----AAGAGCAUGCA--------AA
....(((((((.....)))))))..((((((((.........((((((....))))))...(((((..(((..(((((...)))))..)))..)----)))))).))))--------)) ( -34.90)
>DroGri_CAF1 11050 100 - 1
GCCUCGUUCAGCUUGUUGGAGCGUAUCUGCAGCGACUUGAGCUCAAGCAGAUGCUGAAAGAUCUUGCGCUCCAUGUAGUAUCUGCAAAUAGGG-----------AUGGC--------AG
(((((((((((.((((((.((.....)).)))))).))))))....((((((((((...((........))....)))))))))).......)-----------).)))--------.. ( -34.50)
>DroWil_CAF1 38448 113 - 1
GACUCAUUCAGUUUACUGGAACGUAUCUGUAGGGAUUUCAGCUCCAGCAAAUGCUGAAAGAUCUUGCGCUCCAUGUAAUAUCUGCAAAUGAAACAAACAUAAAUUUCAAGA------GG
..(((...(((.((((((((.((((.....(((..(((((((..........)))))))..))))))).)))).))))...)))....(((((..........))))).))------). ( -27.70)
>DroMoj_CAF1 10849 107 - 1
ACCUCGUUCAGCUUGUUGGAGCGUAUUUGCAGCGACUUGAGCUCCAGCAGAUGCUGGAAGAUCUUGCGCUCCAUGUAGUAUCUGCAAAUAGAAG----UGAAGUGUGCC--------AG
..((.((...((((..(((((((((....(.((.......))((((((....)))))).)....)))))))))(((((...)))))........----..))))..)).--------)) ( -32.60)
>DroAna_CAF1 8546 114 - 1
GCCUCGUUGAGCUUGCUGGAGCGGAUCUGCAGAGAUUUAAGCUCGAGAAGAUGCUGGAAGAUCUUUCGUUCCAUGUAGUAUCUGCAAAUGAAAC----GAGAAAUUAAA-CAAAGUAGG
..((((((..(.((((..((((.(((((....)))))...))))....(((((((((((((....)).))))....))))))))))).)..)))----)))........-......... ( -31.70)
>consensus
GCCUCGUUCAGCUUGCUGGAGCGUAUCUGCAGCGACUUGAGCUCCAGCAGAUGCUGGAAGAUCUUGCGCUCCAUGUAGUAUCUGCAAAUAAAA_______GAGAUUGAA________AG
................((((((((((((.(((((.((...((....)))).)))))..))))...))))))))((((.....))))................................. (-17.49 = -17.38 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:16 2006