Locus 7889

Sequence ID X_DroMel_CAF1
Location 19,665,521 – 19,665,618
Length 97
Max. P 0.949797
window12942 window12943

overview

Window 2

Location 19,665,521 – 19,665,618
Length 97
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 70.66
Mean single sequence MFE -21.19
Consensus MFE -5.32
Energy contribution -5.16
Covariance contribution -0.16
Combinations/Pair 1.14
Mean z-score -2.14
Structure conservation index 0.25
SVM decision value 1.37
SVM RNA-class probability 0.947733
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19665521 97 + 22224390
CAUAUAGUAUAGAAUCAUAUA----UG-----------CAAUGAAUGUAGCAAGGACAUUUUUAAGCUGAUUUA------UUAGCGUACCUGACACAAAUGCACACAUGCACGUACAU
......((((....(((..((----((-----------((((((((.((((..............)))))))))------)).)))))..)))......((((....)))).)))).. ( -18.44)
>DroSec_CAF1 39003 89 + 1
CAUAUAGUAUAGAAUCGUAUA----UGCAUUCAU---GCAAUUUAUGCAGCAAGGACAUUUCCAAGCUGAUUUA----------------------AAAUGCACACACGCACGUACAU
................(((..----(((.....(---(((.((((..((((..(((....)))..))))...))----------------------)).)))).....)))..))).. ( -22.10)
>DroSim_CAF1 30762 89 + 1
CAUAUAGUAUAGAAUCAUAUA----UGCAUUCAU---GCAAUUUAUGCAGCAAGGACAUUUCUAAGCUGAUUUA----------------------AAAUGCACACAUGCACGUACAU
.................((..----(((((...(---(((.((((..((((..(((....)))..))))...))----------------------)).))))...)))))..))... ( -19.30)
>DroEre_CAF1 51105 106 + 1
CAUAUA-----GAAUCAUACAGACUUGCCUACAUGCUGCAAUAAAUGCAGCAACGACACUU--AAGCUGAUAUUC-----UUGGCGUACCAGACACAAAUGCGUACAUGCACGUACAU
......-----...........((.(((.....(((((((.....))))))).........--..((..(.....-----)..))((((((........)).))))..))).)).... ( -21.80)
>DroYak_CAF1 52971 108 + 1
CAUAUA-----GAAUCAUAUAGACUUGCAUAUAU---GCAAUGCGUGCAGCAACGACAUUU--AAGCUGAUAUUCUGAUAUUGGCGUAACGUACACAAAUGCACACAUGCACGUACAU
......-----.............(((((....)---))))((((((((.....(.(((((--..((..((((....))))..))(((...)))..)))))).....))))))))... ( -24.30)
>consensus
CAUAUAGUAUAGAAUCAUAUA____UGCAUACAU___GCAAUGAAUGCAGCAAGGACAUUU__AAGCUGAUUUA______UU_GCGUA_C__ACACAAAUGCACACAUGCACGUACAU
...............................................((((..............))))..............................(((......)))....... ( -5.32 =  -5.16 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,665,521 – 19,665,618
Length 97
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 70.66
Mean single sequence MFE -25.36
Consensus MFE -6.07
Energy contribution -5.63
Covariance contribution -0.44
Combinations/Pair 1.29
Mean z-score -2.15
Structure conservation index 0.24
SVM decision value 1.39
SVM RNA-class probability 0.949797
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19665521 97 - 22224390
AUGUACGUGCAUGUGUGCAUUUGUGUCAGGUACGCUAA------UAAAUCAGCUUAAAAAUGUCCUUGCUACAUUCAUUG-----------CA----UAUAUGAUUCUAUACUAUAUG
.((((....((((((((((..((((.((((.(((((..------......)))........)).)))).)))).....))-----------))----))))))....))))....... ( -19.60)
>DroSec_CAF1 39003 89 - 1
AUGUACGUGCGUGUGUGCAUUU----------------------UAAAUCAGCUUGGAAAUGUCCUUGCUGCAUAAAUUGC---AUGAAUGCA----UAUACGAUUCUAUACUAUAUG
.((((..(((((.((((((.((----------------------((...((((..(((....)))..))))..)))).)))---))).)))))----..))))............... ( -28.00)
>DroSim_CAF1 30762 89 - 1
AUGUACGUGCAUGUGUGCAUUU----------------------UAAAUCAGCUUAGAAAUGUCCUUGCUGCAUAAAUUGC---AUGAAUGCA----UAUAUGAUUCUAUACUAUAUG
..(((..(((((.((((((.((----------------------((...((((...((....))...))))..)))).)))---))).)))))----..)))................ ( -21.00)
>DroEre_CAF1 51105 106 - 1
AUGUACGUGCAUGUACGCAUUUGUGUCUGGUACGCCAA-----GAAUAUCAGCUU--AAGUGUCGUUGCUGCAUUUAUUGCAGCAUGUAGGCAAGUCUGUAUGAUUC-----UAUAUG
.....(((((....((((....))))...)))))...(-----((((..(((((.--...((((..(((((((.....)))))))....)))))).)))....))))-----)..... ( -30.30)
>DroYak_CAF1 52971 108 - 1
AUGUACGUGCAUGUGUGCAUUUGUGUACGUUACGCCAAUAUCAGAAUAUCAGCUU--AAAUGUCGUUGCUGCACGCAUUGC---AUAUAUGCAAGUCUAUAUGAUUC-----UAUAUG
(((.((.((((((((((((..((((((.((.(((.((.....((........)).--...)).))).))))))))...)))---))))))))).)).))).......-----...... ( -27.90)
>consensus
AUGUACGUGCAUGUGUGCAUUUGUGU__G_UACGC_AA______UAAAUCAGCUU__AAAUGUCCUUGCUGCAUAAAUUGC___AUGAAUGCA____UAUAUGAUUCUAUACUAUAUG
......(((((.(((.((((((...................................))))))...))))))))............................................ ( -6.07 =  -5.63 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:04 2006