Locus 6515

Sequence ID 2R_DroMel_CAF1
Location 20,366,805 – 20,366,923
Length 118
Max. P 0.847349
window10373 window10374

overview

Window 3

Location 20,366,805 – 20,366,923
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.09
Mean single sequence MFE -19.55
Consensus MFE -16.40
Energy contribution -17.40
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.84
SVM decision value 0.35
SVM RNA-class probability 0.698915
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20366805 118 + 20766785
U-GCGCAGCCAAAUGAUUCUGCACAUCAAUUUCUCACGCACUAAGUGAGCCACUUAGCACACAUCAAAAAUCAAUAAUCGAUUAAAUAAUUAGAAAAUUGUGAAAAUUACUGUAAUUUU-
.-..((((..........))))(((..(((((.(((((..(((((((...)))))))..)........((((.......))))................)))))))))..)))......- ( -17.10)
>DroVir_CAF1 112082 117 + 1
--GCAGAGCCAAAUGAUUUCUCACAUCAAUUUCUCACGCACUAAGUGAGCCACUUAGCGCACAUCAAAAAUCAAUAAUCGAUUAAAUAAUUAGAAAAUUGUGAAAAUUACUGUAAUUUU-
--((((.......((((((.(((((....(((((...((.(((((((...))))))).))........((((.......))))........)))))..)))))))))))))))......- ( -22.01)
>DroGri_CAF1 106256 120 + 1
GCGCACAUCCAAAUGAUUUCUCACAUCAAUUUCUCACGCACUAAGUGAGCCACUUAGCGCACAUCAAAAAUCAAUAAUCGAUUAAAUAAUUAGAAAAUUGUGAAAAUUACAGUAAUUUUG
.............((((((.(((((....(((((...((.(((((((...))))))).))........((((.......))))........)))))..)))))))))))........... ( -20.50)
>DroWil_CAF1 159206 107 + 1
A-UUGUGGCCAAAUGAUUUCUCACAUCAAUUUCUCACGCACUAAGUGAGCCACUUAG-----------AAUCAAUAAUCGAUUAAAUAAUUAGAAAAUUGUGAAAAUUACUGUAAUUUU-
(-(((..(.....((((((.(((((....(((((......(((((((...)))))))-----------((((.......))))........)))))..))))))))))))..))))...- ( -17.30)
>DroMoj_CAF1 126186 105 + 1
--------------GAUUUCUCACAUCAAUUUCUCACGCACUAAGUGAGCCACUUAGCGCACAUCAAAAAUCAAUAAUCGAUUAAAUAAUUAGAAAAUUGUGAAAAUUACUGUAAUUUU-
--------------(((((.(((((....(((((...((.(((((((...))))))).))........((((.......))))........)))))..))))))))))...........- ( -19.40)
>DroPer_CAF1 97792 118 + 1
G-GCGCAACCAAAUGAUUUCUCACAUCAAUUUCUCACGCACUAAGUGAGCCACUUAGCGCACAUCAAAAAUCAAUAAUCGAUUAAAUAAUUAGAAAAUUGUGAAAAUUACUGUAAUUUU-
(-(.....))...((((((.(((((....(((((...((.(((((((...))))))).))........((((.......))))........)))))..)))))))))))..........- ( -21.00)
>consensus
__GCGCAGCCAAAUGAUUUCUCACAUCAAUUUCUCACGCACUAAGUGAGCCACUUAGCGCACAUCAAAAAUCAAUAAUCGAUUAAAUAAUUAGAAAAUUGUGAAAAUUACUGUAAUUUU_
.............((((((.(((((....(((((...((.(((((((...))))))).))........((((.......))))........)))))..)))))))))))........... (-16.40 = -17.40 +   1.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 20,366,805 – 20,366,923
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.09
Mean single sequence MFE -27.68
Consensus MFE -23.06
Energy contribution -24.45
Covariance contribution 1.39
Combinations/Pair 1.03
Mean z-score -2.29
Structure conservation index 0.83
SVM decision value 0.77
SVM RNA-class probability 0.847349
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20366805 118 - 20766785
-AAAAUUACAGUAAUUUUCACAAUUUUCUAAUUAUUUAAUCGAUUAUUGAUUUUUGAUGUGUGCUAAGUGGCUCACUUAGUGCGUGAGAAAUUGAUGUGCAGAAUCAUUUGGCUGCGC-A
-.......((((..(((((((.........((((...((((((...))))))..))))..(..(((((((...)))))))..)))))))))))).(((((((..........))))))-) ( -31.10)
>DroVir_CAF1 112082 117 - 1
-AAAAUUACAGUAAUUUUCACAAUUUUCUAAUUAUUUAAUCGAUUAUUGAUUUUUGAUGUGCGCUAAGUGGCUCACUUAGUGCGUGAGAAAUUGAUGUGAGAAAUCAUUUGGCUCUGC--
-.......(((...(((((((.........((((...((((((...))))))..))))..((((((((((...))))))))))))))))).(..(.((((....)))))..)..))).-- ( -28.60)
>DroGri_CAF1 106256 120 - 1
CAAAAUUACUGUAAUUUUCACAAUUUUCUAAUUAUUUAAUCGAUUAUUGAUUUUUGAUGUGCGCUAAGUGGCUCACUUAGUGCGUGAGAAAUUGAUGUGAGAAAUCAUUUGGAUGUGCGC
..........(((.(((((((.........((((...((((((...))))))..))))..((((((((((...)))))))))))))))))(((.(.((((....)))).).))).))).. ( -30.10)
>DroWil_CAF1 159206 107 - 1
-AAAAUUACAGUAAUUUUCACAAUUUUCUAAUUAUUUAAUCGAUUAUUGAUU-----------CUAAGUGGCUCACUUAGUGCGUGAGAAAUUGAUGUGAGAAAUCAUUUGGCCACAA-U
-.......((((..(((((((................((((((...))))))-----------(((((((...)))))))...)))))))))))..((((....))))(((....)))-. ( -18.50)
>DroMoj_CAF1 126186 105 - 1
-AAAAUUACAGUAAUUUUCACAAUUUUCUAAUUAUUUAAUCGAUUAUUGAUUUUUGAUGUGCGCUAAGUGGCUCACUUAGUGCGUGAGAAAUUGAUGUGAGAAAUC--------------
-....(((((.((((((((((.........((((...((((((...))))))..))))..((((((((((...))))))))))))))).))))).)))))......-------------- ( -28.10)
>DroPer_CAF1 97792 118 - 1
-AAAAUUACAGUAAUUUUCACAAUUUUCUAAUUAUUUAAUCGAUUAUUGAUUUUUGAUGUGCGCUAAGUGGCUCACUUAGUGCGUGAGAAAUUGAUGUGAGAAAUCAUUUGGUUGCGC-C
-.........(((.(((((((.........((((...((((((...))))))..))))..((((((((((...)))))))))))))))))((..(.((((....)))))..)))))..-. ( -29.70)
>consensus
_AAAAUUACAGUAAUUUUCACAAUUUUCUAAUUAUUUAAUCGAUUAUUGAUUUUUGAUGUGCGCUAAGUGGCUCACUUAGUGCGUGAGAAAUUGAUGUGAGAAAUCAUUUGGCUGCGC__
.....(((((.((((((((((.........((((...((((((...))))))..))))..((((((((((...))))))))))))))).))))).))))).................... (-23.06 = -24.45 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:41 2006