Locus 5201

Sequence ID 2R_DroMel_CAF1
Location 16,920,584 – 16,920,678
Length 94
Max. P 0.985293
window8312 window8313

overview

Window 2

Location 16,920,584 – 16,920,678
Length 94
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 77.68
Mean single sequence MFE -31.92
Consensus MFE -17.86
Energy contribution -19.58
Covariance contribution 1.72
Combinations/Pair 1.04
Mean z-score -2.82
Structure conservation index 0.56
SVM decision value 2.00
SVM RNA-class probability 0.985293
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16920584 94 + 20766785
CUUGCCCAUCCGGUCCUAGGAGCUGUCCGCAUUUUAUGACCAAACAUAAAAAGCAGAAGCAGCAGCAGAAGAA--CGGAGGGAUUGGA--UGUCGGGG
((((..(((((((((((....((((((.((.(((((((......))))))).)).)..)))))....(.....--)...)))))))))--)).)))). ( -29.90)
>DroSec_CAF1 18155 93 + 1
CUUGCCCAUCCGGUCCUAGGAGCUGUCCGCAUUUUAUGACCAAACAUAAAAAGCAGAAGCAGCAGCAGAAGAA--CUGAGGGAUUGGA--UGGCGGU-
.(((((.((((((((((....((((((.((.(((((((......))))))).)).)..)))))..(((.....--))).)))))))))--)))))).- ( -35.40)
>DroSim_CAF1 18199 95 + 1
CUUGCCCAUCCGGUCCUAGGAGCUGUCCGCAUUUUAUGACCAAACAUAAAAAGCAGAAGCAGCAGCAGCAGCAGAGGGAGGGAUUGGA--UGGCGGU-
.(((((.((((((((((....((((((.((.(((((((......))))))).)).)..))))).((....)).......)))))))))--)))))).- ( -35.60)
>DroEre_CAF1 18606 84 + 1
CUUGCCCAUCCGGUCCUAGGAGCUGUCCGCAUUUUAUGACCAAACAUAAAAAGCAGAUUCA------GAGGAA--CGGAGGGAUUGGA--UGGA----
.....((((((((((((.(((....)))((.(((((((......))))))).)).......------......--....)))))))))--))).---- ( -30.00)
>DroYak_CAF1 18950 84 + 1
CUUGCCCAUCCGGUCGUAGGAGCUGUCCGCAGUUUAUGACCAAACAUAAAAAGCAGAAGCA------GAAGAA--CGACGGGAUUGGA--UGGG----
....(((((((((((((((..((((....))))))))))))...........((....)).------......--..........)))--))))---- ( -28.10)
>DroPer_CAF1 24483 92 + 1
CGCUCAAGUCCAGGGCUAGGAGUUGUCCGCAUUUUAUGGACAAACAUAAAAAA---AAACACAGACAGGAGGU--UUGGGGCAGGGGCGGGGGCGGG-
(((((..((((.((((........))))((.(((((((......)))))))..---.....(((((.....))--)))..))..))))..)))))..- ( -32.50)
>consensus
CUUGCCCAUCCGGUCCUAGGAGCUGUCCGCAUUUUAUGACCAAACAUAAAAAGCAGAAGCAGCAGCAGAAGAA__CGGAGGGAUUGGA__UGGCGG__
.....((((((((((((.(((....)))((.(((((((......))))))).)).........................)))))))))..)))..... (-17.86 = -19.58 +   1.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,920,584 – 16,920,678
Length 94
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 77.68
Mean single sequence MFE -28.38
Consensus MFE -14.53
Energy contribution -15.67
Covariance contribution 1.14
Combinations/Pair 1.10
Mean z-score -2.65
Structure conservation index 0.51
SVM decision value 1.61
SVM RNA-class probability 0.967694
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16920584 94 - 20766785
CCCCGACA--UCCAAUCCCUCCG--UUCUUCUGCUGCUGCUUCUGCUUUUUAUGUUUGGUCAUAAAAUGCGGACAGCUCCUAGGACCGGAUGGGCAAG
........--......(((((((--.((((..(..((((..(((((.(((((((......))))))).)))))))))..).)))).)))).))).... ( -30.90)
>DroSec_CAF1 18155 93 - 1
-ACCGCCA--UCCAAUCCCUCAG--UUCUUCUGCUGCUGCUUCUGCUUUUUAUGUUUGGUCAUAAAAUGCGGACAGCUCCUAGGACCGGAUGGGCAAG
-...((((--(((..(((..(((--(......))))..((((((((.(((((((......))))))).))))).))).....)))..)))).)))... ( -31.70)
>DroSim_CAF1 18199 95 - 1
-ACCGCCA--UCCAAUCCCUCCCUCUGCUGCUGCUGCUGCUUCUGCUUUUUAUGUUUGGUCAUAAAAUGCGGACAGCUCCUAGGACCGGAUGGGCAAG
-...((((--(((..(((........((....)).((((..(((((.(((((((......))))))).))))))))).....)))..)))).)))... ( -31.80)
>DroEre_CAF1 18606 84 - 1
----UCCA--UCCAAUCCCUCCG--UUCCUC------UGAAUCUGCUUUUUAUGUUUGGUCAUAAAAUGCGGACAGCUCCUAGGACCGGAUGGGCAAG
----....--......(((((((--.(((((------((..(((((.(((((((......))))))).)))))))).....)))).)))).))).... ( -28.10)
>DroYak_CAF1 18950 84 - 1
----CCCA--UCCAAUCCCGUCG--UUCUUC------UGCUUCUGCUUUUUAUGUUUGGUCAUAAACUGCGGACAGCUCCUACGACCGGAUGGGCAAG
----((((--(((......((((--(.....------.((((((((..((((((......))))))..))))).)))....))))).))))))).... ( -31.00)
>DroPer_CAF1 24483 92 - 1
-CCCGCCCCCGCCCCUGCCCCAA--ACCUCCUGUCUGUGUUU---UUUUUUAUGUUUGUCCAUAAAAUGCGGACAACUCCUAGCCCUGGACUUGAGCG
-..(((..((((.........((--(((........).))))---..(((((((......))))))).)))).(((.(((.......))).))).))) ( -16.80)
>consensus
__CCGCCA__UCCAAUCCCUCCG__UUCUUCUGCUGCUGCUUCUGCUUUUUAUGUUUGGUCAUAAAAUGCGGACAGCUCCUAGGACCGGAUGGGCAAG
................(((...................((((((((.(((((((......))))))).))))).)))(((.......))).))).... (-14.53 = -15.67 +   1.14)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:02 2006