Locus 1999

Sequence ID 3R_DroMel_CAF1
Location 5,660,194 – 5,660,333
Length 139
Max. P 0.986719
window3271 window3272 window3273

overview

Window 1

Location 5,660,194 – 5,660,293
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.78
Mean single sequence MFE -19.38
Consensus MFE -1.76
Energy contribution -2.44
Covariance contribution 0.68
Combinations/Pair 1.38
Mean z-score -1.60
Structure conservation index 0.09
SVM decision value 0.02
SVM RNA-class probability 0.544549
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5660194 99 + 27905053
UAAAAAAUGUAUCAGAUGUGAAU--GGAGUUGGAGUAUA---AUAGA-AGAAUCUGUAGAAUAAUCAAUAAGGUACAGACUCCUA---UAGAAUACUG----------CAG--CACAAUA
.......(((.(((....)))..--...((((.(((((.---.((..-.((.((((((...............)))))).))...---))..))))).----------)))--))))... ( -17.56)
>DroSec_CAF1 13830 99 + 1
UAAAAAAUGUAUCAGAUGUGAAU--GGAGUAGGAGUAUA---AUAGA-CAAAUCUGCAGAAUAAUCAAUAAUGUCCAGUAUCCUA---UAGAAUACUG----------CAG--CACAAUA
................((((..(--(.((((..((.(((---...((-((.....................))))...))).)).---.....)))).----------)).--))))... ( -11.20)
>DroSim_CAF1 13825 102 + 1
UAAAAAAUGUAUCUGAUGUGAAU--GGAAUAGGAGUAUAGGAAUAGA-CGAAUCUGCAGAAUAAUCAAUAAUGUCCAGUAUCCUA---UAGAAUACUG----------CAG--CACAAUA
.......(((..(((..(((...--...((((((.(((.(((.((((-....))))..((....)).......))).))))))))---)....)))..----------)))--.)))... ( -13.00)
>DroEre_CAF1 10774 105 + 1
UAAAAUACGUAACAAUUGUGAAU--GGAGUAGGAGCAUG---AUAGAAGGUAUCUGCAGAA-AAUUAAUCAUUUGCAGAAUUCUU-UUAAAAAUAAUGAUACUACUCG--------UAUA
....((((...((....))....--.((((((...(((.---.(((((((..((((((((.-.........))))))))..))))-)))......)))...)))))))--------))). ( -24.80)
>DroYak_CAF1 14172 110 + 1
UAAAAUACG-----AGUAUGUAUGAGGUGUAGGAGAAUA---AUAGA-GGCUUCUGCAGAA-AAUCAAUAAUAUGCAGAAGCCUUUUUUAAAAUAAUGAUAUUACUCGCGGCUCACUAUA
.........-----....((((((((.(((..(((..((---(.(((-((((((((((...-...........))))))))))))).))).((((....)))).)))))).)))).)))) ( -30.34)
>consensus
UAAAAAAUGUAUCAGAUGUGAAU__GGAGUAGGAGUAUA___AUAGA_CGAAUCUGCAGAAUAAUCAAUAAUGUCCAGAAUCCUA___UAGAAUACUG__________CAG__CACAAUA
.................................................((.((((((...............)))))).))...................................... ( -1.76 =  -2.44 +   0.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,660,194 – 5,660,293
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.78
Mean single sequence MFE -17.17
Consensus MFE -2.36
Energy contribution -3.36
Covariance contribution 1.00
Combinations/Pair 1.44
Mean z-score -1.88
Structure conservation index 0.14
SVM decision value 0.63
SVM RNA-class probability 0.806865
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5660194 99 - 27905053
UAUUGUG--CUG----------CAGUAUUCUA---UAGGAGUCUGUACCUUAUUGAUUAUUCUACAGAUUCU-UCUAU---UAUACUCCAACUCC--AUUCACAUCUGAUACAUUUUUUA
...((((--.((----------.(((((..((---.(((((((((((...((.....))...))))))))))-).)).---.))))).)).....--..(((....)))))))....... ( -18.10)
>DroSec_CAF1 13830 99 - 1
UAUUGUG--CUG----------CAGUAUUCUA---UAGGAUACUGGACAUUAUUGAUUAUUCUGCAGAUUUG-UCUAU---UAUACUCCUACUCC--AUUCACAUCUGAUACAUUUUUUA
...((((--...----------((((((((..---..))))))))((((...(((.........)))...))-))...---..............--...))))................ ( -14.60)
>DroSim_CAF1 13825 102 - 1
UAUUGUG--CUG----------CAGUAUUCUA---UAGGAUACUGGACAUUAUUGAUUAUUCUGCAGAUUCG-UCUAUUCCUAUACUCCUAUUCC--AUUCACAUCAGAUACAUUUUUUA
...((((--(((----------((((((((..---..)))))))).........(((...((....))...)-))....................--........))).))))....... ( -14.40)
>DroEre_CAF1 10774 105 - 1
UAUA--------CGAGUAGUAUCAUUAUUUUUAA-AAGAAUUCUGCAAAUGAUUAAUU-UUCUGCAGAUACCUUCUAU---CAUGCUCCUACUCC--AUUCACAAUUGUUACGUAUUUUA
.(((--------(((((((...(((......((.-(((...((((((...((......-.))))))))...))).)).---.)))...))))))(--(........))....)))).... ( -14.30)
>DroYak_CAF1 14172 110 - 1
UAUAGUGAGCCGCGAGUAAUAUCAUUAUUUUAAAAAAGGCUUCUGCAUAUUAUUGAUU-UUCUGCAGAAGCC-UCUAU---UAUUCUCCUACACCUCAUACAUACU-----CGUAUUUUA
...........((((((((((....)))........(((((((((((...........-...))))))))))-)....---.....................))))-----)))...... ( -24.44)
>consensus
UAUUGUG__CUG__________CAGUAUUCUA___UAGGAUUCUGCACAUUAUUGAUUAUUCUGCAGAUUCC_UCUAU___UAUACUCCUACUCC__AUUCACAUCUGAUACAUUUUUUA
.....................................(((.((((((...............)))))).)))................................................ ( -2.36 =  -3.36 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,660,231 – 5,660,333
Length 102
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 76.92
Mean single sequence MFE -24.36
Consensus MFE -13.50
Energy contribution -15.38
Covariance contribution 1.88
Combinations/Pair 1.07
Mean z-score -2.67
Structure conservation index 0.55
SVM decision value 2.05
SVM RNA-class probability 0.986719
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5660231 102 - 27905053
UUUCUUUGCAGAAAAAUCGAAAUUUGAAAUGAAUUAUUCUUAUUGUG--CUG----------CAGUAUUCUA---UAGGAGUCUGUACCUUAUUGAUUAUUCUACAGAUUCUUCUAU--
.....((((((...(((.(((((((.....))))..)))..)))...--)))----------))).......---.(((((((((((...((.....))...)))))))))))....-- ( -18.10)
>DroSec_CAF1 13867 95 - 1
UUUCUUUGCAGAAAAAUCGAA-------AUGAAUUAUUCUUAUUGUG--CUG----------CAGUAUUCUA---UAGGAUACUGGACAUUAUUGAUUAUUCUGCAGAUUUGUCUAU--
....(((((((((.(((((((-------((((.......)))))(((--.(.----------((((((((..---..)))))))).))))..)))))).))))))))).........-- ( -26.30)
>DroSim_CAF1 13863 104 - 1
UUUCUUUGCAGAAAAAUCGAAAUUUUAAAUGAAUUAUUCUUAUUGUG--CUG----------CAGUAUUCUA---UAGGAUACUGGACAUUAUUGAUUAUUCUGCAGAUUCGUCUAUUC
....(((((((((.(((((((((((.....))))).........(((--.(.----------((((((((..---..)))))))).))))..)))))).)))))))))........... ( -26.80)
>DroYak_CAF1 14206 116 - 1
UUUCUUUCCAGGCAAAGCGAAAUUUGGAAUUCAUUAUUCAUAUAGUGAGCCGCGAGUAAUAUCAUUAUUUUAAAAAAGGCUUCUGCAUAUUAUUGAUU-UUCUGCAGAAGCCUCUAU--
.....(((((((..........)))))))((((((((....))))))))....(((((((...)))))))......(((((((((((...........-...)))))))))))....-- ( -26.24)
>consensus
UUUCUUUGCAGAAAAAUCGAAAUUUGAAAUGAAUUAUUCUUAUUGUG__CUG__________CAGUAUUCUA___UAGGAUACUGGACAUUAUUGAUUAUUCUGCAGAUUCGUCUAU__
....(((((((((.((((((..............(((.......)))...............(((((((((.....))))))))).......)))))).)))))))))........... (-13.50 = -15.38 +   1.88)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:49 2006