Locus 4747

Sequence ID 3L_DroMel_CAF1
Location 13,348,604 – 13,348,783
Length 179
Max. P 0.976499
window7470 window7471 window7472 window7473

overview

Window 0

Location 13,348,604 – 13,348,724
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.18
Mean single sequence MFE -20.95
Consensus MFE -18.01
Energy contribution -18.40
Covariance contribution 0.39
Combinations/Pair 1.07
Mean z-score -1.57
Structure conservation index 0.86
SVM decision value 0.25
SVM RNA-class probability 0.654349
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13348604 120 + 23771897
UGCUGACAUGACAUGAACUGUAGUUUAUUUAUUAUUUCUCUGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGU
.....((((.(((.((...(((((......)))))...)))))(((.............)))..........................(((((((((((....))))))))))))))).. ( -21.02)
>DroSec_CAF1 20221 120 + 1
UGCUGACAUGACAUGAACUGUAGUUUAUUUAUUAUUUCUCUGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGU
.....((((.(((.((...(((((......)))))...)))))(((.............)))..........................(((((((((((....))))))))))))))).. ( -21.02)
>DroSim_CAF1 19995 120 + 1
UGCUGAAAUGACAUGAACUGUAGUUUAUUUAUUAUUUCUCUGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUAU
(((((((((((.((((((....))))))...............(((.............)))......))))))))............(((((((((((....)))))))))))..))). ( -24.52)
>DroEre_CAF1 20496 117 + 1
UGCUGACAUGACAUGAACUGUAGUUUAUUUAUUAUUUCUCUGUGCCUCAUUCUUCUUCUGGCUCCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGCA---
.(((((.((((.((((((....))))))...............(((.............)))......)))).)))............(((((((((((....))))))))))))).--- ( -22.52)
>DroYak_CAF1 21285 117 + 1
UGCUGACAUGACAUGAGCUGUAGUUUAUUUAUUAUUUCUCUGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUU---
...(((.((((((.(((..(((((......)))))..))))))(((.............))).......))).)))............(((((((((((....)))))))))))...--- ( -23.62)
>DroAna_CAF1 19271 111 + 1
UACUGACAUGACAUGAACUGUAGUUUAUUUAUUAUUUCUCUGUGCCUCGGUCUCCAUCUUGCUUCCCUCCAUUUUAUUUAUAUCCUUAACGCAUGCAAACAU--UUGUAUGUC-------
.(((((....(((.((...(((((......)))))...)))))...))))).......................................((((((((....--)))))))).------- ( -13.00)
>consensus
UGCUGACAUGACAUGAACUGUAGUUUAUUUAUUAUUUCUCUGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUG___
.((.((.((((.((((((....))))))...)))).))...))(((.............)))..........................(((((((((((....)))))))))))...... (-18.01 = -18.40 +   0.39)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,348,644 – 13,348,757
Length 113
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 82.54
Mean single sequence MFE -25.86
Consensus MFE -16.73
Energy contribution -16.98
Covariance contribution 0.25
Combinations/Pair 1.17
Mean z-score -2.19
Structure conservation index 0.65
SVM decision value 0.87
SVM RNA-class probability 0.870518
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13348644 113 + 23771897
UGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGUGUGCGUGUGCGAAUCGGGUCAUGCACUCACACA--
...(((.............)))..........................(((((((((((....)))))))))))(((((.((((((((.((...)).).))))))).))))).-- ( -35.92)
>DroSec_CAF1 20261 107 + 1
UGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGUG------GGCGAAUCGGGUCAUACACUCACACA--
...(((.............)))..........................(((((((((((....)))))))))))(((((((------(.(......).)))))))).......-- ( -27.22)
>DroSim_CAF1 20035 109 + 1
UGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUAUG------UGCGAAUCGGGUCAUACACUCACACACA
...(((.............)))..........................(((((((((((....)))))))))))(((((((------(.((...)).).)))))))......... ( -24.92)
>DroAna_CAF1 19311 99 + 1
UGUGCCUCGGUCUCCAUCUUGCUUCCCUCCAUUUUAUUUAUAUCCUUAACGCAUGCAAACAU--UUGUAUGUC--------------UGCGAAUCAGGUCAUACAUAUAUGUAUG
...((((.((..................))...................((((.(((.((..--..)).))).--------------))))....))))((((((....)))))) ( -15.37)
>consensus
UGUGCCUCAUUCUUCUUCUGGCUUCUUUUCAUUUUAUUUAUAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGUG______UGCGAAUCGGGUCAUACACUCACACA__
(((((((.((((..........................((......))(((((((((((....)))))))))))................)))).))).))))............ (-16.73 = -16.98 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,348,684 – 13,348,783
Length 99
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 77.48
Mean single sequence MFE -29.92
Consensus MFE -13.79
Energy contribution -14.23
Covariance contribution 0.44
Combinations/Pair 1.15
Mean z-score -3.27
Structure conservation index 0.46
SVM decision value 1.77
SVM RNA-class probability 0.976499
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13348684 99 + 23771897
UAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGUGUGCGUGUGCGAAUCGGGUCAUGCACUCACACA--CACUCAUUUGUAU---GUCCUGUACUUUA
........(((((((((((....)))))))))))(((((((((.((((..((......))..)))).))))))--)))......((((---.....)))).... ( -36.10)
>DroSec_CAF1 20301 93 + 1
UAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGUG------GGCGAAUCGGGUCAUACACUCACACA--CACACAUUUGUAU---GUCCUGUAGUUUA
..........(((((((((((....)))(((((((((((((------((.(.((......)).).))))))))--)))))))))))))---))........... ( -31.50)
>DroSim_CAF1 20075 95 + 1
UAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUAUG------UGCGAAUCGGGUCAUACACUCACACACACACACAUUUGUAU---GUCCUGUAGUUUA
..........(((((((((..(((.(((.((((.(((((((------(.((...)).).))))))).)))).))).)))..)))))))---))........... ( -30.00)
>DroAna_CAF1 19351 88 + 1
UAUCCUUAACGCAUGCAAACAU--UUGUAUGUC--------------UGCGAAUCAGGUCAUACAUAUAUGUAUGGCGCUGUUAGUACGUCGUCUUGUAGUUUA
.........((((.(((.((..--..)).))).--------------))))...(((((((((((....)))))))).)))....((((......))))..... ( -22.10)
>consensus
UAUCCUUGACGCAUGCAAACAUGUUUGUAUGUGUGUGUGUG______UGCGAAUCGGGUCAUACACUCACACA__CACACAUUUGUAU___GUCCUGUAGUUUA
........(((((((((((....)))))))))))....................((((.(((((....................))))...).))))....... (-13.79 = -14.23 +   0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,348,684 – 13,348,783
Length 99
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 77.48
Mean single sequence MFE -28.57
Consensus MFE -10.81
Energy contribution -12.62
Covariance contribution 1.81
Combinations/Pair 1.22
Mean z-score -3.69
Structure conservation index 0.38
SVM decision value 1.07
SVM RNA-class probability 0.910795
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13348684 99 - 23771897
UAAAGUACAGGAC---AUACAAAUGAGUG--UGUGUGAGUGCAUGACCCGAUUCGCACACGCACACACACACACAUACAAACAUGUUUGCAUGCGUCAAGGAUA
..........(((---..........(((--((((((.((((.((............)).)))).))))))))).......((((....)))).)))....... ( -28.30)
>DroSec_CAF1 20301 93 - 1
UAAACUACAGGAC---AUACAAAUGUGUG--UGUGUGAGUGUAUGACCCGAUUCGCC------CACACACACACAUACAAACAUGUUUGCAUGCGUCAAGGAUA
..........(((---.......((((((--((((((.(((..(((......)))..------))).))))))))))))..((((....)))).)))....... ( -30.70)
>DroSim_CAF1 20075 95 - 1
UAAACUACAGGAC---AUACAAAUGUGUGUGUGUGUGAGUGUAUGACCCGAUUCGCA------CAUACACACACAUACAAACAUGUUUGCAUGCGUCAAGGAUA
..........(((---.......((((((((((((((.((((..((......)))))------).))))))))))))))..((((....)))).)))....... ( -31.60)
>DroAna_CAF1 19351 88 - 1
UAAACUACAAGACGACGUACUAACAGCGCCAUACAUAUAUGUAUGACCUGAUUCGCA--------------GACAUACAA--AUGUUUGCAUGCGUUAAGGAUA
.............((((((....(((.(.((((((....)))))).))))....(((--------------(((((....--)))))))).))))))....... ( -23.70)
>consensus
UAAACUACAGGAC___AUACAAAUGUGUG__UGUGUGAGUGUAUGACCCGAUUCGCA______CACACACACACAUACAAACAUGUUUGCAUGCGUCAAGGAUA
..........(((...((.(((((((((...((((((.(((..........................))).))))))...))))))))).))..)))....... (-10.81 = -12.62 +   1.81)

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 11:32:10 2006