Locus 147

Sequence ID 3L_DroMel_CAF1
Location 458,953 – 459,143
Length 190
Max. P 0.993992
window208 window209 window210

overview

Window 8

Location 458,953 – 459,044
Length 91
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 82.44
Mean single sequence MFE -25.58
Consensus MFE -12.84
Energy contribution -13.15
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.78
Structure conservation index 0.50
SVM decision value 0.22
SVM RNA-class probability 0.638490
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 458953 91 + 23771897
AUCUGCCCACAGAUGCGAGUACAACAUGCAACAUUCGAGGACGGUAUGGGAUGGGAUGGC---CACCGAACCAUCUUAGACC-----AUCCCAUUCCAA------
.((((....))))((((.(.....).))))............((.((((((((((((((.---.......))))).....))-----))))))).))..------ ( -28.50)
>DroSec_CAF1 39977 81 + 1
AUCUGCCCACAGAUGCGAGUACAACAUGCAACAUUCGAGG----------AUGGGAUGGC---CACCGAACCAUACUAUACC-----AUCCCAUUCGAA------
.((((....))))((((.(.....).))))........((----------(((((((((.---.................))-----)))))))))...------ ( -22.57)
>DroSim_CAF1 40876 81 + 1
AUCUGCCCACAGAUGCGAGUACAACAUGCAACAUUCGAGG----------AUGGGAUGGC---CACCGAACCAUACUAGACC-----AUCCCAUUCGAA------
.((((....))))((((.(.....).))))........((----------(((((((((.---(..............).))-----)))))))))...------ ( -22.84)
>DroYak_CAF1 41379 95 + 1
AUCUGCCCACAGAUGCGAGUACAACAUGCAACAUCUGAGG----------AUGGGAUGGUGGCCAUCGAACCAUCCUAGACCAUCCCAUCCCAUUCCAAAUCCAA
.........((((((...(((.....)))..)))))).((----------((((((((((((........)).......)))))))))))).............. ( -28.41)
>consensus
AUCUGCCCACAGAUGCGAGUACAACAUGCAACAUUCGAGG__________AUGGGAUGGC___CACCGAACCAUACUAGACC_____AUCCCAUUCCAA______
.((((....))))((((.(.....).))))......(.((...........((((((((...........))))))))...........)))............. (-12.84 = -13.15 +   0.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 459,015 – 459,105
Length 90
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 81.83
Mean single sequence MFE -24.24
Consensus MFE -22.40
Energy contribution -22.24
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.53
Structure conservation index 0.92
SVM decision value 2.44
SVM RNA-class probability 0.993992
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 459015 90 + 23771897
CCGAACCAUCUUAGACC-----AUCCCAUUCCAA------------AUCCAAUCGCAGCAAUCCCAUUCCAUGACGUUGUCAUUUGGGAUUGCGUGACGAUGGCGCA
..(..(((((...(...-----..).........------------......((((.(((((((((....(((((...))))).))))))))))))).)))))..). ( -27.30)
>DroSec_CAF1 40029 90 + 1
CCGAACCAUACUAUACC-----AUCCCAUUCGAA------------AUCCAAUCGCAGCAAUUCCAUUCCAUGACGUUGUCAUUUGGGAUUGCGUGACGAUGGCGCA
...............((-----(((......(..------------...)..((((.(((((((((....(((((...))))).))))))))))))).))))).... ( -23.20)
>DroSim_CAF1 40928 90 + 1
CCGAACCAUACUAGACC-----AUCCCAUUCGAA------------AUCCAAUCGCAGCAAUUCCAUUCCAUGACGUUGUCAUUUGGGAUUGCGUGACGAUGGCGCA
.............(.((-----(((......(..------------...)..((((.(((((((((....(((((...))))).))))))))))))).))))))... ( -23.80)
>DroEre_CAF1 41964 75 + 1
--------------------CCAUCCCAUUCCCA------------AUCCAAUCGCAGCAAUUCCAACCCAUGACGUUGUCAUUUGGGAUUGCGUGACGAUGGCGCA
--------------------..............------------..(((.(((((((((((((((...(((((...))))))))))))))).)).)))))).... ( -22.50)
>DroYak_CAF1 41434 107 + 1
UCGAACCAUCCUAGACCAUCCCAUCCCAUUCCAAAUCCAACUACAAAUCCAAUCGCAGCAAUUCCAUCCCAUGACGUUGUCAUUUGGGAUUGCGUGACGAUGGCGCA
..(..(((((...((........))...........................((((.(((((((((....(((((...))))).))))))))))))).)))))..). ( -24.40)
>consensus
CCGAACCAUACUAGACC_____AUCCCAUUCCAA____________AUCCAAUCGCAGCAAUUCCAUUCCAUGACGUUGUCAUUUGGGAUUGCGUGACGAUGGCGCA
................................................(((.((((((((((((((....(((((...))))).))))))))).)).)))))).... (-22.40 = -22.24 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 459,044 – 459,143
Length 99
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.42
Mean single sequence MFE -31.80
Consensus MFE -14.14
Energy contribution -15.81
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.44
SVM decision value 0.02
SVM RNA-class probability 0.542748
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 459044 99 + 23771897
------AUCCAAUCGCAGCAAUCCCAUUCCAUGACGUUGUCAUUUG---GGAUUGCGUGACGAUGGCGCAUUUCUCU--CAAGGAAUCAAAUUGAAUCUUCGUUUUGGGU
------((((((((((.(((((((((....(((((...))))).))---)))))))))))((((...(.((((((..--..)))))))..))))..........)))))) ( -29.90)
>DroPse_CAF1 101536 89 + 1
------UACCAAU---ACCAAUUCCAUUCCAUGACGUUGUCAUUUGUGGGGAUUGCGUGACGAUUGCGCAUUUCUCGAGCUCGGAAU------G------GGUAUUGGGU
------..(((((---(((.(((((.....(((((...)))))...((((((.((((..(...)..)))).)))))).....)))))------.------)))))))).. ( -34.70)
>DroSim_CAF1 40957 99 + 1
------AUCCAAUCGCAGCAAUUCCAUUCCAUGACGUUGUCAUUUG---GGAUUGCGUGACGAUGGCGCAUUUCUCG--CAAGGAAUCAAAUUGAAUCUUCGUUUUGGGU
------((((((((((.(((((((((....(((((...))))).))---)))))))))))(((.((..((.(((.(.--...))))......))..)).)))..)))))) ( -29.00)
>DroEre_CAF1 41978 99 + 1
------AUCCAAUCGCAGCAAUUCCAACCCAUGACGUUGUCAUUUG---GGAUUGCGUGACGAUGGCGCAUUUCUCG--CAAGGAAUCAAAUUGAAUCUUCGUUUUGGGU
------((((((((((.((((((((((...(((((...))))))))---)))))))))))(((.((..((.(((.(.--...))))......))..)).)))..)))))) ( -29.70)
>DroYak_CAF1 41474 105 + 1
CUACAAAUCCAAUCGCAGCAAUUCCAUCCCAUGACGUUGUCAUUUG---GGAUUGCGUGACGAUGGCGCAUUUCUCG--CCAGGAAUCAAAUUGAAUCUUCGUUUCGGGU
......((((.......(((((((((....(((((...))))).))---)))))))(.((((((((((.......))--)))(((.((.....)).)))))))).))))) ( -31.70)
>DroPer_CAF1 98746 89 + 1
------UACCAAU---ACCAAUUCCAUUCCAUGACGUUGUCAUUUGUGGGGAUUGCGUGACGAUUGCGCAUUUCUCGGUCUCGGAAU------G------GGUAUUGGGU
------..(((((---(((.(((((...(((((((...)))))....(((((.((((..(...)..)))).)))))))....)))))------.------)))))))).. ( -35.80)
>consensus
______AUCCAAUCGCAGCAAUUCCAUUCCAUGACGUUGUCAUUUG___GGAUUGCGUGACGAUGGCGCAUUUCUCG__CAAGGAAUCAAAUUGAAUCUUCGUUUUGGGU
........((((......((((...((((((((((...)))))......(((.(((((.......))))).)))........)))))...))))..........)))).. (-14.14 = -15.81 +   1.67)

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 09:33:49 2006