Locus 218

Sequence ID 2R_DroMel_CAF1
Location 1,554,415 – 1,554,614
Length 199
Max. P 0.978015
window486 window487 window488 window489 window490

overview

Window 6

Location 1,554,415 – 1,554,534
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.69
Mean single sequence MFE -38.08
Consensus MFE -28.64
Energy contribution -29.52
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.75
SVM decision value 0.87
SVM RNA-class probability 0.871230
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1554415 119 + 20766785
UUGUGCUCAAUUGUGCCAUGAAGGCCCAUAAGGUUUCAC-UGCCCAUGGGCUUGUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAAACAUUUGACCAGGUUGCAUCUGGUCAA
..........(((.((((.((((((((((..(((.....-.))).))))))))((((.(((..(((((((((...((((.....))))...)))))))))..))).)))).))))))))) ( -40.00)
>DroSec_CAF1 4238 119 + 1
UUGUGCUCAAUUGUGCAUUGAAGGCCCAUAAGGUUCCAC-UGCCCAUGGGCUUGUUAGCUGUGCAAAUGUUUUUUUCUGCGAUUCAGGUCAAAACACUUGACCAGGUCGCAUCUGGUCAA
..........(((..((((((((((((((..(((.....-.))).)))))))).)))).))..))).((((((..((((.....))))..))))))..(((((((((...))))))))). ( -39.80)
>DroSim_CAF1 4724 118 + 1
UUGUGCUCAAUUGUGCAUUGAAGGCCCACAAGGUUCCAC-UGCCCAUGGGCUUGUUAGCUGUGCAAAUGUUUUUUUCUGCGAUUCAGGUCA-AACACUUGACCAGGUCGCAUCUGGUCAA
...((..((.(((..(((((((((((((...(((.....-.)))..))))))).)))).))..)))...........(((((((..(((((-(....)))))).)))))))..))..)). ( -37.50)
>DroEre_CAF1 4657 118 + 1
CUGGGCUCAAUUGUGCAUUGGCGGCC-UAAAGGUUCCAC-UGCCCCUGGGCUCGUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAGCCAUUUGACCAGGUUGCAUCUGGUCAA
...((((((.(((..((...((((((-((..(((.....-.)))..))))).)))....))..))).))......((((.....))))...))))..((((((((((...)))))))))) ( -39.90)
>DroYak_CAF1 10224 120 + 1
UUGGGCUCACUUGCGCAUUAAAGGCCUUAAAGGUUUCAUUUGGCAAUGGGCUUCUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAGACAUUUGACCAGGUUGCAUCUGAUCAA
..(((((((.((((.((....(((((.....)))))....))))))))))))).(((.(((..(((((((((...((((.....))))...)))))))))..))).)))........... ( -33.20)
>consensus
UUGUGCUCAAUUGUGCAUUGAAGGCCCAAAAGGUUCCAC_UGCCCAUGGGCUUGUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAAACAUUUGACCAGGUUGCAUCUGGUCAA
.......((.(((((((....(((((((...(((.......)))..)))))))......))))))).))........(((((((..((((((.....)))))).)))))))......... (-28.64 = -29.52 +   0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,554,415 – 1,554,534
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.69
Mean single sequence MFE -34.34
Consensus MFE -24.22
Energy contribution -24.26
Covariance contribution 0.04
Combinations/Pair 1.17
Mean z-score -2.05
Structure conservation index 0.71
SVM decision value 0.31
SVM RNA-class probability 0.681522
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1554415 119 - 20766785
UUGACCAGAUGCAACCUGGUCAAAUGUUUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUACAAGCCCAUGGGCA-GUGAAACCUUAUGGGCCUUCAUGGCACAAUUGAGCACAA
..((((((.......))))))((((((((....(((.....)))....)))))))).....(((((...(((....))).-((....((....))(((.....)))))...))))).... ( -34.00)
>DroSec_CAF1 4238 119 - 1
UUGACCAGAUGCGACCUGGUCAAGUGUUUUGACCUGAAUCGCAGAAAAAAACAUUUGCACAGCUAACAAGCCCAUGGGCA-GUGGAACCUUAUGGGCCUUCAAUGCACAAUUGAGCACAA
((((((((.......))))))))(((((((...(((.....)))...))))))).(((...........(((((((((..-......)).)))))))..(((((.....))))))))... ( -35.70)
>DroSim_CAF1 4724 118 - 1
UUGACCAGAUGCGACCUGGUCAAGUGUU-UGACCUGAAUCGCAGAAAAAAACAUUUGCACAGCUAACAAGCCCAUGGGCA-GUGGAACCUUGUGGGCCUUCAAUGCACAAUUGAGCACAA
((((((((.......))))))))(((((-..(..((....(((((........)))))...((......(((((..((..-.......))..))))).......)).)).)..))))).. ( -36.92)
>DroEre_CAF1 4657 118 - 1
UUGACCAGAUGCAACCUGGUCAAAUGGCUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUACGAGCCCAGGGGCA-GUGGAACCUUUA-GGCCGCCAAUGCACAAUUGAGCCCAG
((((((((.......))))))))..((((..(((((....(((((........)))))...(((....))).)))).(((-.(((..((....-))...))).)))....)..))))... ( -39.90)
>DroYak_CAF1 10224 120 - 1
UUGAUCAGAUGCAACCUGGUCAAAUGUCUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUAGAAGCCCAUUGCCAAAUGAAACCUUUAAGGCCUUUAAUGCGCAAGUGAGCCCAA
((((((((.......))))))))..........(((.....))).......(((((((.((..(((((.(((((((....))))..........))).))))))).)))))))....... ( -25.20)
>consensus
UUGACCAGAUGCAACCUGGUCAAAUGUUUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUACAAGCCCAUGGGCA_GUGGAACCUUAUGGGCCUUCAAUGCACAAUUGAGCACAA
((((((((.......)))))))).(((.............(((((........)))))...(((((...(((....)))...((((.((.....))..)))).........)))))))). (-24.22 = -24.26 +   0.04)

alignment

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secondary structure

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Window 8

Location 1,554,454 – 1,554,574
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.83
Mean single sequence MFE -34.16
Consensus MFE -25.42
Energy contribution -25.70
Covariance contribution 0.28
Combinations/Pair 1.14
Mean z-score -1.55
Structure conservation index 0.74
SVM decision value -0.05
SVM RNA-class probability 0.509550
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1554454 120 + 20766785
UGCCCAUGGGCUUGUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAAACAUUUGACCAGGUUGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGGGCACCUAUAAAUUAACGAUC
(((((.(..(((((....((((..((((((((...((((.....))))...))))))))((((((((...))))))))..))))....)))))..)..)))))................. ( -36.70)
>DroSec_CAF1 4277 120 + 1
UGCCCAUGGGCUUGUUAGCUGUGCAAAUGUUUUUUUCUGCGAUUCAGGUCAAAACACUUGACCAGGUCGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGAGCACAUAUAAAUUAGCGAUC
.(((....)))(((((((.(((((...((((((.((((((((((..((((((.....)))))).)))))))...((((.....))))..))).)))))).)))))......))))))).. ( -35.60)
>DroSim_CAF1 4763 119 + 1
UGCCCAUGGGCUUGUUAGCUGUGCAAAUGUUUUUUUCUGCGAUUCAGGUCA-AACACUUGACCAGGUCGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGAGCACCUAUAAAUUAGCGAUC
.(((....)))(((((((..((((...((((((.((((((((((..(((((-(....)))))).)))))))...((((.....))))..))).)))))).)))).......))))))).. ( -34.00)
>DroEre_CAF1 4695 119 + 1
UGCCCCUGGGCUCGUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAGCCAUUUGACCAGGUUGCAUCUGGUCAAAUAGAACUC-GGCAACCCGAGCGCCUAUAAAGUAGCGAUC
.(((....)))((((..((...)).....(((((....(((.(((.(((...(((((((((((((((...)))))))))))).(....)-))).))).))))))..)))))...)))).. ( -35.90)
>DroYak_CAF1 10264 120 + 1
UGGCAAUGGGCUUCUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAGACAUUUGACCAGGUUGCAUCUGAUCAAAUAGAACUAAAGCAACCCGAGCUCCUAUAAAUUUGCGAUC
..((((.((((((......((..(((((((((...((((.....))))...)))))))))..))((((((....(.((.....)).)....)))))).)))).)).......)))).... ( -28.60)
>consensus
UGCCCAUGGGCUUGUAAGCUGUGCAAAUGUUUAUUUCUGCGAUUCAGGUCAAAACAUUUGACCAGGUUGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGAGCACCUAUAAAUUAGCGAUC
.......((((((((..(((.................(((((((..((((((.....)))))).)))))))((((......)))).....)))...)))))).))............... (-25.42 = -25.70 +   0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,554,454 – 1,554,574
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -34.97
Consensus MFE -27.60
Energy contribution -28.04
Covariance contribution 0.44
Combinations/Pair 1.18
Mean z-score -1.91
Structure conservation index 0.79
SVM decision value 0.95
SVM RNA-class probability 0.887835
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1554454 120 - 20766785
GAUCGUUAAUUUAUAGGUGCCCGCUUUGCUCGAGAUCUAUUUGACCAGAUGCAACCUGGUCAAAUGUUUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUACAAGCCCAUGGGCA
.................(((((((((.(((((((((..((((((((((.......)))))))))))))))))........(((((........)))))...))....))))....))))) ( -33.00)
>DroSec_CAF1 4277 120 - 1
GAUCGCUAAUUUAUAUGUGCUCGCUUUGCUCGAGAUCUAUUUGACCAGAUGCGACCUGGUCAAGUGUUUUGACCUGAAUCGCAGAAAAAAACAUUUGCACAGCUAACAAGCCCAUGGGCA
((.(((..........))).))(((.((((((((((..((((((((((.......))))))))))))))))).(((.....)))............))).)))......(((....))). ( -34.40)
>DroSim_CAF1 4763 119 - 1
GAUCGCUAAUUUAUAGGUGCUCGCUUUGCUCGAGAUCUAUUUGACCAGAUGCGACCUGGUCAAGUGUU-UGACCUGAAUCGCAGAAAAAAACAUUUGCACAGCUAACAAGCCCAUGGGCA
....(((......(((((.((((.......))))...(((((((((((.......)))))))))))..-..)))))....(((((........)))))..)))......(((....))). ( -34.80)
>DroEre_CAF1 4695 119 - 1
GAUCGCUACUUUAUAGGCGCUCGGGUUGCC-GAGUUCUAUUUGACCAGAUGCAACCUGGUCAAAUGGCUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUACGAGCCCAGGGGCA
....(((......(((((((((((....))-))))..(((((((((((.......)))))))))))))))).((((....(((((........)))))...(((....))).))))))). ( -42.40)
>DroYak_CAF1 10264 120 - 1
GAUCGCAAAUUUAUAGGAGCUCGGGUUGCUUUAGUUCUAUUUGAUCAGAUGCAACCUGGUCAAAUGUCUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUAGAAGCCCAUUGCCA
....((((........(((((((((((.....((...(((((((((((.......))))))))))).)).)))))))...(((((........)))))...)))).........)))).. ( -30.23)
>consensus
GAUCGCUAAUUUAUAGGUGCUCGCUUUGCUCGAGAUCUAUUUGACCAGAUGCAACCUGGUCAAAUGUUUUGACCUGAAUCGCAGAAAUAAACAUUUGCACAGCUUACAAGCCCAUGGGCA
....(((......((((.((.......))((((((..(((((((((((.......)))))))))))))))))))))....(((((........)))))..)))......(((....))). (-27.60 = -28.04 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,554,494 – 1,554,614
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.17
Mean single sequence MFE -33.98
Consensus MFE -25.64
Energy contribution -26.08
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -2.77
Structure conservation index 0.75
SVM decision value 1.80
SVM RNA-class probability 0.978015
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1554494 120 + 20766785
GAUUCAGGUCAAAACAUUUGACCAGGUUGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGGGCACCUAUAAAUUAACGAUCAAUCCGAAAGCUUGCGAACUUUAACUCGCAACCAUGGAUA
.(((((((((((.....)))))).((((((.((((......))))((.(((((....((((.....................))))...))))).))..........)))))).))))). ( -32.30)
>DroSec_CAF1 4317 120 + 1
GAUUCAGGUCAAAACACUUGACCAGGUCGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGAGCACAUAUAAAUUAGCGAUCAAUGCGACCACUUGCGAACUUUAACUUGCAAUUAUGGAUA
.(((((((((((.....)))))).((((((((.(((((.........(((.......)))((............)))))))))))))))..((((((........))))))...))))). ( -35.50)
>DroSim_CAF1 4803 119 + 1
GAUUCAGGUCA-AACACUUGACCAGGUCGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGAGCACCUAUAAAUUAGCGAUCAAUGCGACCACUUGCGAACUUUAACUCGCAAUCAUGGAUA
.((((((((((-(....)))))).((((((((.(((((........((((.......))))...(((.....))).)))))))))))))..((((((........))))))...))))). ( -39.30)
>DroEre_CAF1 4735 119 + 1
GAUUCAGGUCAAGCCAUUUGACCAGGUUGCAUCUGGUCAAAUAGAACUC-GGCAACCCGAGCGCCUAUAAAGUAGCGAUCAUUGCGACAGCUUGCGAACUUUAACUCGCAACCAUGGAUA
.((((((((.((((.((((((((((((...)))))))))))).(..(((-((....)))))..).......((.((((...)))).)).))))((((........)))).))).))))). ( -37.00)
>DroYak_CAF1 10304 120 + 1
GAUUCAGGUCAAGACAUUUGACCAGGUUGCAUCUGAUCAAAUAGAACUAAAGCAACCCGAGCUCCUAUAAAUUUGCGAUCAAUCCGACAGCUUGCGAACUUUAAUUUGCAACUAUGAAUA
.((((((((((((...))))))).(((((((((((......)))).....(((.......)))..........)))))))........((.(((((((......))))))))).))))). ( -25.80)
>consensus
GAUUCAGGUCAAAACAUUUGACCAGGUUGCAUCUGGUCAAAUAGAUCUCGAGCAAAGCGAGCACCUAUAAAUUAGCGAUCAAUGCGACAGCUUGCGAACUUUAACUCGCAACCAUGGAUA
.(((((((((.......((((((((((...))))))))))((((..((((.......))))...))))........))))...........((((((........))))))...))))). (-25.64 = -26.08 +   0.44)

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 09:32:46 2006