Locus 3344

Sequence ID 3L_DroMel_CAF1
Location 9,815,746 – 9,815,941
Length 195
Max. P 0.998829
window5207 window5208 window5209

overview

Window 7

Location 9,815,746 – 9,815,861
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.70
Mean single sequence MFE -22.68
Consensus MFE -20.22
Energy contribution -20.46
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.50
Structure conservation index 0.89
SVM decision value 1.16
SVM RNA-class probability 0.924006
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9815746 115 + 23771897
UUGCCUUACUACC----UUCA-AAUGGCAAUAACAAUAGCGUACGCAAAGCGGAGCUCCGCCAGUUCAUCUGCAUAAUAAUGCUAAUUAUUUUUAAUUGCCGCAACUUGUCAUUUGCCAC
.............----....-..((((((..((((..(((...((((.((((....))))..........((((....)))).............)))))))...))))...)))))). ( -25.60)
>DroSec_CAF1 109874 115 + 1
UUAUCUUACUACC----UCCA-AAUAGCAAUAACAAUAGCGUACGCAAAGCGGAGCUCCGCCAGUUCAUCUGCAUAAUAAUGCUAAUUAUUUUUAAUUGCCGCAACUUGUCAUUUGCCAC
.............----....-....((((..((((..(((...((((.((((....))))..........((((....)))).............)))))))...))))...))))... ( -20.90)
>DroSim_CAF1 113208 116 + 1
UUGUCUUACUACC----UCCANAAUAGCAAUAACAAUAGCGUACGCAAAGCGGAGCUUCGCCAGUUCAUUUGCAUAAUAAUGCUAAUUAUUUUUAAUUGCCGCAACUUGUCAUUUGCCAC
.............----.........((((..((((..(((...(((((...(((((.....))))).)))))........((.(((((....))))))))))...))))...))))... ( -21.10)
>DroEre_CAF1 112711 115 + 1
UUGUCUUACCACC----UCCA-AAUGGCAAUAACAAUAGCGUACGCAAAGCGGAGCUUCGCCAGUUCAUCUGCAUAAUAAUACUAAUUAUUUUUAAUUGCCGCAACUUGUCAUUUGCCAC
.............----....-..((((((..((((..(((...((((.(((((....(....)....)))))..((((((....)))))).....)))))))...))))...)))))). ( -22.90)
>DroYak_CAF1 122788 119 + 1
UUGUCUUACUACCGCCCUCAA-AAUGGCAAUAACAAUAGCGUACGCAAAGCGGAGCUUCGCCAGUUCAUCUGCAUAAUAAUACUAAUUAUUUUUAAUUGCCGCAACUUGUCAUUUGCCAC
.....................-..((((((..((((..(((...((((.(((((....(....)....)))))..((((((....)))))).....)))))))...))))...)))))). ( -22.90)
>consensus
UUGUCUUACUACC____UCCA_AAUGGCAAUAACAAUAGCGUACGCAAAGCGGAGCUUCGCCAGUUCAUCUGCAUAAUAAUGCUAAUUAUUUUUAAUUGCCGCAACUUGUCAUUUGCCAC
........................((((((..((((..(((...((((.(((((....(....)....)))))..((((((....)))))).....)))))))...))))...)))))). (-20.22 = -20.46 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,815,746 – 9,815,861
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.70
Mean single sequence MFE -31.48
Consensus MFE -30.84
Energy contribution -30.12
Covariance contribution -0.72
Combinations/Pair 1.10
Mean z-score -1.85
Structure conservation index 0.98
SVM decision value 3.24
SVM RNA-class probability 0.998829
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9815746 115 - 23771897
GUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCAUUAUUAUGCAGAUGAACUGGCGGAGCUCCGCUUUGCGUACGCUAUUGUUAUUGCCAUU-UGAA----GGUAGUAAGGCAA
(((((((.((((((...((((((((((....))))).)).....(((((((.......(((((....)))))))))))))))..))))))))))))).-....----............. ( -34.21)
>DroSec_CAF1 109874 115 - 1
GUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCAUUAUUAUGCAGAUGAACUGGCGGAGCUCCGCUUUGCGUACGCUAUUGUUAUUGCUAUU-UGGA----GGUAGUAAGAUAA
(((((((.((((((...((((((((((....))))).)).....(((((((.......(((((....)))))))))))))))..))))))))))))).-....----............. ( -31.91)
>DroSim_CAF1 113208 116 - 1
GUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCAUUAUUAUGCAAAUGAACUGGCGAAGCUCCGCUUUGCGUACGCUAUUGUUAUUGCUAUUNUGGA----GGUAGUAAGACAA
(((((((.((((((...(((((...............((((....))))..........(((((((...))))))))).)))..)))))))))))))......----............. ( -29.70)
>DroEre_CAF1 112711 115 - 1
GUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGUAUUAUUAUGCAGAUGAACUGGCGAAGCUCCGCUUUGCGUACGCUAUUGUUAUUGCCAUU-UGGA----GGUGGUAAGACAA
(((((((.((((((...(((((.............((((.(((((.....)))))))))(((((((...))))))))).)))..))))))))))))).-....----............. ( -30.80)
>DroYak_CAF1 122788 119 - 1
GUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGUAUUAUUAUGCAGAUGAACUGGCGAAGCUCCGCUUUGCGUACGCUAUUGUUAUUGCCAUU-UUGAGGGCGGUAGUAAGACAA
(((((((.((((((...(((((.............((((.(((((.....)))))))))(((((((...))))))))).)))..))))))))))))).-..................... ( -30.80)
>consensus
GUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCAUUAUUAUGCAGAUGAACUGGCGAAGCUCCGCUUUGCGUACGCUAUUGUUAUUGCCAUU_UGGA____GGUAGUAAGACAA
(((((((.((((((...(((((...............((((....))))..........(((((((...))))))))).)))..)))))))))))))....................... (-30.84 = -30.12 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,815,821 – 9,815,941
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.61
Mean single sequence MFE -29.67
Consensus MFE -25.14
Energy contribution -25.58
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.85
SVM decision value 1.19
SVM RNA-class probability 0.928082
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9815821 120 - 23771897
GCCCAUCCUCGGCGACAGUGAAAACCGAACCUCCAGUCAGUUGCCCGCGAAACUUUCACUAAUCACUCACAGAGUUUUGUGUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCA
((((......)(((((.((....))..........((((.((((((((((((((((..............))))))))))).))))).))))..)))))))).................. ( -34.34)
>DroSec_CAF1 109949 119 - 1
GCCAAUCCUAGGCGACAGUGAAAACCGAACCUC-AGUCAGUUGCCCGCGAAACUUUCACUAAUCACUCACAGAGUUUUGUGUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCA
...........(((((.((....))........-.((((.((((((((((((((((..............))))))))))).))))).))))..))))).(((((((....))))).)). ( -34.04)
>DroSim_CAF1 113284 119 - 1
GCCAAUCCUCGGCGACAGUGAAAACCGAACCUC-AAUCAGUUGCCCGCGAAACUUUCACUAAUCACUCACAGAGUUUUGUGUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCA
...........(((((.((....))........-..(((.((((((((((((((((..............))))))))))).))))).)))...))))).(((((((....))))).)). ( -30.24)
>DroEre_CAF1 112786 115 - 1
GCUUAUCCUCUCCGACUGUGAAAACCGAACCU-----CAGUUGCCCGAGAAACUUUCACUAAUCACUCACAGAGUUUUGUGUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGUA
........((((((((((.(..........).-----))))))...)))).......((((((.((((...))))....(((.((((........)))).)))..........)))))). ( -20.00)
>DroYak_CAF1 122867 115 - 1
GCCCAUCGUCUGCGACAGUGGAAACCGUAGCU-----CAGUUGCCCGAGAAACUUUCACUAAUCACUCACAGAGUUUUGUGUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGUA
..((((.(((...))).))))...((((((((-----((.(((((((.((((((((..............)))))))).)).))))).)))...)))))))................... ( -29.74)
>consensus
GCCAAUCCUCGGCGACAGUGAAAACCGAACCUC_A_UCAGUUGCCCGCGAAACUUUCACUAAUCACUCACAGAGUUUUGUGUGGCAAAUGACAAGUUGCGGCAAUUAAAAAUAAUUAGCA
(((........(((((.((....))............((.((((((((((((((((..............))))))))))).))))).))....)))))))).................. (-25.14 = -25.58 +   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 10:55:31 2006