Locus 4964

Sequence ID X_DroMel_CAF1
Location 12,957,970 – 12,958,123
Length 153
Max. P 0.997907
window8094 window8095 window8096

overview

Window 4

Location 12,957,970 – 12,958,090
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.00
Mean single sequence MFE -31.00
Consensus MFE -25.36
Energy contribution -25.56
Covariance contribution 0.20
Combinations/Pair 1.16
Mean z-score -3.03
Structure conservation index 0.82
SVM decision value 2.96
SVM RNA-class probability 0.997907
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12957970 120 + 22224390
AAUAUUUUACAUAUGCUUCGGAUGCACGUGUCCAACGCCACACGUGUCCUAAUUCUGUUAAUAAUACGUUGGCCAUUUUAAAUGGUCAACAUAUGCUACAAUUCAAGCAACCGCAACCGG
.............(((((.((((((((((((........))))))))........(((.....(((.(((((((((.....))))))))).)))...)))))))))))).(((....))) ( -32.00)
>DroSec_CAF1 3376 120 + 1
AAUAUUUUACAUAUGCUUCGGAUGCACGUGUCCAACGACACACGUGUCCUAAUUCUGCUAAUAAUACGUUGGCCAACUAAAUUGGUCAACAUAUGCUACAAUUCAAGCAACCAGGCCCGG
..................(((..((((((((........)))))))).........(((........(((((((((.....)))))))))...((((........))))....)))))). ( -31.20)
>DroSim_CAF1 2408 120 + 1
AAUAUUUUACAUAUGCUUCGGAUGCACGUGUCCAACGACACACGUGUCCUAAUUCUGCUAAUAAUACGUUGGCCAACUAAAAUGGUCAACAUAUGCUACAAUUCAAGCAACCAGACCCGG
..................(((..((((((((........))))))))......((((..........((((((((.......))))))))...((((........))))..)))).))). ( -30.90)
>DroEre_CAF1 3525 119 + 1
GAUAUUUUACAUAUGCCUUGGAUACACGUAUCCAACGCCACACGUGCCCCAAUUCUGAUAAUAAUACGUUGGCUACUC-GAAUGGUCAGCAUAUGCUACAAUUCAAGCAACCAGAGCCGG
..............((.(((((((....))))))).))....((.((......((((..........((((((((...-...))))))))...((((........))))..)))))))). ( -27.80)
>DroYak_CAF1 3504 112 + 1
AAUAAUUUACAUAUGCUGAGGAUACACGUGUCCCACGACACACGUGUCCCAAUUCUGUUAAUAAUACGUUGGCCAAGCUAAAUGGCCAACAUAUGCUACAAUUCAAGCAACC--------
.............((((((((((((..(((((....)))))..))))))......(((.....(((.((((((((.......)))))))).)))...)))..)).))))...-------- ( -33.10)
>consensus
AAUAUUUUACAUAUGCUUCGGAUGCACGUGUCCAACGACACACGUGUCCUAAUUCUGCUAAUAAUACGUUGGCCAACUAAAAUGGUCAACAUAUGCUACAAUUCAAGCAACCAGACCCGG
.............(((((.((((((((((((........))))))))....................((((((((.......))))))))..........)))))))))........... (-25.36 = -25.56 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,957,970 – 12,958,090
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.00
Mean single sequence MFE -36.58
Consensus MFE -25.34
Energy contribution -25.70
Covariance contribution 0.36
Combinations/Pair 1.19
Mean z-score -2.35
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.825726
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12957970 120 - 22224390
CCGGUUGCGGUUGCUUGAAUUGUAGCAUAUGUUGACCAUUUAAAAUGGCCAACGUAUUAUUAACAGAAUUAGGACACGUGUGGCGUUGGACACGUGCAUCCGAAGCAUAUGUAAAAUAUU
....(((((..(((((...((((...((((((((.((((.....)))).)))))))).....)))).....((((((((((........)))))))..))).)))))..)))))...... ( -33.20)
>DroSec_CAF1 3376 120 - 1
CCGGGCCUGGUUGCUUGAAUUGUAGCAUAUGUUGACCAAUUUAGUUGGCCAACGUAUUAUUAGCAGAAUUAGGACACGUGUGUCGUUGGACACGUGCAUCCGAAGCAUAUGUAAAAUAUU
.((((((((((((((........)))((((((((.(((((...))))).)))))))).........))))))).(((((((........)))))))..)))).................. ( -33.80)
>DroSim_CAF1 2408 120 - 1
CCGGGUCUGGUUGCUUGAAUUGUAGCAUAUGUUGACCAUUUUAGUUGGCCAACGUAUUAUUAGCAGAAUUAGGACACGUGUGUCGUUGGACACGUGCAUCCGAAGCAUAUGUAAAAUAUU
((...(((((((((.......)))))((((((((.(((.......))).))))))))......))))....))..((((((((..(((((........))))).))))))))........ ( -33.90)
>DroEre_CAF1 3525 119 - 1
CCGGCUCUGGUUGCUUGAAUUGUAGCAUAUGCUGACCAUUC-GAGUAGCCAACGUAUUAUUAUCAGAAUUGGGGCACGUGUGGCGUUGGAUACGUGUAUCCAAGGCAUAUGUAAAAUAUC
...(((((((((((((((((.(((((....))).)).))))-))))))))...(((....))).......)))))(((((((.(.(((((((....))))))).))))))))........ ( -43.40)
>DroYak_CAF1 3504 112 - 1
--------GGUUGCUUGAAUUGUAGCAUAUGUUGGCCAUUUAGCUUGGCCAACGUAUUAUUAACAGAAUUGGGACACGUGUGUCGUGGGACACGUGUAUCCUCAGCAUAUGUAAAUUAUU
--------.(((((.......)))))((((((((((((.......)))))))))))).....(((...((((((.(((((((((....))))))))).))).)))....)))........ ( -38.60)
>consensus
CCGGGUCUGGUUGCUUGAAUUGUAGCAUAUGUUGACCAUUUAAAUUGGCCAACGUAUUAUUAACAGAAUUAGGACACGUGUGUCGUUGGACACGUGCAUCCGAAGCAUAUGUAAAAUAUU
...........(((((...((((...((((((((.((((.....)))).)))))))).....)))).....((((((((((........)))))))..))).)))))............. (-25.34 = -25.70 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,958,010 – 12,958,123
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 88.00
Mean single sequence MFE -23.90
Consensus MFE -21.67
Energy contribution -21.80
Covariance contribution 0.13
Combinations/Pair 1.21
Mean z-score -1.77
Structure conservation index 0.91
SVM decision value 0.98
SVM RNA-class probability 0.893731
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12958010 113 + 22224390
CACGUGUCCUAAUUCUGUUAAUAAUACGUUGGCCAUUUUAAAUGGUCAACAUAUGCUACAAUUCAAGCAACCGCAACCGGGAAAAUCCUUCACCCACUAUGCCCAGCGCACUG
...((((.((.................(((((((((.....)))))))))...((((........))))...(((...(((...........)))....)))..)).)))).. ( -24.60)
>DroSec_CAF1 3416 112 + 1
CACGUGUCCUAAUUCUGCUAAUAAUACGUUGGCCAACUAAAUUGGUCAACAUAUGCUACAAUUCAAGCAACCAGGCCCGGGAAAAUCCUUCACCCACUAUGACCA-UGCACUG
...((((.........(((........(((((((((.....)))))))))...((((........))))....)))..(((...........)))..........-.)))).. ( -23.90)
>DroSim_CAF1 2448 112 + 1
CACGUGUCCUAAUUCUGCUAAUAAUACGUUGGCCAACUAAAAUGGUCAACAUAUGCUACAAUUCAAGCAACCAGACCCGGGAAAAUCCUUCACCCACUAUGACCA-UGCACUG
...((((.........((((((.....))))))........(((((((.....((((........)))).........(((...........)))....))))))-))))).. ( -23.70)
>DroEre_CAF1 3565 111 + 1
CACGUGCCCCAAUUCUGAUAAUAAUACGUUGGCUACUC-GAAUGGUCAGCAUAUGCUACAAUUCAAGCAACCAGAGCCGGGAAAAUCCCACACCCACUUAGCCCA-GCCACUG
...(((......(((((..........((((((((...-...))))))))...((((........))))..)))))..(((.....))).....)))........-....... ( -23.40)
>consensus
CACGUGUCCUAAUUCUGCUAAUAAUACGUUGGCCAACUAAAAUGGUCAACAUAUGCUACAAUUCAAGCAACCAGACCCGGGAAAAUCCUUCACCCACUAUGACCA_UGCACUG
...((((......((((..........(((((((((.....)))))))))...((((........))))..))))...(((...........)))............)))).. (-21.67 = -21.80 +   0.13)

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 11:37:08 2006