Locus 5231

Sequence ID 3L_DroMel_CAF1
Location 14,425,989 – 14,426,176
Length 187
Max. P 0.998602
window8273 window8274 window8275 window8276 window8277

overview

Window 3

Location 14,425,989 – 14,426,081
Length 92
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.40
Mean single sequence MFE -20.80
Consensus MFE -12.13
Energy contribution -13.30
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.58
SVM decision value 0.84
SVM RNA-class probability 0.864597
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14425989 92 - 23771897
--GAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGU-AAAACCAUUUGGCAACUUGUUAAUAAGCA-AUUGCAC----------------------AGCA-CAAAU
--...(((............((((.....))))....((((((((.(..-....)))))))))..)))........((.-...))..----------------------....-..... ( -19.60)
>DroPse_CAF1 49223 116 - 1
--AGAAAGACCUAGCCUAAAGCCAAUAAAUGGCAUUAGCCAAAUGCGGUUAAGACAAUUUUGAAACUUGUUAAUAAGCG-AUUGCACUCACACGAUCGGCAUCAGCACCAGCACCCAAG
--...........(((....((((.....)))).((((((......))))))(((((.........))))).......(-((((........))))))))....((....))....... ( -21.20)
>DroSec_CAF1 28342 92 - 1
--GAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUGGCCAAAUGUGGU-AAAACCAUUUGGCAACUUGUUAAUAAGCA-AUUGCAC----------------------AGCA-CAAAU
--..................((((.....)))).(((((((((((.(..-....)))))))((((.(((((....))))-)))))..----------------------.)).-))).. ( -19.90)
>DroYak_CAF1 33838 94 - 1
GCGAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGU-AAAACCAUUUGGCAACUUGUUAAUAAGCA-AUUGCAC----------------------AGCA-CAAAU
((((................((((.....))))....((((((((.(..-....)))))))))...(((((....))))-)))))..----------------------....-..... ( -22.20)
>DroAna_CAF1 43570 91 - 1
--GAAAAGACCUAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGC-AAAACCAUUUGGCAACUUGUUAAUAAGCAAAUUGCAU----------------------A--A-ACAAU
--..................((((.....((((....))))....))))-...........((((.(((((....))))).))))..----------------------.--.-..... ( -20.70)
>DroPer_CAF1 49389 116 - 1
--AGAAAGACCUAGCCUAAAGCCAAUAAAUGGCAUUAGCCAAAUGCGGUUAAGACAAUUUUUAAACUUGUUAAUAAGCG-AUUGCACUCACACGAUCGGCAUCAGCACCAGCACCCAAG
--...........(((....((((.....)))).((((((......))))))(((((.........))))).......(-((((........))))))))....((....))....... ( -21.20)
>consensus
__GAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGU_AAAACCAUUUGGCAACUUGUUAAUAAGCA_AUUGCAC______________________AGCA_CAAAU
.....(((............((((.....))))....((((((((.(.......)))))))))..)))........((.....)).................................. (-12.13 = -13.30 +   1.17)

alignment

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secondary structure

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Window 4

Location 14,426,005 – 14,426,100
Length 95
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 79.75
Mean single sequence MFE -17.79
Consensus MFE -12.65
Energy contribution -13.60
Covariance contribution 0.95
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.71
SVM decision value 0.75
SVM RNA-class probability 0.839639
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14426005 95 + 23771897
UGCUUAUUAACAAGUUGCCAAAUGGUUUU-ACCACAUUUGGCUAAUGCCACUUAUUGGCUUUAGGUUUGGUCUUUUCGU-UUU-UCAUUUUGCUAUUU
.((.....((((((..(((((((((....-.))........((((.((((.....)))).)))))))))))..))).))-)..-.......))..... ( -18.44)
>DroPse_CAF1 49262 78 + 1
CGCUUAUUAACAAGUUUCAAAAUUGUCUUAACCGCAUUUGGCUAAUGCCAUUUAUUGGCUUUAGGCUAGGUCUUUCUG--------------------
.((......((((.........)))).......))((((((((...((((.....))))....)))))))).......-------------------- ( -13.92)
>DroSec_CAF1 28358 96 + 1
UGCUUAUUAACAAGUUGCCAAAUGGUUUU-ACCACAUUUGGCCAAUGCCACUUAUUGGCUUUAGGUUUGGUCUUUUCCUUUUU-UCAUUUUGCUAUUU
.(((((.......(((((((((((.....-....))))))).))))((((.....))))..)))))..((......)).....-.............. ( -18.10)
>DroEre_CAF1 43582 95 + 1
UGCUUAUUAACAAGUUGCCAAAUGGUUUU-ACCACAUUUGGCUAAUGCCACUUAUUGGCUUUAGGUUUGGUCUUUUCGU-UUU-UCAUUUUGCUAUUU
.((.....((((((..(((((((((....-.))........((((.((((.....)))).)))))))))))..))).))-)..-.......))..... ( -18.44)
>DroAna_CAF1 43585 94 + 1
UGCUUAUUAACAAGUUGCCAAAUGGUUUU-GCCACAUUUGGCUAAUGCCACUUAUUGGCUUUAGGUUAGGUCUUUUCGU-UUUCUUGUUUUAGC--UU
.(((....((((((..((((((((.....-....))))))))(((.((((.....)))).)))................-...))))))..)))--.. ( -23.90)
>DroPer_CAF1 49428 78 + 1
CGCUUAUUAACAAGUUUAAAAAUUGUCUUAACCGCAUUUGGCUAAUGCCAUUUAUUGGCUUUAGGCUAGGUCUUUCUG--------------------
.((......((((.........)))).......))((((((((...((((.....))))....)))))))).......-------------------- ( -13.92)
>consensus
UGCUUAUUAACAAGUUGCCAAAUGGUUUU_ACCACAUUUGGCUAAUGCCACUUAUUGGCUUUAGGUUAGGUCUUUUCGU_UUU_UCAUUUUGCU__UU
.(((((..........((((((((..........))))))))....((((.....))))..)))))................................ (-12.65 = -13.60 +   0.95)

alignment

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secondary structure

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Window 5

Location 14,426,005 – 14,426,100
Length 95
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 79.75
Mean single sequence MFE -19.35
Consensus MFE -10.87
Energy contribution -12.03
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -3.19
Structure conservation index 0.56
SVM decision value 1.72
SVM RNA-class probability 0.973704
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14426005 95 - 23771897
AAAUAGCAAAAUGA-AAA-ACGAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGU-AAAACCAUUUGGCAACUUGUUAAUAAGCA
...((((((.....-...-....................((((.....))))....((((((((.(..-....)))))))))...))))))....... ( -21.40)
>DroPse_CAF1 49262 78 - 1
--------------------CAGAAAGACCUAGCCUAAAGCCAAUAAAUGGCAUUAGCCAAAUGCGGUUAAGACAAUUUUGAAACUUGUUAAUAAGCG
--------------------............((.....((((.....)))).((((((......))))))(((((.........))))).....)). ( -12.90)
>DroSec_CAF1 28358 96 - 1
AAAUAGCAAAAUGA-AAAAAGGAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUGGCCAAAUGUGGU-AAAACCAUUUGGCAACUUGUUAAUAAGCA
...((((((.....-.....((......)).........((((.....))))....((((((((.(..-....)))))))))...))))))....... ( -21.70)
>DroEre_CAF1 43582 95 - 1
AAAUAGCAAAAUGA-AAA-ACGAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGU-AAAACCAUUUGGCAACUUGUUAAUAAGCA
...((((((.....-...-....................((((.....))))....((((((((.(..-....)))))))))...))))))....... ( -21.40)
>DroAna_CAF1 43585 94 - 1
AA--GCUAAAACAAGAAA-ACGAAAAGACCUAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGC-AAAACCAUUUGGCAACUUGUUAAUAAGCA
..--(((..((((((...-....................((((.....))))....((((((((.(..-....)))))))))..))))))....))). ( -25.80)
>DroPer_CAF1 49428 78 - 1
--------------------CAGAAAGACCUAGCCUAAAGCCAAUAAAUGGCAUUAGCCAAAUGCGGUUAAGACAAUUUUUAAACUUGUUAAUAAGCG
--------------------............((.....((((.....)))).((((((......))))))(((((.........))))).....)). ( -12.90)
>consensus
AA__AGCAAAAUGA_AAA_ACGAAAAGACCAAACCUAAAGCCAAUAAGUGGCAUUAGCCAAAUGUGGU_AAAACCAUUUGGCAACUUGUUAAUAAGCA
........................(((............((((.....))))....((((((((.(.......)))))))))..)))........... (-10.87 = -12.03 +   1.17)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,426,081 – 14,426,176
Length 95
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 91.37
Mean single sequence MFE -21.96
Consensus MFE -18.26
Energy contribution -19.14
Covariance contribution 0.88
Combinations/Pair 1.10
Mean z-score -2.19
Structure conservation index 0.83
SVM decision value 2.09
SVM RNA-class probability 0.987591
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14426081 95 + 23771897
GU-UUU-UCAUUUUGCUAUUUGUAUUU-UAUCUCUUUUUCCAUAUUUCCAAUUGGAUGUCAGUGUGGGCUGUCGUCACGCCCACAAUCUCGGUAGCAG
..-...-......(((((((.......-..........((((..........))))......(((((((((....)).))))))).....))))))). ( -22.50)
>DroSec_CAF1 28434 96 + 1
CUUUUU-UCAUUUUGCUAUUUGUAUUU-UAUCUCUUUUUCCAUAUUUCCAAUUGGAUGUCAGUGUGGGCUGUCGUCACGCCCACAAUCUCGGUAGCAG
......-......(((((((.......-..........((((..........))))......(((((((((....)).))))))).....))))))). ( -22.50)
>DroSim_CAF1 43238 95 + 1
GU-UUU-UCAUUUUGCUAUUUGUAUUU-UAUCUCUUUUUCCAUAUUUCCAAUUGGAUGUCAGUGUGGGCUGUCGUCACGCCCACAAUCUCGGUAGCAG
..-...-......(((((((.......-..........((((..........))))......(((((((((....)).))))))).....))))))). ( -22.50)
>DroEre_CAF1 43658 94 + 1
GU-UUU-UCAUUUUGCUAUUUGU-UUU-UAUCUCUUUUUCCAUAUUUCCAAUUGGAUGUCAGUGUGGGCUGUCGUCACGCCCACAAUCUCGGUAGCAG
..-...-......(((((((...-...-..........((((..........))))......(((((((((....)).))))))).....))))))). ( -22.50)
>DroAna_CAF1 43661 95 + 1
GU-UUUCUUGUUUUAGC--UUGCGUUUUCUUAUAUUUUUUCAUAUUUCCAAUUGGAUGUCAGCGUGGGCUGUCGUCACGCCCACAAUCUCAGUAGCAG
..-.....((((...((--(.((((((....((((......))))........)))))).)))((((((((....)).)))))).........)))). ( -19.80)
>consensus
GU_UUU_UCAUUUUGCUAUUUGUAUUU_UAUCUCUUUUUCCAUAUUUCCAAUUGGAUGUCAGUGUGGGCUGUCGUCACGCCCACAAUCUCGGUAGCAG
.............(((((((..................((((..........))))......(((((((((....)).))))))).....))))))). (-18.26 = -19.14 +   0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,426,081 – 14,426,176
Length 95
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 91.37
Mean single sequence MFE -20.34
Consensus MFE -18.20
Energy contribution -18.12
Covariance contribution -0.08
Combinations/Pair 1.18
Mean z-score -2.24
Structure conservation index 0.89
SVM decision value 3.16
SVM RNA-class probability 0.998602
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14426081 95 - 23771897
CUGCUACCGAGAUUGUGGGCGUGACGACAGCCCACACUGACAUCCAAUUGGAAAUAUGGAAAAAGAGAUA-AAAUACAAAUAGCAAAAUGA-AAA-AC
.(((((.......(((((((((....)).)))))))((....((((..(....)..))))...)).....-.........)))))......-...-.. ( -20.60)
>DroSec_CAF1 28434 96 - 1
CUGCUACCGAGAUUGUGGGCGUGACGACAGCCCACACUGACAUCCAAUUGGAAAUAUGGAAAAAGAGAUA-AAAUACAAAUAGCAAAAUGA-AAAAAG
.(((((.......(((((((((....)).)))))))((....((((..(....)..))))...)).....-.........)))))......-...... ( -20.60)
>DroSim_CAF1 43238 95 - 1
CUGCUACCGAGAUUGUGGGCGUGACGACAGCCCACACUGACAUCCAAUUGGAAAUAUGGAAAAAGAGAUA-AAAUACAAAUAGCAAAAUGA-AAA-AC
.(((((.......(((((((((....)).)))))))((....((((..(....)..))))...)).....-.........)))))......-...-.. ( -20.60)
>DroEre_CAF1 43658 94 - 1
CUGCUACCGAGAUUGUGGGCGUGACGACAGCCCACACUGACAUCCAAUUGGAAAUAUGGAAAAAGAGAUA-AAA-ACAAAUAGCAAAAUGA-AAA-AC
.(((((.......(((((((((....)).)))))))((....((((..(....)..))))...)).....-...-.....)))))......-...-.. ( -20.60)
>DroAna_CAF1 43661 95 - 1
CUGCUACUGAGAUUGUGGGCGUGACGACAGCCCACGCUGACAUCCAAUUGGAAAUAUGAAAAAAUAUAAGAAAACGCAA--GCUAAAACAAGAAA-AC
..(((.........((((((((....)).))))))((.....(((....))).((((......))))........)).)--))............-.. ( -19.30)
>consensus
CUGCUACCGAGAUUGUGGGCGUGACGACAGCCCACACUGACAUCCAAUUGGAAAUAUGGAAAAAGAGAUA_AAAUACAAAUAGCAAAAUGA_AAA_AC
.(((((.......(((((((((....)).)))))))......(((....)))............................)))))............. (-18.20 = -18.12 +  -0.08)

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 11:45:06 2006