Locus 3889

Sequence ID 3L_DroMel_CAF1
Location 11,259,066 – 11,259,211
Length 145
Max. P 0.999945
window6051 window6052 window6053 window6054 window6055 window6056

overview

Window 1

Location 11,259,066 – 11,259,159
Length 93
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.35
Mean single sequence MFE -17.78
Consensus MFE -3.42
Energy contribution -4.62
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.19
SVM decision value 2.81
SVM RNA-class probability 0.997153
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259066 93 + 23771897
AAGAAAACCAACAAUACUUGUAAAUAACAUUAUGGCCCAUACAGCAGCAAC---------------------------AAUAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUAAAGUC
...............((((...............((.......))(((.((---------------------------(((.((((((.(.......).))))))))))).))).)))). ( -15.80)
>DroSec_CAF1 59916 93 + 1
AAGAAAACCAACAAUACUUGUAAAUAACAUUAUGGCCCAUACAGCAGCAAC---------------------------AAUAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUACAGUC
.................(((((............((.......)).((.((---------------------------(((.((((((.(.......).))))))))))).))))))).. ( -15.90)
>DroSim_CAF1 61586 93 + 1
AAGAAAACCAACAAUACUUGUAAAUAACAUUAUGGCCCAUACAGCAGCAAC---------------------------AAUAGUUGCUACAAUAACAGCAGCAACAUUGUUGCUACAGUC
.................(((((............((.......)).(((((---------------------------(((.((((((.(.......).))))))))))))))))))).. ( -20.00)
>DroYak_CAF1 63485 118 + 1
AUGAAAACCAACAACACUUUUAAAUAACAUUAUGGCC-AAACAGCAGCAACAAUAGUUGCUACAAUAACAGCAGAUACAAUAGUUGCUACCAUAACAGCAGCAACAUUGUGUCUA-AGUA
...............((((.............((((.-.....))((((((....)))))).))........(((((((((.((((((.(.......).))))))))))))))))-))). ( -25.30)
>DroAna_CAF1 60037 92 + 1
-GCAACACCAGCAGUAUUUGUAAAUAACAGUAUUGCCAGUGCAACAACAGC---------------------------AACAAAAACCAUGAAGAAAACAACAAAUUUGAAGCCCAAGUU
-....(((..((((((((.((.....))))))))))..)))..........---------------------------.........................((((((.....)))))) ( -11.90)
>consensus
AAGAAAACCAACAAUACUUGUAAAUAACAUUAUGGCCCAUACAGCAGCAAC___________________________AAUAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUAAAGUC
..................................................................................((((((........)))))).................. ( -3.42 =  -4.62 +   1.20)

alignment

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secondary structure

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Window 2

Location 11,259,066 – 11,259,159
Length 93
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.35
Mean single sequence MFE -28.84
Consensus MFE -12.24
Energy contribution -12.44
Covariance contribution 0.20
Combinations/Pair 1.31
Mean z-score -3.73
Structure conservation index 0.42
SVM decision value 4.74
SVM RNA-class probability 0.999945
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259066 93 - 23771897
GACUUUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU---------------------------GUUGCUGCUGUAUGGGCCAUAAUGUUAUUUACAAGUAUUGUUGGUUUUCUU
.((..((((.(((((((((((((.......)))))))).)))---------------------------)).))))..))..(((((((((((((.......))))))).)))))).... ( -26.40)
>DroSec_CAF1 59916 93 - 1
GACUGUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU---------------------------GUUGCUGCUGUAUGGGCCAUAAUGUUAUUUACAAGUAUUGUUGGUUUUCUU
.((.(((((.(((((((((((((.......)))))))).)))---------------------------)).))))).))..(((((((((((((.......))))))).)))))).... ( -29.40)
>DroSim_CAF1 61586 93 - 1
GACUGUAGCAACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU---------------------------GUUGCUGCUGUAUGGGCCAUAAUGUUAUUUACAAGUAUUGUUGGUUUUCUU
.((.(((((((((((((((((((.......)))))))).)))---------------------------)))))))).))..(((((((((((((.......))))))).)))))).... ( -33.50)
>DroYak_CAF1 63485 118 - 1
UACU-UAGACACAAUGUUGCUGCUGUUAUGGUAGCAACUAUUGUAUCUGCUGUUAUUGUAGCAACUAUUGUUGCUGCUGUUU-GGCCAUAAUGUUAUUUAAAAGUGUUGUUGGUUUUCAU
....-((((.((((((((((((((.....))))))))).))))).))))........((((((((....))))))))((...-((((((((..((.......))..))).)))))..)). ( -37.70)
>DroAna_CAF1 60037 92 - 1
AACUUGGGCUUCAAAUUUGUUGUUUUCUUCAUGGUUUUUGUU---------------------------GCUGUUGUUGCACUGGCAAUACUGUUAUUUACAAAUACUGCUGGUGUUGC-
......(((..((((.....((.......)).....))))..---------------------------)))...((.((((..(((.((.(((.....)))..)).)))..)))).))- ( -17.20)
>consensus
GACUGUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU___________________________GUUGCUGCUGUAUGGGCCAUAAUGUUAUUUACAAGUAUUGUUGGUUUUCUU
...........(((((.(((((((..(((.((((((((...............................)))))))).)))..))).....(((.....))))))).)))))........ (-12.24 = -12.44 +   0.20)

alignment

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secondary structure

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Window 3

Location 11,259,106 – 11,259,196
Length 90
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.10
Mean single sequence MFE -23.71
Consensus MFE -10.20
Energy contribution -11.20
Covariance contribution 1.00
Combinations/Pair 1.14
Mean z-score -2.85
Structure conservation index 0.43
SVM decision value 3.54
SVM RNA-class probability 0.999365
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259106 90 + 23771897
ACAGCAGCAAC---------------------------AAUAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUAAAGUCGUAGCCCUCUUUUGGCAGUGUCUA-AACAAUGAGAA--AA
.....(((.((---------------------------(((.((((((.(.......).))))))))))).)))..((.((..(((.......)))..)).)).-...........--.. ( -20.40)
>DroSec_CAF1 59956 90 + 1
ACAGCAGCAAC---------------------------AAUAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUACAGUCGUAGCCCUCAUUUGGCAGUGUCUA-AACACUGAAAA--AA
.........((---------------------------(((.((((((.(.......).))))))))))).(((((....))))).....(((..((((((...-.))))))..))--). ( -24.20)
>DroSim_CAF1 61626 92 + 1
ACAGCAGCAAC---------------------------AAUAGUUGCUACAAUAACAGCAGCAACAUUGUUGCUACAGUCGUAGCCCUCUUUUGGCAGUGUCUA-AACACUGAAAAAAAA
...(.((((((---------------------------(((.((((((.(.......).))))))))))))))).).............((((..((((((...-.))))))..)))).. ( -27.80)
>DroYak_CAF1 63524 116 + 1
ACAGCAGCAACAAUAGUUGCUACAAUAACAGCAGAUACAAUAGUUGCUACCAUAACAGCAGCAACAUUGUGUCUA-AGUAGUAGCCCUCUUUUGGCAGUGUCUG-UACACUGAGAA--AA
...((((((((....))))))......((.(((((((((((.((((((.(.......).))))))))))))))).-.)).)).))....((((..((((((...-.)))))).)))--). ( -33.20)
>DroAna_CAF1 60076 91 + 1
GCAACAACAGC---------------------------AACAAAAACCAUGAAGAAAACAACAAAUUUGAAGCCCAAGUUGUUGUCCAAGUUUGGCAUUAGUUAGGGUACUGAGAA--AA
((.......))---------------------------........(((........(((((((.((((.....))))))))))).......)))..(((((......)))))...--.. ( -12.96)
>consensus
ACAGCAGCAAC___________________________AAUAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUAAAGUCGUAGCCCUCUUUUGGCAGUGUCUA_AACACUGAGAA__AA
.............................................(((((.((...(((.(((....))).)))...)).)))))((......))((((((.....))))))........ (-10.20 = -11.20 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,259,106 – 11,259,196
Length 90
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.10
Mean single sequence MFE -29.84
Consensus MFE -13.84
Energy contribution -13.92
Covariance contribution 0.08
Combinations/Pair 1.35
Mean z-score -3.44
Structure conservation index 0.46
SVM decision value 4.43
SVM RNA-class probability 0.999895
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259106 90 - 23771897
UU--UUCUCAUUGUU-UAGACACUGCCAAAAGAGGGCUACGACUUUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU---------------------------GUUGCUGCUGU
..--...........-........(((.......)))....((..((((.(((((((((((((.......)))))))).)))---------------------------)).))))..)) ( -24.90)
>DroSec_CAF1 59956 90 - 1
UU--UUUUCAGUGUU-UAGACACUGCCAAAUGAGGGCUACGACUGUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU---------------------------GUUGCUGCUGU
..--.....(((((.-...)))))(((.......)))....((.(((((.(((((((((((((.......)))))))).)))---------------------------)).))))).)) ( -31.90)
>DroSim_CAF1 61626 92 - 1
UUUUUUUUCAGUGUU-UAGACACUGCCAAAAGAGGGCUACGACUGUAGCAACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU---------------------------GUUGCUGCUGU
((((((..((((((.-...))))))..))))))........((.(((((((((((((((((((.......)))))))).)))---------------------------)))))))).)) ( -37.20)
>DroYak_CAF1 63524 116 - 1
UU--UUCUCAGUGUA-CAGACACUGCCAAAAGAGGGCUACUACU-UAGACACAAUGUUGCUGCUGUUAUGGUAGCAACUAUUGUAUCUGCUGUUAUUGUAGCAACUAUUGUUGCUGCUGU
((--((..((((((.-...))))))..))))((.(((.......-.(((.((((((((((((((.....))))))))).))))).)))))).))...((((((((....))))))))... ( -39.90)
>DroAna_CAF1 60076 91 - 1
UU--UUCUCAGUACCCUAACUAAUGCCAAACUUGGACAACAACUUGGGCUUCAAAUUUGUUGUUUUCUUCAUGGUUUUUGUU---------------------------GCUGUUGUUGC
..--....(((((.....((....((((.....(((((((((.((........)).)))))))))......))))....)))---------------------------))))....... ( -15.30)
>consensus
UU__UUCUCAGUGUU_UAGACACUGCCAAAAGAGGGCUACGACUGUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUAUU___________________________GUUGCUGCUGU
........((((((.....))))))......((.(((..((((............))))..))).))...((((((((...............................))))))))... (-13.84 = -13.92 +   0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,259,119 – 11,259,211
Length 92
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 86.20
Mean single sequence MFE -21.95
Consensus MFE -15.38
Energy contribution -16.88
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.60
Structure conservation index 0.70
SVM decision value 1.23
SVM RNA-class probability 0.933996
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259119 92 + 23771897
UAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUAAAGUCGUAGCCCUCUUUUGGCAGUGUCUAAACAAUGAGAA--AAAUGUAUCCAAAAACG
..((((((........))))))..((((((......((.((..(((.......)))..)).))..))))))....--................. ( -16.80)
>DroSec_CAF1 59969 92 + 1
UAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUACAGUCGUAGCCCUCAUUUGGCAGUGUCUAAACACUGAAAA--AAAUGUAUCCAAAAAUA
..((((((........)))))).(((((...(((((....))))).....(((..((((((....))))))..))--))))))........... ( -23.90)
>DroSim_CAF1 61639 94 + 1
UAGUUGCUACAAUAACAGCAGCAACAUUGUUGCUACAGUCGUAGCCCUCUUUUGGCAGUGUCUAAACACUGAAAAAAAAAUAUACCCAAAAAUA
.....(((((.((...(((((((....)))))))...)).)))))....((((..((((((....))))))..))))................. ( -22.90)
>DroYak_CAF1 63564 86 + 1
UAGUUGCUACCAUAACAGCAGCAACAUUGUGUCUA-AGUAGUAGCCCUCUUUUGGCAGUGUCUGUACACUGAGAA--AACUGUGGCUAA-----
..((((((........)))))).............-.....((((((..((((..((((((....))))))..))--))..).))))).----- ( -24.20)
>consensus
UAGUUGCUACAAUAACAGCAGCAACAUUGUAGCUACAGUCGUAGCCCUCUUUUGGCAGUGUCUAAACACUGAAAA__AAAUGUAUCCAAAAAUA
..((((((........)))))).(((((...(((((....)))))((......))((((((....)))))).......)))))........... (-15.38 = -16.88 +   1.50)

alignment

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secondary structure

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Window 6

Location 11,259,119 – 11,259,211
Length 92
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 86.20
Mean single sequence MFE -25.95
Consensus MFE -19.30
Energy contribution -20.30
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.74
SVM decision value 1.75
SVM RNA-class probability 0.975597
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259119 92 - 23771897
CGUUUUUGGAUACAUUU--UUCUCAUUGUUUAGACACUGCCAAAAGAGGGCUACGACUUUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUA
..(((((((.....(((--..(.....)...))).....)))))))..(((((......))))).....((((((((.......)))))))).. ( -19.60)
>DroSec_CAF1 59969 92 - 1
UAUUUUUGGAUACAUUU--UUUUCAGUGUUUAGACACUGCCAAAUGAGGGCUACGACUGUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUA
.....(((....(((((--....((((((....))))))..)))))..((((((....)))))).))).((((((((.......)))))))).. ( -27.70)
>DroSim_CAF1 61639 94 - 1
UAUUUUUGGGUAUAUUUUUUUUUCAGUGUUUAGACACUGCCAAAAGAGGGCUACGACUGUAGCAACAAUGUUGCUGCUGUUAUUGUAGCAACUA
........(((...(((((((..((((((....))))))..))))))).((((((((.((((((((...)))))))).)))...))))).))). ( -28.90)
>DroYak_CAF1 63564 86 - 1
-----UUAGCCACAGUU--UUCUCAGUGUACAGACACUGCCAAAAGAGGGCUACUACU-UAGACACAAUGUUGCUGCUGUUAUGGUAGCAACUA
-----.(((((.(..((--((..((((((....))))))..))))..)))))).....-..........(((((((((.....))))))))).. ( -27.60)
>consensus
UAUUUUUGGAUACAUUU__UUCUCAGUGUUUAGACACUGCCAAAAGAGGGCUACGACUGUAGCUACAAUGUUGCUGCUGUUAUUGUAGCAACUA
.......................((((((....))))))((......))(((((....)))))......((((((((.......)))))))).. (-19.30 = -20.30 +   1.00)

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 11:09:16 2006