Locus 1879

Sequence ID 3R_DroMel_CAF1
Location 5,398,700 – 5,398,912
Length 212
Max. P 0.992174
window3085 window3086 window3087 window3088

overview

Window 5

Location 5,398,700 – 5,398,794
Length 94
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.03
Mean single sequence MFE -27.27
Consensus MFE -15.90
Energy contribution -15.80
Covariance contribution -0.10
Combinations/Pair 1.25
Mean z-score -1.37
Structure conservation index 0.58
SVM decision value 0.15
SVM RNA-class probability 0.609624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5398700 94 - 27905053
CUUGAUAACAACCGCAUACGGUUGUGUUCGUGAGCGGAUUGCCUUCUG-----------UUGUGGAACCCUAUGAAAAAAAGUUUCCCAAAA---------AAAUCAAAAACUU------
.(((((.(((((((....)))))))((((...((((((......))))-----------))...))))........................---------..)))))......------ ( -20.20)
>DroSim_CAF1 8429 100 - 1
CUUGAUA---ACCGCAUGCGGUUGUGUUCGUGAGCGGAUUGCCUUCUG-----------UUAUGGAACCCUAUGAAAAAAGGUUCCCCAAAAUCGCGAUAAUUAUCAAAAACUG------
.((((((---((((....)))).....((((((..((...(((((...-----------((((((....))))))...)))))...))....))))))....))))))......------ ( -27.70)
>DroYak_CAF1 8761 116 - 1
CUUGAUA---ACCGCAUGCGGUUGUGUUUGUGAGCGGAUUGCUUUCUGGUUGCUUUCAGCUGUGGAGGCCUAAACAGAAAGAUUCCCGAAUAUCGCUUGA-AAAUCCGAAAGUUAAAGGA
....(((---((((....)))))))....((((.(((....(((((((...(((((((....))))))).....)))))))....)))....))))....-...(((..........))) ( -33.90)
>consensus
CUUGAUA___ACCGCAUGCGGUUGUGUUCGUGAGCGGAUUGCCUUCUG___________UUGUGGAACCCUAUGAAAAAAGGUUCCCCAAAAUCGC___A_AAAUCAAAAACUU______
.(((((.....((((.(((((......))))).))))..........................((((((...........)))))).................)))))............ (-15.90 = -15.80 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,398,754 – 5,398,874
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.11
Mean single sequence MFE -32.19
Consensus MFE -24.67
Energy contribution -24.29
Covariance contribution -0.38
Combinations/Pair 1.15
Mean z-score -2.93
Structure conservation index 0.77
SVM decision value 2.31
SVM RNA-class probability 0.992174
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5398754 120 + 27905053
AAUCCGCUCACGAACACAACCGUAUGCGGUUGUUAUCAAGCGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCUCAGAUUUGUCUACCGUCGUUUCGGAUUUAU
((((((...((((..(((((((....))))))).(((.(((((((((.(((..((((..............))))...))))))))))))..)))..........))))..))))))... ( -38.14)
>DroSim_CAF1 8492 117 + 1
AAUCCGCUCACGAACACAACCGCAUGCGGU---UAUCAAGCGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCUCAGAUUUGUCUACCGUCGUUUCGGAUUUAU
((((((...((((....(((((....))))---)(((.(((((((((.(((..((((..............))))...))))))))))))..)))..........))))..))))))... ( -34.64)
>DroYak_CAF1 8840 117 + 1
AAUCCGCUCACAAACACAACCGCAUGCGGU---UAUCAAGCGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCACAGAUUUGUCUACCGUCGUUUCGGAUUUAU
((((((.....(((((((((((....))))---).....((((((((.(((..((((..............))))...)))))))))))...............)).))))))))))... ( -31.54)
>DroAna_CAF1 8407 99 + 1
------------GACACA--C---GGCAGU---UAUCAAGCGCAGGUUGCUCAAAAUAAUCAAAUAAUUUCGUUUAAUAGCACCUGCGCACAGAUUUGUAUACUACUGCUU-GGAUUGAC
------------....((--.---((((((---......((((((((.(((..((((..............))))...)))))))))))((......)).....)))))))-)....... ( -24.44)
>consensus
AAUCCGCUCACGAACACAACCGCAUGCGGU___UAUCAAGCGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCACAGAUUUGUCUACCGUCGUUUCGGAUUUAU
...................(((...(((((....(((..((((((((.(((..((((..............))))...)))))))))))...)))......))))).....)))...... (-24.67 = -24.29 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,398,754 – 5,398,874
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.11
Mean single sequence MFE -36.93
Consensus MFE -25.58
Energy contribution -27.57
Covariance contribution 2.00
Combinations/Pair 1.10
Mean z-score -3.17
Structure conservation index 0.69
SVM decision value 2.16
SVM RNA-class probability 0.989267
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5398754 120 - 27905053
AUAAAUCCGAAACGACGGUAGACAAAUCUGAGCGCAGGUGCCAUUAAAUGAAAUUAUUUGAUUAUUUCGAGCAACCUGCGCUUGAUAACAACCGCAUACGGUUGUGUUCGUGAGCGGAUU
...((((((..((((..........(((.(((((((((((((((((((((....))))))))......).)).))))))))))))).(((((((....)))))))..))))...)))))) ( -43.00)
>DroSim_CAF1 8492 117 - 1
AUAAAUCCGAAACGACGGUAGACAAAUCUGAGCGCAGGUGCCAUUAAAUGAAAUUAUUUGAUUAUUUCGAGCAACCUGCGCUUGAUA---ACCGCAUGCGGUUGUGUUCGUGAGCGGAUU
...((((((..((((..............(((((((((((((((((((((....))))))))......).)).)))))))))).(((---((((....)))))))..))))...)))))) ( -41.30)
>DroYak_CAF1 8840 117 - 1
AUAAAUCCGAAACGACGGUAGACAAAUCUGUGCGCAGGUGCCAUUAAAUGAAAUUAUUUGAUUAUUUCGAGCAACCUGCGCUUGAUA---ACCGCAUGCGGUUGUGUUUGUGAGCGGAUU
...((((((..((((................(((((((((((((((((((....))))))))......).)).))))))))...(((---((((....)))))))..))))...)))))) ( -36.60)
>DroAna_CAF1 8407 99 - 1
GUCAAUCC-AAGCAGUAGUAUACAAAUCUGUGCGCAGGUGCUAUUAAACGAAAUUAUUUGAUUAUUUUGAGCAACCUGCGCUUGAUA---ACUGCC---G--UGUGUC------------
........-..(((((.(....)..(((...(((((((((((..(((.((((....)))).))).....))).))))))))..))).---))))).---.--......------------ ( -26.80)
>consensus
AUAAAUCCGAAACGACGGUAGACAAAUCUGAGCGCAGGUGCCAUUAAAUGAAAUUAUUUGAUUAUUUCGAGCAACCUGCGCUUGAUA___ACCGCAUGCGGUUGUGUUCGUGAGCGGAUU
...((((((..((((.(((......(((.(((((((((((((((((((((....))))))))......).)).)))))))))))))....)))(((......)))..))))...)))))) (-25.58 = -27.57 +   2.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,398,794 – 5,398,912
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.46
Mean single sequence MFE -31.64
Consensus MFE -25.16
Energy contribution -24.40
Covariance contribution -0.75
Combinations/Pair 1.23
Mean z-score -1.52
Structure conservation index 0.80
SVM decision value 0.02
SVM RNA-class probability 0.541254
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5398794 118 + 27905053
CGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCUCAGAUUUGUCUACCGUCGUUUCGGAUUUAUGGUG--AACUAUAGUAUGUGUGCGAUAAUGAAAAUCAGCG
.((((((.(((..((((..............))))...)))))))))(((..(((((.((....(((((..((.((((((((..--..)))))).)).)).)))))...)))))))))). ( -29.94)
>DroSim_CAF1 8529 118 + 1
CGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCUCAGAUUUGUCUACCGUCGUUUCGGAUUUAUGGUG--AACUAUAGUAUGUGUGCGAUAAUGAAAAUCAGCG
.((((((.(((..((((..............))))...)))))))))(((..(((((.((....(((((..((.((((((((..--..)))))).)).)).)))))...)))))))))). ( -29.94)
>DroYak_CAF1 8877 118 + 1
CGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCACAGAUUUGUCUACCGUCGUUUCGGAUUUAUGGUG--AACUAUAGUAUGUGUGCGAUAAUGAAAAUCAGCG
.((((((.(((..((((..............))))...)))))))))(((((.((.......(((......)))..((((((..--..)))))).)).)))))(((.......))).... ( -28.84)
>DroAna_CAF1 8427 119 + 1
CGCAGGUUGCUCAAAAUAAUCAAAUAAUUUCGUUUAAUAGCACCUGCGCACAGAUUUGUAUACUACUGCUU-GGAUUGACAGUGCGGGCGGUAGUAUGUGUGCGAUAAUGAAAAUCAGCG
.((((((.(((..((((..............))))...)))))))))(((((......(((((((((((((-(.((.....)).)))))))))))))))))))(((.......))).... ( -37.84)
>consensus
CGCAGGUUGCUCGAAAUAAUCAAAUAAUUUCAUUUAAUGGCACCUGCGCACAGAUUUGUCUACCGUCGUUUCGGAUUUAUGGUG__AACUAUAGUAUGUGUGCGAUAAUGAAAAUCAGCG
(((((((.(((..((((..............))))...))))))))))....(((((.......(((((.......(((((((....))))))).......))))).....))))).... (-25.16 = -24.40 +  -0.75)

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 10:21:46 2006