Locus 8955

Sequence ID 3R_DroMel_CAF1
Location 24,019,159 – 24,019,328
Length 169
Max. P 0.869975
window14353 window14354 window14355 window14356

overview

Window 3

Location 24,019,159 – 24,019,254
Length 95
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 88.95
Mean single sequence MFE -23.85
Consensus MFE -22.10
Energy contribution -22.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.93
SVM decision value 0.87
SVM RNA-class probability 0.869975
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24019159 95 + 27905053
GGAAAAUCGUCUGGCAUGUGGAUAAUUUCCAGCAGACUUGCCGCUGCAUUAGUGCACAGACAUACACACA------UAUACUCGUAUAGACAAUCACACAU
.((...(((((((((((.((((.....))))((((........))))....)))).))))).........------((((....))))))...))...... ( -22.70)
>DroSec_CAF1 214543 87 + 1
GGAAAAUCGUCUGGCAUGUGGAUAAUUUCCAGCAGACUUGUCGCUGCAUUAGUGCACAGACACA--------------CACUCGUAAAGACAAUCACACAU
........(((((((((.((((.....))))((((........))))....)))).)))))...--------------....................... ( -22.10)
>DroSim_CAF1 211929 95 + 1
GGAAAAUCGUCUGGCAUGUGGAUAAUUUCCAGCAGACUUGUCGCUGCAUUAGUGCACAGACACAGACACA------UAUACUCGUAUAGACAAUCACACAU
........(((((((((.((((.....))))((((........))))....)))).)))))...((....------((((....)))).....))...... ( -22.80)
>DroEre_CAF1 225844 101 + 1
GGAAAAUCGUCUGGCAUGUGGAUAAUUUCCAGCAGACUUGCCGCUGCAUUAGUGCACAGACAGACACACAUACGUGUAUGCUGGUAUAGACAAUCACACAU
........(((((((((.((((.....))))((((........))))....)))).(((.((.((((......)))).)))))...))))).......... ( -27.80)
>consensus
GGAAAAUCGUCUGGCAUGUGGAUAAUUUCCAGCAGACUUGCCGCUGCAUUAGUGCACAGACACACACACA______UAUACUCGUAUAGACAAUCACACAU
........(((((((((.((((.....))))((((........))))....)))).)))))........................................ (-22.10 = -22.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,019,194 – 24,019,288
Length 94
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 87.80
Mean single sequence MFE -27.33
Consensus MFE -21.92
Energy contribution -21.93
Covariance contribution 0.00
Combinations/Pair 1.04
Mean z-score -1.49
Structure conservation index 0.80
SVM decision value 0.15
SVM RNA-class probability 0.608594
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24019194 94 - 27905053
UGUCGGCAGAUUAUAUUGUCCUGGCUGUCAGGAUAUGUGUGAUUGUCUAUACGAGUAUA------UGUGUGUAUGUCUGUGCACUAAUGCAGCGGCAAGU
(((((((((.(((((((((((((.....))))))).))))))))))).......((((.------.(((..((....))..)))..))))...))))... ( -28.20)
>DroSec_CAF1 214578 86 - 1
UGUCGGCAGAUUAUAUUGUCCUGCCUGUCACGAUAUGUGUGAUUGUCUUUACGAGUG--------------UGUGUCUGUGCACUAAUGCAGCGACAAGU
(((((((((((......)).))))).(.(((.((((.(((((......))))).)))--------------)))).)..((((....))))..))))... ( -22.60)
>DroSim_CAF1 211964 94 - 1
UGUCGGCAGAUUAUAUUGUCCUGCCUGUCAGGAUAUGUGUGAUUGUCUAUACGAGUAUA------UGUGUCUGUGUCUGUGCACUAAUGCAGCGACAAGU
(((((((((.(((((((((((((.....))))))).)))))))))))............------(((((..((((....))))..)))))..))))... ( -27.10)
>DroEre_CAF1 225879 100 - 1
UGUCGGCAGAUUAUAUUGUCCUGCCUGUCAGGAUAUGUGUGAUUGUCUAUACCAGCAUACACGUAUGUGUGUCUGUCUGUGCACUAAUGCAGCGGCAAGU
(((((((((((((((((((((((.....))))))).))))))..........(((.((((((....))))))))))))))(((....)))..)))))... ( -31.40)
>consensus
UGUCGGCAGAUUAUAUUGUCCUGCCUGUCAGGAUAUGUGUGAUUGUCUAUACGAGUAUA______UGUGUGUGUGUCUGUGCACUAAUGCAGCGACAAGU
(((((((((.(((((((((((((.....))))))).)))))))))))...........................(.((((........)))))))))... (-21.92 = -21.93 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,019,227 – 24,019,328
Length 101
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 78.71
Mean single sequence MFE -23.00
Consensus MFE -13.19
Energy contribution -15.28
Covariance contribution 2.09
Combinations/Pair 1.05
Mean z-score -1.85
Structure conservation index 0.57
SVM decision value 0.29
SVM RNA-class probability 0.670098
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24019227 101 + 27905053
CA------UAUACUCGUAUAGA--CAAUCACACAUAUCCUGACAGCCAGGACAAUAUAAUCUGCCGACAAUUUGCGCCUAAAAGUUGGCUGCAUUUUGUUGAAAUGCAA
..------.......((((...--............(((((.....))))).............((((((..((((((........))).)))..))))))..)))).. ( -24.50)
>DroVir_CAF1 235321 84 + 1
------------------CAUACGCAAACACACAC----CAACUGCA--AAUAUCAUAAUCAGUGGCAAUUUUGCGCCUAAAAGUUGGCUGCAUUUUGU-GAAAUGCGC
------------------....((((..((((..(----((.(((..--...........))))))......((((((........))).)))...)))-)...)))). ( -17.92)
>DroSec_CAF1 214607 97 + 1
----------CACUCGUAAAGA--CAAUCACACAUAUCGUGACAGGCAGGACAAUAUAAUCUGCCGACAAUUUGCGCCUAAAAGUUGGCUGCAUUUUGUUGAAAUGCAA
----------.....(((....--...((((.......))))..((((((.........))))))(((((..((((((........))).)))..)))))....))).. ( -25.00)
>DroSim_CAF1 211997 101 + 1
CA------UAUACUCGUAUAGA--CAAUCACACAUAUCCUGACAGGCAGGACAAUAUAAUCUGCCGACAAUUUGCGCCUAAAAGUUGGCUGCAUUUUGUUGAAAUGCAA
..------.......((((...--............(((((.....))))).............((((((..((((((........))).)))..))))))..)))).. ( -24.30)
>DroEre_CAF1 225912 107 + 1
CAUACGUGUAUGCUGGUAUAGA--CAAUCACACAUAUCCUGACAGGCAGGACAAUAUAAUCUGCCGACAAUUUGCGCCUAAAAGUUGGCUGCAUUUUGCUGAAAUGCAA
.....((.((((....)))).)--).......(((.((......((((((.........))))))(.(((..((((((........))).)))..)))).)).)))... ( -23.30)
>consensus
CA______UAUACUCGUAUAGA__CAAUCACACAUAUCCUGACAGGCAGGACAAUAUAAUCUGCCGACAAUUUGCGCCUAAAAGUUGGCUGCAUUUUGUUGAAAUGCAA
....................................(((((.....)))))...........((((((((..((((((........))).)))..))))))....)).. (-13.19 = -15.28 +   2.09)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,019,227 – 24,019,328
Length 101
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 78.71
Mean single sequence MFE -25.98
Consensus MFE -16.29
Energy contribution -17.82
Covariance contribution 1.53
Combinations/Pair 1.08
Mean z-score -1.59
Structure conservation index 0.63
SVM decision value -0.04
SVM RNA-class probability 0.510923
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24019227 101 - 27905053
UUGCAUUUCAACAAAAUGCAGCCAACUUUUAGGCGCAAAUUGUCGGCAGAUUAUAUUGUCCUGGCUGUCAGGAUAUGUGUGAUUG--UCUAUACGAGUAUA------UG
.(((((((.....)))))))(((........))).....((((.(((((.(((((((((((((.....))))))).)))))))))--))...)))).....------.. ( -27.30)
>DroVir_CAF1 235321 84 - 1
GCGCAUUUC-ACAAAAUGCAGCCAACUUUUAGGCGCAAAAUUGCCACUGAUUAUGAUAUU--UGCAGUUG----GUGUGUGUUUGCGUAUG------------------
(((((...(-(((...(((.(((........)))))).....(((((((...........--..))).))----)).))))..)))))...------------------ ( -24.02)
>DroSec_CAF1 214607 97 - 1
UUGCAUUUCAACAAAAUGCAGCCAACUUUUAGGCGCAAAUUGUCGGCAGAUUAUAUUGUCCUGCCUGUCACGAUAUGUGUGAUUG--UCUUUACGAGUG----------
.(((((((.....)))))))(((........)))(((.(((((.(((((((......)).)))))....))))).)))((((...--...)))).....---------- ( -23.70)
>DroSim_CAF1 211997 101 - 1
UUGCAUUUCAACAAAAUGCAGCCAACUUUUAGGCGCAAAUUGUCGGCAGAUUAUAUUGUCCUGCCUGUCAGGAUAUGUGUGAUUG--UCUAUACGAGUAUA------UG
.(((((((.....)))))))(((........))).....((((.(((((.(((((((((((((.....))))))).)))))))))--))...)))).....------.. ( -26.60)
>DroEre_CAF1 225912 107 - 1
UUGCAUUUCAGCAAAAUGCAGCCAACUUUUAGGCGCAAAUUGUCGGCAGAUUAUAUUGUCCUGCCUGUCAGGAUAUGUGUGAUUG--UCUAUACCAGCAUACACGUAUG
.(((......((((..(((.(((........))))))..)))).(((((.(((((((((((((.....))))))).)))))))))--)).......))).......... ( -28.30)
>consensus
UUGCAUUUCAACAAAAUGCAGCCAACUUUUAGGCGCAAAUUGUCGGCAGAUUAUAUUGUCCUGCCUGUCAGGAUAUGUGUGAUUG__UCUAUACGAGUAUA______UG
.(((((((.....)))))))(((........)))..............(((((((((((((((.....))))))).))))))))......................... (-16.29 = -17.82 +   1.53)

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 13:23:31 2006