Locus 1370

Sequence ID X_DroMel_CAF1
Location 4,104,717 – 4,104,858
Length 141
Max. P 0.998980
window2178 window2179 window2180

overview

Window 8

Location 4,104,717 – 4,104,825
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 71.30
Mean single sequence MFE -36.55
Consensus MFE -22.54
Energy contribution -22.35
Covariance contribution -0.19
Combinations/Pair 1.17
Mean z-score -2.32
Structure conservation index 0.62
SVM decision value 2.39
SVM RNA-class probability 0.993337
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4104717 108 + 22224390
UUCUGCGCUCCACG----------CCGCUCCCGUUGUCCUUGCAGACAAUUAAGCAAGGACAAUGCG-CCGCACAGGCUUUGUAAAAGCUCAUGCAUGCACACUGGCAUCGCAGCUCU-G
..(((((......(----------((.....((((((((((((..........)))))))))))).(-(.(((..(((((.....)))))..)))..)).....)))..)))))....-. ( -37.70)
>DroVir_CAF1 189857 100 + 1
-GCUGCCUGCCUAA---CU--G--CCUG-CCAGUUGUCCUUGCAGACAAUUAAGCAGGAACAAUGCAGCAACAGAAGCUUUACAAAUGCUCAUGCAUGC-CACAGCGAGU----------
-(((((((((.(((---.(--(--.(((-(.((.....)).)))).)).))).)))))......((((((...((.((.........)))).))).)))-..))))....---------- ( -29.30)
>DroSec_CAF1 116598 108 + 1
UUCUGCGCUCCACG----------CCGCUCCCGUUGUCCUUGCAGACAAUUAAGCAAGGACAAUGCG-CCGCACAGGCUUUGUAAAAGCUCAUGCAUGCACACUGGCAUCGCAGGUCU-G
.((((((......(----------((.....((((((((((((..........)))))))))))).(-(.(((..(((((.....)))))..)))..)).....)))..))))))...-. ( -39.00)
>DroEre_CAF1 122869 118 + 1
CUCUGCGCUCCCUGACACUCCACUCUGCUCCCGUUGUCCUUGCAGACAAUUAAGCAGGGACAAUGCG-CCGCACAGGCUUUGUAAAAGCUCAUGCAUGCACACUGGCAGCGCUGGUCU-G
.((.(((((.((.(.................((((((((((((..........)))))))))))).(-(.(((..(((((.....)))))..)))..))...).)).))))).))...-. ( -38.80)
>DroMoj_CAF1 176863 102 + 1
-GCUGCCUGUC------CU--G--CCUC-UGCCUUGUCCUUGCACACAAUUAGGCAGGAACAAUGCAGCAGCACAAGCUUUGCAAAUGCUCAUGCAUGC-CACAGCGAGUA--ACU---G
-(((((.((((------((--(--(((.-....((((........))))..))))))).)))..)))))...((..(((.((...((((....))))..-)).)))..)).--...---. ( -32.90)
>DroAna_CAF1 145509 119 + 1
UGCUCCUGCUCCUGUAACUCCAGCUAGUGCCUGUUGUCCUUGCAGACAAUUAAGCAAGGACAAUGCG-CUGCACUGGCUUUGUAAAAGCUCAUGCAUGCAGACUGCCAGUCCUUCUAUGG
.((....))..........(((((.(((((..(((((((((((..........))))))))))))))-))))((((((((((((...((....)).))))))..)))))).......))) ( -41.60)
>consensus
UGCUGCGCUCCACG___CU_____CCGCUCCCGUUGUCCUUGCAGACAAUUAAGCAAGGACAAUGCG_CCGCACAGGCUUUGUAAAAGCUCAUGCAUGCACACUGCCAGCGC_GCUCU_G
.((.............................(((((((((((..........)))))))))))(((...(((..(((((.....)))))..))).))).....)).............. (-22.54 = -22.35 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,104,717 – 4,104,825
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 71.30
Mean single sequence MFE -45.02
Consensus MFE -18.86
Energy contribution -19.28
Covariance contribution 0.42
Combinations/Pair 1.25
Mean z-score -3.23
Structure conservation index 0.42
SVM decision value 3.31
SVM RNA-class probability 0.998980
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4104717 108 - 22224390
C-AGAGCUGCGAUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG-CGCAUUGUCCUUGCUUAAUUGUCUGCAAGGACAACGGGAGCGG----------CGUGGAGCGCAGAA
.-....(((((((((((((((((.(((((..((((.....))))..))))))-))))))((((((((..........)))))))).........))----------)))....))))).. ( -46.90)
>DroVir_CAF1 189857 100 - 1
----------ACUCGCUGUG-GCAUGCAUGAGCAUUUGUAAAGCUUCUGUUGCUGCAUUGUUCCUGCUUAAUUGUCUGCAAGGACAACUGG-CAGG--C--AG---UUAGGCAGGCAGC-
----------......((..-(((.(((.((((.........)))).))))))..))..((((((((((((((((((((.((.....)).)-))))--)--))---))))))))).)))- ( -44.80)
>DroSec_CAF1 116598 108 - 1
C-AGACCUGCGAUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG-CGCAUUGUCCUUGCUUAAUUGUCUGCAAGGACAACGGGAGCGG----------CGUGGAGCGCAGAA
.-....(((((((((((((((((.(((((..((((.....))))..))))))-))))))((((((((..........)))))))).........))----------)))....))))).. ( -47.00)
>DroEre_CAF1 122869 118 - 1
C-AGACCAGCGCUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG-CGCAUUGUCCCUGCUUAAUUGUCUGCAAGGACAACGGGAGCAGAGUGGAGUGUCAGGGAGCGCAGAG
.-......(((((.(((((((((.(((((..((((.....))))..))))))-)))))).(((((((((..((((((....))))))...))))))...)))......)).))))).... ( -50.30)
>DroMoj_CAF1 176863 102 - 1
C---AGU--UACUCGCUGUG-GCAUGCAUGAGCAUUUGCAAAGCUUGUGCUGCUGCAUUGUUCCUGCCUAAUUGUGUGCAAGGACAAGGCA-GAGG--C--AG------GACAGGCAGC-
.---.((--(((.....)))-))..(((..(((.........)))..))).(((((.((((.(((((((..((((.(....).))))....-.)))--)--))------))))))))))- ( -41.30)
>DroAna_CAF1 145509 119 - 1
CCAUAGAAGGACUGGCAGUCUGCAUGCAUGAGCUUUUACAAAGCCAGUGCAG-CGCAUUGUCCUUGCUUAAUUGUCUGCAAGGACAACAGGCACUAGCUGGAGUUACAGGAGCAGGAGCA
((......((((.....))))..........((((((..((..(((((..((-.((.((((((((((..........))))))))))...)).)).)))))..))..)))))).)).... ( -39.80)
>consensus
C_AGAGC_GCACUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG_CGCAUUGUCCCUGCUUAAUUGUCUGCAAGGACAACGGGAGCGG_____AG___CAGGGAGCGCAGAA
........((((.....))))((.(((((..((((.....))))..)))))...)).((((((.(((..........))).))))))................................. (-18.86 = -19.28 +   0.42)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,104,747 – 4,104,858
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 67.89
Mean single sequence MFE -32.10
Consensus MFE -13.09
Energy contribution -12.87
Covariance contribution -0.22
Combinations/Pair 1.25
Mean z-score -2.22
Structure conservation index 0.41
SVM decision value 1.67
SVM RNA-class probability 0.971319
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4104747 111 - 22224390
-------AUGUGAAUUUAUUUUCUUAGCGUGUAGAUUUUGC-AGAGCUGCGAUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG-CGCAUUGUCCUUGCUUAAUUGUCUGCA
-------....((((((((...........))))))))(((-(((...((((.(.((((((((.(((((..((((.....))))..))))))-))))))).).)))).......)))))) ( -34.60)
>DroGri_CAF1 153765 87 - 1
---------------------------CAGGUGGGUGUUGCAAUAGU--UACUCGCAGUG-GCAUGCAUGAGCAUUUAUAAGACUUGUG---CUGCAUUGUUCCUGCUUAAUUGUCUGCA
---------------------------...........(((((((((--((...((((..-(((((((...((((...........)))---))))).)))..)))).))))))).)))) ( -23.00)
>DroSec_CAF1 116628 104 - 1
--------------CUAAUUUUCUUCGCGUGUAGAUUUUGC-AGACCUGCGAUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG-CGCAUUGUCCUUGCUUAAUUGUCUGCA
--------------........................(((-((((..((((.(.((((((((.(((((..((((.....))))..))))))-))))))).).))))......))))))) ( -35.80)
>DroEre_CAF1 122909 118 - 1
AUAUAAUAUGUGAAUCCGUUUUCUUCAUGUGUAGAUUUUGC-AGACCAGCGCUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG-CGCAUUGUCCCUGCUUAAUUGUCUGCA
.....(((((((((.........)))))))))......(((-((((.((((..(.((((((((.(((((..((((.....))))..))))))-))))))).)..)))).....))))))) ( -39.50)
>DroMoj_CAF1 176891 87 - 1
---------------------------CAGGGAACUGCUGC---AGU--UACUCGCUGUG-GCAUGCAUGAGCAUUUGCAAAGCUUGUGCUGCUGCAUUGUUCCUGCCUAAUUGUGUGCA
---------------------------..((((((.((..(---(((--.....))))..-))(((((..(((((..((...))..)))))..))))).))))))(((.......).)). ( -32.00)
>DroAna_CAF1 145549 104 - 1
--------------AUAAUUUUUUUCA-GUGCAACCAUUGCCAUAGAAGGACUGGCAGUCUGCAUGCAUGAGCUUUUACAAAGCCAGUGCAG-CGCAUUGUCCUUGCUUAAUUGUCUGCA
--------------...........((-((((....(((((((.........)))))))..((.(((((..((((.....))))..))))))-)))))))....(((..........))) ( -27.70)
>consensus
_______________U_AUUUUCUUC_CGUGUAGAUUUUGC_AGAGC_GCACUGCCAGUGUGCAUGCAUGAGCUUUUACAAAGCCUGUGCGG_CGCAUUGUCCCUGCUUAAUUGUCUGCA
................................................((((.....))))(((..(((((((....((((.((..........)).))))....)))))..))..))). (-13.09 = -12.87 +  -0.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:34 2006