Locus 1436

Sequence ID X_DroMel_CAF1
Location 4,326,770 – 4,326,860
Length 90
Max. P 0.569431
window2293 window2294

overview

Window 3

Location 4,326,770 – 4,326,860
Length 90
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 76.76
Mean single sequence MFE -18.18
Consensus MFE -10.15
Energy contribution -12.02
Covariance contribution 1.86
Combinations/Pair 1.07
Mean z-score -1.59
Structure conservation index 0.56
SVM decision value 0.07
SVM RNA-class probability 0.569431
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4326770 90 + 22224390
--U-GGCCAAAGCGAGCAGACACUAAAUUACACUAACGUGUUUUGAAUUAUUUUUCAAUUUCAUUGUCAGCCGCAGACAGA-CU--------ACGGACGUAC
--.-.......(((.((.((((.......((((....)))).(((((......)))))......)))).))))).......-(.--------...)...... ( -18.50)
>DroVir_CAF1 167889 75 + 1
UAC-GGCCA----GUGCAGACACUAAAUUACACUAACGUGUUUUGAAUUAUUUUUCAAUUUCAUUGUCGGCC-CAGACACA---------------------
...-(((((----(((....)))).....((((....)))).(((((......)))))..........))))-........--------------------- ( -16.90)
>DroPse_CAF1 133751 95 + 1
--AGGCCCA----GUGCAGACACUAAAUUACACUAACGUGUUUUGAAUUAUUUUUCAAUUUCAUUGUCAGCCCCAGACAUAGCUAUAGAGACACGGCCGUA-
--.((((.(----(((....)))).............((((((((((......)))........((((.......))))........)))))))))))...- ( -21.70)
>DroGri_CAF1 133864 75 + 1
UAC-GGACA----GUGCAGACACUAAAUUACACUAACGUGUUUUGAAUUAUUUUUCAAUUUCAUUGUCGGCC-CAGACACA---------------------
..(-.((((----(((.(((.........((((....)))).(((((......))))))))))))))).)..-........--------------------- ( -15.70)
>DroAna_CAF1 134077 75 + 1
-------------GCGCAGGCACUAAAUUACACUAACGUGUUUUGAAUUAUUUUUCAAUUUCAUUGUCAGCCGCAGACAUA-C-------------ACGCCG
-------------.....(((........((((....)))).(((((......)))))......((((.......))))..-.-------------..))). ( -14.60)
>DroPer_CAF1 135535 95 + 1
--AGGCCCA----GUGCAGACACUAAAUUACACUAACGUGUUUUGAAUUAUUUUUCAAUUUCAUUGUCAGCCCCAGACAUAGCCAUAGAGACACGGCCGUA-
--.((((.(----(((....)))).............((((((((((......)))........((((.......))))........)))))))))))...- ( -21.70)
>consensus
__A_GGCCA____GUGCAGACACUAAAUUACACUAACGUGUUUUGAAUUAUUUUUCAAUUUCAUUGUCAGCC_CAGACAUA_C______________CGUA_
...............((.((((.......((((....)))).(((((......)))))......)))).))............................... (-10.15 = -12.02 +   1.86)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,326,770 – 4,326,860
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 76.76
Mean single sequence MFE -20.50
Consensus MFE -13.28
Energy contribution -13.45
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.20
Structure conservation index 0.65
SVM decision value 0.06
SVM RNA-class probability 0.561935
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4326770 90 - 22224390
GUACGUCCGU--------AG-UCUGUCUGCGGCUGACAAUGAAAUUGAAAAAUAAUUCAAAACACGUUAGUGUAAUUUAGUGUCUGCUCGCUUUGGCC-A--
.(((....))--------).-...(((.(((((.((((.((((.(((((......))))).((((....))))..)))).)))).)).)))...))).-.-- ( -21.80)
>DroVir_CAF1 167889 75 - 1
---------------------UGUGUCUG-GGCCGACAAUGAAAUUGAAAAAUAAUUCAAAACACGUUAGUGUAAUUUAGUGUCUGCAC----UGGCC-GUA
---------------------...(.(..-(((.((((.((((.(((((......))))).((((....))))..)))).)))).)).)----..).)-... ( -17.60)
>DroPse_CAF1 133751 95 - 1
-UACGGCCGUGUCUCUAUAGCUAUGUCUGGGGCUGACAAUGAAAUUGAAAAAUAAUUCAAAACACGUUAGUGUAAUUUAGUGUCUGCAC----UGGGCCU--
-...((((((((......((((........))))((((.((((.(((((......))))).((((....))))..)))).)))).))))----..)))).-- ( -24.50)
>DroGri_CAF1 133864 75 - 1
---------------------UGUGUCUG-GGCCGACAAUGAAAUUGAAAAAUAAUUCAAAACACGUUAGUGUAAUUUAGUGUCUGCAC----UGUCC-GUA
---------------------...(..((-(((.((((.((((.(((((......))))).((((....))))..)))).)))).)).)----))..)-... ( -15.00)
>DroAna_CAF1 134077 75 - 1
CGGCGU-------------G-UAUGUCUGCGGCUGACAAUGAAAUUGAAAAAUAAUUCAAAACACGUUAGUGUAAUUUAGUGCCUGCGC-------------
.(((((-------------(-(.((((.......))))......(((((......))))).))))))).(((((..........)))))------------- ( -15.10)
>DroPer_CAF1 135535 95 - 1
-UACGGCCGUGUCUCUAUGGCUAUGUCUGGGGCUGACAAUGAAAUUGAAAAAUAAUUCAAAACACGUUAGUGUAAUUUAGUGUCUGCAC----UGGGCCU--
-...(((((((....)))))))..(((..(.((.((((.((((.(((((......))))).((((....))))..)))).)))).)).)----..)))..-- ( -29.00)
>consensus
_UACG______________G_UAUGUCUG_GGCUGACAAUGAAAUUGAAAAAUAAUUCAAAACACGUUAGUGUAAUUUAGUGUCUGCAC____UGGCC_G__
...............................((.((((.((((.(((((......))))).((((....))))..)))).)))).))............... (-13.28 = -13.45 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:26 2006