Locus 6440

Sequence ID X_DroMel_CAF1
Location 16,140,135 – 16,140,279
Length 144
Max. P 0.944748
window10511 window10512

overview

Window 1

Location 16,140,135 – 16,140,243
Length 108
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 69.41
Mean single sequence MFE -26.09
Consensus MFE -16.10
Energy contribution -16.52
Covariance contribution 0.42
Combinations/Pair 1.29
Mean z-score -1.21
Structure conservation index 0.62
SVM decision value 0.31
SVM RNA-class probability 0.684837
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16140135 108 - 22224390
-AAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCCCAUUCCCCAUUCCUACGCAAUGCACGCUCUCUAUCCUCUAGCCGGAACCG------CUC
-............((((.(((((((.....(((....)))..(((((..................))))).)))))))..)))).....(((.......)))....------... ( -24.07)
>DroSec_CAF1 2800 108 - 1
-AAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCCAUGCCCCCAUUCCUACGCAAUGCACGCCCUAUAUCCUCUAGCCGGAACCG------CUC
-............((((.(((((((.....(((....)))..(((((..((.......)).....))))).)))))))..)))).....(((.......)))....------... ( -28.60)
>DroSim_CAF1 339 99 - 1
-AAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCCAUGGCCCCAUUCCUAC---------CCUCUCUAUCCUCUAGCCGGAACCG------CUC
-............((((......))))...((....((((((.((.........)).)))))).........---------........(((.......)))...)------).. ( -23.90)
>DroEre_CAF1 3091 93 - 1
-AAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCUAAGAAAGUGCUCCCC--------ACUCCUAUGCAAUGUAC-------AAUGUCUAUCCGGAGCCG------CUC
-....(((((((.((((......))))...(((....)))...)))))))......--------.((((((.(((......-------..))).))...))))...------... ( -24.70)
>DroWil_CAF1 10580 102 - 1
UUAUUCACUUUCGCACGACAUUGUCCCGU-GCU----GGCU-----GGUGGUCGCACGGGACCAAUUACUGAUCAUCGUUCGAUGUCCA---UUUAGCCGGAACCUCCACCAGUU
............(((((.........)))-)).----((((-----((((((((.((((((.((.....)).)).)))).)))..(((.---.......)))....))))))))) ( -29.40)
>DroYak_CAF1 354 91 - 1
-AAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGAAAGUGCUCCCC--------AUGUCUACGCAAUG--C-------AUUGUCUAUCCGGAGCCG------GUU
-.....((((((.((((......))))...(((....)))...))))))(((((..--------..(..((.((((..--.-------.)))).))..))))))..------... ( -25.90)
>consensus
_AAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCC__G_CCCCAUUCCUACGCAAUG_ACGCUCUCUAUCCUCUAGCCGGAACCG______CUC
.....(((((((.((((......))))...(((....)))...)))))))................................................................. (-16.10 = -16.52 +   0.42)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,140,164 – 16,140,279
Length 115
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 76.70
Mean single sequence MFE -26.30
Consensus MFE -18.03
Energy contribution -19.20
Covariance contribution 1.17
Combinations/Pair 1.14
Mean z-score -1.81
Structure conservation index 0.69
SVM decision value 1.35
SVM RNA-class probability 0.944748
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16140164 115 - 22224390
GCAAGGUUAAAAAC-UUGACCUCAGACAUCACAUUCGAAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCCCAUUCCCCAUUCCUACGCAAUGCA
((((((((((....-)))))))...................(((((((.((((......))))...(((....)))...)))))))..........................))). ( -28.70)
>DroSec_CAF1 2829 115 - 1
GCAAGGUUAAAAAC-UUGACCUCAGACAUCACAUUCGAAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCCAUGCCCCCAUUCCUACGCAAUGCA
((.(((((((....-)))))))..............(((......)))..))(.(((((((.....(((....)))..(((((..((.......)).....))))).)))))))). ( -29.20)
>DroSim_CAF1 367 107 - 1
GCAAGGUUAAAAAC-UUGACCUCAGACAUCACAUUCGAAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCCAUGGCCCCAUUCCUAC--------
((.(((((((....-)))))))..............(((......))).((((......))))...))....((((((.((.........)).)))))).........-------- ( -28.50)
>DroEre_CAF1 3113 108 - 1
UCAAGGUUAACAACGUCGACCUCAGACAUCACAUUUUAAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCUAAGAAAGUGCUCCCC--------ACUCCUAUGCAAUGUA
...((((..((...))..))))...((((..(((.......(((((((.((((......))))...(((....)))...)))))))......--------......)))..)))). ( -26.91)
>DroYak_CAF1 376 105 - 1
UCAAGGUUACCAAC-UUGACCUCAGACAUCACAUUUUAAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGAAAGUGCUCCCC--------AUGUCUACGCAAUG--
...((((((.....-.)))))).((((((............(((((((.((((......))))...(((....)))...)))))))......--------))))))........-- ( -28.07)
>DroAna_CAF1 20224 94 - 1
UCAAGGUCAAUAAC-UUAACCUUGGACAUAACAAAUAAAUUCACUUUCAAGCGACAUUGGCCC--UAUUUAUAGGACAAUGCAGGGAUU-------------------GCAAUGCG
(((((((.((....-)).))))))).........................(((((((((..((--((....)))).)))))......))-------------------))...... ( -16.40)
>consensus
GCAAGGUUAAAAAC_UUGACCUCAGACAUCACAUUCGAAUUCACUUUCAGGCGACAUUGCGCCACCGCCCACGGGCCAAGGAAGUGCUCCCC________AUUCCUACGCAAUGCA
...(((((((.....)))))))...................(((((((.((((......))))...(((....)))...))))))).............................. (-18.03 = -19.20 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:46 2006