Locus 2010

Sequence ID	3L_DroMel_CAF1
Location	5,521,328 – 5,521,423
Length	95
Max. P	0.898687

overview

Window 7

Location	5,521,328 – 5,521,423
Length	95
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	79.69
Mean single sequence MFE	-21.80
Consensus MFE	-13.29
Energy contribution	-13.05
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-1.93
Structure conservation index	0.61
SVM decision value	0.53
SVM RNA-class probability	0.772362
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5521328 95 + 23771897
UAUGGCUACGCCUUGAGAACCAAAGCGUUCUAUAGUUACUAUCCAAUAUACUCGUA-GAUGCACUGAAGUGGUAGUAUGCUCUAUGAGCCAAUGAA
(((((..((((.(((.....))).)))).)))))................((((((-((.((((((......))))..))))))))))........ ( -22.10)
>DroSec_CAF1 82996 89 + 1
UAUGGCUACGCCUUGAGAACCAAAGCGUUCUAUAGUUACUAUGCACCAUACUAGUA-GU------AACAUACUUGUAUAUACUAUGAGCCAAUGAA
..(((((((((.(((.....))).))))..((((((...((((((.......((((-..------....)))))))))).)))))))))))..... ( -21.51)
>DroSim_CAF1 84739 89 + 1
UAUGGCUACGCCUUGAGAACCAAAGCGUUCUAUAGUUACUAUGCACCAUACUAGUA-GU------AACAUACUUGUAUAUACUAUGAGCCAAUGAA
..(((((((((.(((.....))).))))..((((((...((((((.......((((-..------....)))))))))).)))))))))))..... ( -21.51)
>DroEre_CAF1 83647 75 + 1
CAUGGCUACGCCUUGAGAACCAAAGCGUUCUAUGGGUACCAUCCAGCAUGC---------------------UAGUAUGCUCUAUGAGCCAAUGAA
..(((((..((((..(((((......)))))..))))..(((..((((((.---------------------...))))))..))))))))..... ( -24.00)
>DroYak_CAF1 71912 88 + 1
UAUGGCUACGCCUUGAGAACCAAAGCGUUCUAUGGUUACUAUCCAGUAUGU-AGUAUGU------AGUAU-GUAGUAUGCUCUAUGAGCCAAUGAA
..(((((((((.(((.....))).))))..(((((.((((((..(.(((((-...))))------).)..-))))))....))))))))))..... ( -19.90)
>consensus
UAUGGCUACGCCUUGAGAACCAAAGCGUUCUAUAGUUACUAUCCACCAUACUAGUA_GU______AACAU_CUAGUAUGCUCUAUGAGCCAAUGAA
..(((((((((.(((.....))).))))..(((((.(((...................................)))....))))))))))..... (-13.29 = -13.05 +  -0.24)

alignment

secondary structure

dotplot

Window 8

Location	5,521,328 – 5,521,423
Length	95
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	79.69
Mean single sequence MFE	-22.70
Consensus MFE	-15.32
Energy contribution	-15.28
Covariance contribution	-0.04
Combinations/Pair	1.06
Mean z-score	-2.01
Structure conservation index	0.67
SVM decision value	1.00
SVM RNA-class probability	0.898687
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5521328 95 - 23771897
UUCAUUGGCUCAUAGAGCAUACUACCACUUCAGUGCAUC-UACGAGUAUAUUGGAUAGUAACUAUAGAACGCUUUGGUUCUCAAGGCGUAGCCAUA
.....((((((((((....((((((((.....((((...-.....))))..))).))))).)))).))((((((((.....)))))))).)))).. ( -23.70)
>DroSec_CAF1 82996 89 - 1
UUCAUUGGCUCAUAGUAUAUACAAGUAUGUU------AC-UACUAGUAUGGUGCAUAGUAACUAUAGAACGCUUUGGUUCUCAAGGCGUAGCCAUA
.....(((((....((((((((.((((....------..-)))).)))).))))..............((((((((.....))))))))))))).. ( -24.20)
>DroSim_CAF1 84739 89 - 1
UUCAUUGGCUCAUAGUAUAUACAAGUAUGUU------AC-UACUAGUAUGGUGCAUAGUAACUAUAGAACGCUUUGGUUCUCAAGGCGUAGCCAUA
.....(((((....((((((((.((((....------..-)))).)))).))))..............((((((((.....))))))))))))).. ( -24.20)
>DroEre_CAF1 83647 75 - 1
UUCAUUGGCUCAUAGAGCAUACUA---------------------GCAUGCUGGAUGGUACCCAUAGAACGCUUUGGUUCUCAAGGCGUAGCCAUG
.....((((((((..(((((....---------------------..)))))..)))...........((((((((.....))))))))))))).. ( -23.30)
>DroYak_CAF1 71912 88 - 1
UUCAUUGGCUCAUAGAGCAUACUAC-AUACU------ACAUACU-ACAUACUGGAUAGUAACCAUAGAACGCUUUGGUUCUCAAGGCGUAGCCAUA
.....(((((...............-.....------...((((-((......).)))))........((((((((.....))))))))))))).. ( -18.10)
>consensus
UUCAUUGGCUCAUAGAGCAUACUAC_AUGUU______AC_UACUAGUAUGCUGGAUAGUAACUAUAGAACGCUUUGGUUCUCAAGGCGUAGCCAUA
.....(((((............................................((((...))))...((((((((.....))))))))))))).. (-15.32 = -15.28 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:25 2006