Locus 7830

Sequence ID	3R_DroMel_CAF1
Location	20,981,131 – 20,981,242
Length	111
Max. P	0.874937

overview

Window 2

Location	20,981,131 – 20,981,242
Length	111
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	69.23
Mean single sequence MFE	-33.23
Consensus MFE	-15.06
Energy contribution	-16.78
Covariance contribution	1.72
Combinations/Pair	1.26
Mean z-score	-1.73
Structure conservation index	0.45
SVM decision value	0.51
SVM RNA-class probability	0.762278
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20981131 111 + 27905053
UAC-CAUGUGCAGAGCCCGCAUGCAU--GUGCAU-UGGGUUCCCCGCAUGCACAUGCCCAUGCCCAUUUAUAACUAAGUACCUACUUAUGGACCCCGCUGGCGGGAG-GCUGGCAA
...-....(((..((((.((((((((--((((((-((((...)))).))))))))))..))))(((........(((((....))))))))..((((....)))).)-))).))). ( -42.70)
>DroPse_CAF1 34847 101 + 1
AAG-CAGCUG-AAUGCUUGAAUAUACU-GUACAUUCAAGAU------UU------ACACAUUCCCCUUUCUAAGUAAGUACCUACUUAUGAACCCCGGUGGCGGAAAAUCUGGCAG
..(-(.(.((-(((.(((((((.....-....)))))))))------))------))...((((((..((((((((......)))))).))((....)))).))))......)).. ( -19.70)
>DroSec_CAF1 21139 111 + 1
UAC-CAUGUGCGGAGCCCGCAUGCAU--GUGCAU-UGGGGUUCCCGCAUGCACAUGCCCAUGCCCAUUUAUAACUAAGUACCUACUUAUGGACCCCGCUGGCGGGAG-GCCGGCAA
...-...((((((...))))))((((--((((((-((((...)))).))))))))))...((((..........(((((....))))).((.(((((....)))).)-.)))))). ( -44.90)
>DroEre_CAF1 23544 106 + 1
UAC-CAUGUGCAGUGCCCGCAUAUAUUGGGGUAU-UGGGGUCCC-CCAUGCACA------UGCCCAUUUAUAACUAAGUACCUACUUAUGGACCCCGCUGGCGGGAG-GCCGGCAA
...-((((((((((((((.((.....))))))))-((((....)-)))))))))------)).(((........(((((....)))))))).....((((((.....-)))))).. ( -40.70)
>DroYak_CAF1 22623 89 + 1
CACACAUGUGCAGU-------------------U-UGAGGUCCUUGCAUGCACA------UGCCCAUUUAUAACUAAGUACCUACUUAUGGACCCCGCUGGCGGGAG-GCCGGCAA
....((((((((((-------------------.-.(.....)..)).))))))------)).(((........(((((....)))))))).....((((((.....-)))))).. ( -26.50)
>DroPer_CAF1 33568 101 + 1
AAG-CAGCUG-ACUGCUUGAAUAUACU-GUACAUUUAAGAU------UU------GCACAUGCCCCUUUCUAAGUAAGUACCUACUUAUGAACCCCGGUGGCGGAAAAUCUGGCAG
(((-(((...-.)))))).......((-((.......((((------((------.....((((((.(((((((((......)))))).)))....)).))))..)))))).)))) ( -24.90)
>consensus
UAC_CAUGUGCAGUGCCCGCAUAUAU__GUGCAU_UGAGGUCCC_GCAUGCACA_GC_CAUGCCCAUUUAUAACUAAGUACCUACUUAUGGACCCCGCUGGCGGGAG_GCCGGCAA
.......(((((...((((.(((((....))))).)))).........))))).......((((..........(((((....))))).....((((....))))......)))). (-15.06 = -16.78 +   1.72)

alignment

secondary structure

dotplot

Window 3

Location	20,981,131 – 20,981,242
Length	111
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	69.23
Mean single sequence MFE	-36.35
Consensus MFE	-14.70
Energy contribution	-14.65
Covariance contribution	-0.05
Combinations/Pair	1.27
Mean z-score	-1.96
Structure conservation index	0.40
SVM decision value	0.89
SVM RNA-class probability	0.874937
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20981131 111 - 27905053
UUGCCAGC-CUCCCGCCAGCGGGGUCCAUAAGUAGGUACUUAGUUAUAAAUGGGCAUGGGCAUGUGCAUGCGGGGAACCCA-AUGCAC--AUGCAUGCGGGCUCUGCACAUG-GUA
.(((((((-.....))..(((((((((.(((((....)))))...........((((..((((((((((..(((...))).-))))))--)))))))))))))))))...))-))) ( -47.50)
>DroPse_CAF1 34847 101 - 1
CUGCCAGAUUUUCCGCCACCGGGGUUCAUAAGUAGGUACUUACUUAGAAAGGGGAAUGUGU------AA------AUCUUGAAUGUAC-AGUAUAUUCAAGCAUU-CAGCUG-CUU
..((((.(((..((.((....)).(((.(((((((....)))))))))).))..))).)).------..------..((((((((((.-..))))))))))....-..))..-... ( -24.60)
>DroSec_CAF1 21139 111 - 1
UUGCCGGC-CUCCCGCCAGCGGGGUCCAUAAGUAGGUACUUAGUUAUAAAUGGGCAUGGGCAUGUGCAUGCGGGAACCCCA-AUGCAC--AUGCAUGCGGGCUCCGCACAUG-GUA
.(((((((-.....))).(((((((((.(((((....)))))...........((((..((((((((((..(((...))).-))))))--)))))))))))))))))....)-))) ( -53.00)
>DroEre_CAF1 23544 106 - 1
UUGCCGGC-CUCCCGCCAGCGGGGUCCAUAAGUAGGUACUUAGUUAUAAAUGGGCA------UGUGCAUGG-GGGACCCCA-AUACCCCAAUAUAUGCGGGCACUGCACAUG-GUA
.(((((((-.....))).((((.((((.(((((....)))))...........(((------((((..(((-((.......-...))))).))))))))))).))))....)-))) ( -38.70)
>DroYak_CAF1 22623 89 - 1
UUGCCGGC-CUCCCGCCAGCGGGGUCCAUAAGUAGGUACUUAGUUAUAAAUGGGCA------UGUGCAUGCAAGGACCUCA-A-------------------ACUGCACAUGUGUG
..((.(((-.....))).))(((((((.(((((....)))))...........(((------(....))))..))))))).-.-------------------...(((....))). ( -27.60)
>DroPer_CAF1 33568 101 - 1
CUGCCAGAUUUUCCGCCACCGGGGUUCAUAAGUAGGUACUUACUUAGAAAGGGGCAUGUGC------AA------AUCUUAAAUGUAC-AGUAUAUUCAAGCAGU-CAGCUG-CUU
.(((..........(((.((....(((.(((((((....)))))))))).))))).(((((------(.------........)))))-)))).....((((((.-...)))-))) ( -26.70)
>consensus
UUGCCAGC_CUCCCGCCAGCGGGGUCCAUAAGUAGGUACUUAGUUAUAAAUGGGCAUG_GC_UGUGCAUGC_GGGACCCCA_AUGCAC__AUAUAUGCGGGCACUGCACAUG_GUA
.((((.....(((((....)))))....(((((....)))))..........)))).....................(((..(((((....)))))..)))............... (-14.70 = -14.65 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:50 2006