Locus 6700

Sequence ID	3R_DroMel_CAF1
Location	17,631,617 – 17,631,742
Length	125
Max. P	0.962486

overview

Window 9

Location	17,631,617 – 17,631,710
Length	93
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	82.51
Mean single sequence MFE	-31.40
Consensus MFE	-22.37
Energy contribution	-22.57
Covariance contribution	0.20
Combinations/Pair	1.05
Mean z-score	-2.84
Structure conservation index	0.71
SVM decision value	0.93
SVM RNA-class probability	0.883693
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17631617 93 + 27905053
-----------AGCGAAACAGAAC-UUGGUGGGCUGGCAGGCGAAGGCGGAACGGG--GCGUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCU
-----------..((...(((..(-.....)..)))....((....))....))((--((.((((..((((((((((((....)).))))))))))..)))).)))) ( -30.10)
>DroSec_CAF1 26537 93 + 1
-----------AGCGAAACAGAAC-UUGGUGGGCUGGCAGGCGAAGGCGGAGCAGG--GCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGUCU
-----------.((....(((..(-.....)..)))....((....))...)).((--(((((((..((((((((((((....)).))))))))))..))))))))) ( -33.10)
>DroSim_CAF1 26363 93 + 1
-----------AGCGAAACAGAAC-UUGGUGGGCUGGCAGGCGAAGGCGGAGUAGG--GCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCU
-----------.((....(((..(-.....)..)))....((....))...)).((--(((((((..((((((((((((....)).))))))))))..))))))))) ( -33.50)
>DroEre_CAF1 28353 94 + 1
----------AAGCGAAACAGAAG-UUGGUGGGCUGGCAGGCGGAGGCGGAACAGG--GCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCU
----------..............-....((..(((.(.......).)))..))((--(((((((..((((((((((((....)).))))))))))..))))))))) ( -31.00)
>DroYak_CAF1 30884 91 + 1
CCGAAACCGAAACCGAAACAGAA--------------CAGGCGAAGGCGGAACGGG--GCUGUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCU
......(((...((....(....--------------..)((....))))..)))(--(((.(((..((((((((((((....)).))))))))))..))).)))). ( -28.50)
>DroAna_CAF1 34918 94 + 1
-----------A--AACACAAAACCUUCGGGGAGUCGGCGGCGCGGGCGGAACGGAGCGCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCU
-----------.--..........(((((....(((.((...)).)))....))))).(((((((..((((((((((((....)).))))))))))..))))))).. ( -32.20)
>consensus
___________AGCGAAACAGAAC_UUGGUGGGCUGGCAGGCGAAGGCGGAACAGG__GCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCU
........................................((....))..........(((((((..((((((((((((....)).))))))))))..))))))).. (-22.37 = -22.57 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	17,631,645 – 17,631,742
Length	97
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	81.21
Mean single sequence MFE	-26.30
Consensus MFE	-19.44
Energy contribution	-19.92
Covariance contribution	0.47
Combinations/Pair	1.10
Mean z-score	-3.74
Structure conservation index	0.74
SVM decision value	1.54
SVM RNA-class probability	0.962486
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17631645 97 + 27905053
GCGAAGGCGGA--ACGGGGCGUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCUUAAAAAUAAAAAUAAAAACGGCGG-CAG-GGGAG
((....))...--..(((((.((((..((((((((((((....)).))))))))))..)))).))))).......................-...-..... ( -26.00)
>DroPse_CAF1 22801 82 + 1
AG--AUACGGAGAGGAGGGCU-UUUAUCUAAACGGCUCCAAACAGCAAUCGUUUGGGGAAAAAGCCUUAAAAAUGUAAAUAAAAA----------------
..--.((((......((((((-(((.(((((((((((......)))...))))))))..))))))))).....))))........---------------- ( -22.90)
>DroSec_CAF1 26565 99 + 1
GCGAAGGCGGA--GCAGGGCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGUCUUAAAAAUAAAAAUAAAAACGGCGGGCAGGGGGAG
((....))...--((((((((((((..((((((((((((....)).))))))))))..)))))))))).................(....)))........ ( -27.70)
>DroSim_CAF1 26391 97 + 1
GCGAAGGCGGA--GUAGGGCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCUUAAAAAUAAAAAUAAAAACGGCGG-CAG-GGGAG
((....))...--.(((((((((((..((((((((((((....)).))))))))))..)))))))))))......................-...-..... ( -31.50)
>DroYak_CAF1 30910 97 + 1
GCGAAGGCGGA--ACGGGGCUGUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCUUAAAAAUAAAAAUAAAAACGGCGG-CAG-GGGGA
((....))...--..((((((.(((..((((((((((((....)).))))))))))..))).)))))).......................-...-..... ( -26.60)
>DroPer_CAF1 17895 80 + 1
AG--AUACGGA--GGAGGGCU-UUUAUCUAAACGGCUCCAAACAGCAAUCGUUUGGGGAAAAAGCCUUAAAAAUGUAAAUAAAAA----------------
..--.((((..--..((((((-(((.(((((((((((......)))...))))))))..))))))))).....))))........---------------- ( -23.10)
>consensus
GCGAAGGCGGA__GCAGGGCUUUUUAUCUAAACGGUUCCAAAAGGCAAUCGUUUGGGGAAAAAGCCUUAAAAAUAAAAAUAAAAACGGCGG_CAG_GGGAG
...............((((((.(((..((((((((((((....)).))))))))))..))).))))))................................. (-19.44 = -19.92 +   0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:53 2006