Locus 9662

Sequence ID	3R_DroMel_CAF1
Location	25,548,789 – 25,548,915
Length	126
Max. P	0.852244

overview

Window 2

Location	25,548,789 – 25,548,891
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	84.61
Mean single sequence MFE	-26.46
Consensus MFE	-17.48
Energy contribution	-17.28
Covariance contribution	-0.20
Combinations/Pair	1.18
Mean z-score	-1.79
Structure conservation index	0.66
SVM decision value	0.06
SVM RNA-class probability	0.565048
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25548789 102 + 27905053
AACAGUUAUGUUGCUAGCAGACGUUGUCAAAACAAGUUGGCAGUUUUUACAGCUCCAUGUUAACUCAAUGUUAGCUAACAUACGACACAAGUCAGCUGUUCC
(((((((..((((.((((.(((((((....((((...(((.((((.....)))))))))))....))))))).)))).)).))(((....)))))))))).. ( -27.80)
>DroSec_CAF1 32404 102 + 1
AACAGCUAUGUUCCUAUCAGGCGUUCUCAAAGCAAGUUGGCAGCUUCUACAGCUCCAUGUUAACUUAAUGUUAGCUAACAUAAGACACAAGUCAGCUGUUCC
((((((((((((........((.........))....(((.((((.....))))))).((((((.....)))))).)))))).(((....))).)))))).. ( -24.70)
>DroSim_CAF1 32668 102 + 1
AACAGCUAUGUUGCUAUCAGGCGUUCUCAAAGCAAGUUGGCAGCUCCUACAGCUCCAUGUUAACUCAAUGUUAGCUAACAUAAGACACAAGUCAGCUGUUCC
((((((((((((((((.((.((.........)).(((((((((((.....)))....))))))))...)).)))).)))))).(((....))).)))))).. ( -27.70)
>DroEre_CAF1 33185 101 + 1
AACAGUUAUGUUGCUAGCCUGCAUUCGCAAAACAAGUUGGCAUCUUCAACAGCUGCCUGUUAAGUAAAUGUUAGGUAACAUAG-GCACAAGUCAGCUGUUCC
(((((((((((((((.....(((((..(..((((....((((.((.....)).))))))))..)..)))))..)))))))))(-((....))).)))))).. ( -27.30)
>DroYak_CAF1 36168 101 + 1
AACAGUUAUGUUGCUAGCAUGCGUUCGCGAGGCAAGUUGGCAUCUUCGGCACCGCCCUGUUAAGUCAAUGUUAGGUAACAUACCGCAC-AGUCAGCUGUUUU
....(.((((((((((((((......(((.(((..(((((.....)))))...))).))).......)))))).)))))))).)..((-((....))))... ( -24.82)
>consensus
AACAGUUAUGUUGCUAGCAGGCGUUCUCAAAGCAAGUUGGCAGCUUCUACAGCUCCAUGUUAACUCAAUGUUAGCUAACAUAAGACACAAGUCAGCUGUUCC
((((((((((((((((....(((((.....(((((((((..........)))))...)))).....)))))))).))))))).(((....))).)))))).. (-17.48 = -17.28 +  -0.20)

alignment

secondary structure

dotplot

Window 3

Location	25,548,818 – 25,548,915
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	86.91
Mean single sequence MFE	-26.12
Consensus MFE	-17.04
Energy contribution	-17.28
Covariance contribution	0.24
Combinations/Pair	1.14
Mean z-score	-2.84
Structure conservation index	0.65
SVM decision value	0.79
SVM RNA-class probability	0.852244
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25548818 97 + 27905053
AAACAAGUUGGCAGUUUUUACAGCUCCAUGUUAACUCAAUGUUAGCUAACAUACGACACAAGUCAGCUGUUCCGCGCCGACAGCAACAGCAACAAAA
......((((((.((....((((((....((((((.....))))))........(((....)))))))))...)))))))).((....))....... ( -27.20)
>DroSec_CAF1 32433 97 + 1
AAGCAAGUUGGCAGCUUCUACAGCUCCAUGUUAACUUAAUGUUAGCUAACAUAAGACACAAGUCAGCUGUUCCGCGCCGACAGCAACAGCAACAAAA
......((((((.((....((((((....((((((.....))))))........(((....)))))))))...)))))))).((....))....... ( -28.70)
>DroSim_CAF1 32697 97 + 1
AAGCAAGUUGGCAGCUCCUACAGCUCCAUGUUAACUCAAUGUUAGCUAACAUAAGACACAAGUCAGCUGUUCCGCGCCGACAGCAACAGCAACAAAA
......((((((.((....((((((....((((((.....))))))........(((....)))))))))...)))))))).((....))....... ( -28.70)
>DroEre_CAF1 33214 96 + 1
AAACAAGUUGGCAUCUUCAACAGCUGCCUGUUAAGUAAAUGUUAGGUAACAUAG-GCACAAGUCAGCUGUUCCUCGCCGAUAGCAACAGCAACAAAA
......((((((......(((((((((.(((...((..(((((....)))))..-))))).).))))))))....)))))).((....))....... ( -24.30)
>DroYak_CAF1 36197 95 + 1
AGGCAAGUUGGCAUCUUCGGCACCGCCCUGUUAAGUCAAUGUUAGGUAACAUACCGCAC-AGUCAGCUGUUUUUUGCCGACAG-AACAGCAACAAAA
......((((...(((((((((..((.((....)).........((((...))))))((-((....))))....)))))).))-).))))....... ( -21.70)
>consensus
AAGCAAGUUGGCAGCUUCUACAGCUCCAUGUUAACUCAAUGUUAGCUAACAUAAGACACAAGUCAGCUGUUCCGCGCCGACAGCAACAGCAACAAAA
......((((((.......(((((..............(((((....)))))..(((....))).))))).....)))))).((....))....... (-17.04 = -17.28 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:22 2006