Locus 7514

Sequence ID	X_DroMel_CAF1
Location	18,776,992 – 18,777,128
Length	136
Max. P	0.848369

overview

Window 8

Location	18,776,992 – 18,777,112
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-35.60
Consensus MFE	-32.06
Energy contribution	-32.30
Covariance contribution	0.25
Combinations/Pair	1.17
Mean z-score	-1.82
Structure conservation index	0.90
SVM decision value	0.78
SVM RNA-class probability	0.848369
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18776992 120 + 22224390
GUGGGUUAAGACCACGUUCGAGUCAAGCGAAAAACAGUUAAAUCCUCGCAGGCAAUGGCCCAAAUGAAUUACCACUGGCGCGGUAAUCCCCGCCACAGUUCCAAAGUUAAGACUUCGACU
((((.......))))(((.(((((..((((...............)))).(((....))).....(((((.....(((((.((....)).))))).))))).........))))).))). ( -31.76)
>DroSec_CAF1 23536 120 + 1
GUGGGUUAAGACCACGUUCGAGUCAAGCGAAAAACAGUUAAAUCCGCGCAGGCAAUGGCCCAAAUGAAUUACCACUGGCGCGGUAAUCCCCGCCACAGUUGCCAAGUUAAGACUCGGGCU
((((.......))))(((((((((..(((...............)))...((((((((.............))..(((((.((....)).)))))..)))))).......))))))))). ( -41.08)
>DroEre_CAF1 22120 120 + 1
GUGUGUUAAGACCACGUUCGAGUCAAGCGAAAAACAGUUAAAUCCGCGCAGGUAAUGGCCCAAAUGAAUUACCACUGGCGCGGUAAUCUCCGCCACAGUUCCAAAGUUAAGACUCGAACU
(((.((....)))))(((((((((..(((...............)))((.((((((...........))))))((((..((((......))))..))))......))...))))))))). ( -36.66)
>DroYak_CAF1 21905 120 + 1
GUGGGUUAAGACCACGUUCGAGUCAAGCGAAAAACAGUUAAAUCCGCGCAGGUAAUGGCCCAAAUGAAUUACCACUGGCGCGGUAAUCCCCGUCAUAGUUCCAAAGUUAAGACUCAAACU
((((.......))))(((.(((((.(((........)))....((((((.((((((...........))))))....))))))...........................))))).))). ( -32.90)
>consensus
GUGGGUUAAGACCACGUUCGAGUCAAGCGAAAAACAGUUAAAUCCGCGCAGGCAAUGGCCCAAAUGAAUUACCACUGGCGCGGUAAUCCCCGCCACAGUUCCAAAGUUAAGACUCGAACU
((((.......))))(((((((((..(((.................))).((((((...........))))))((((..((((......))))..))))...........))))))))). (-32.06 = -32.30 +   0.25)

alignment

secondary structure

dotplot

Window 9

Location	18,777,032 – 18,777,128
Length	96
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.64
Mean single sequence MFE	-39.23
Consensus MFE	-28.23
Energy contribution	-28.35
Covariance contribution	0.12
Combinations/Pair	1.11
Mean z-score	-1.55
Structure conservation index	0.72
SVM decision value	0.07
SVM RNA-class probability	0.568874
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18777032 96 - 22224390
AGGGCCUCGA------------------------AGUCCGAGUCGAAGUCUUAACUUUGGAACUGUGGCGGGGAUUACCGCGCCAGUGGUAAUUCAUUUGGGCCAUUGCCUGCGAGGAUU
....(((((.------------------------.(((((..(((((((....)))))))...)).)))..((((((((((....))))))))))....((((....)))).)))))... ( -34.20)
>DroSec_CAF1 23576 120 - 1
AGGGCCUAGAGCCCAGGAAACCAGUCCGAGUUCGAGUUCGAGCCCGAGUCUUAACUUGGCAACUGUGGCGGGGAUUACCGCGCCAGUGGUAAUUCAUUUGGGCCAUUGCCUGCGCGGAUU
..(((((((((((..(....)(((((((((((.(((((((....)))).))))))))))..)))).)))..((((((((((....)))))))))).)))))))).((((....))))... ( -49.10)
>DroEre_CAF1 22160 108 - 1
AGGGCCUAGAACCCAGGAAACCAGUC------------CGAGUUCGAGUCUUAACUUUGGAACUGUGGCGGAGAUUACCGCGCCAGUGGUAAUUCAUUUGGGCCAUUACCUGCGCGGAUU
..((((((((..((.(....)..(((------------..(((((.((........)).)))))..))))).(((((((((....)))))))))..))))))))....((.....))... ( -35.40)
>DroYak_CAF1 21945 108 - 1
AGGGCCUAGAACCCAGGAAACCAGUC------------UGAGUUUGAGUCUUAACUUUGGAACUAUGACGGGGAUUACCGCGCCAGUGGUAAUUCAUUUGGGCCAUUACCUGCGCGGAUU
..((((((((.(((.(....)..(((------------..(((((.((........)).)))))..))))))(((((((((....)))))))))..))))))))....((.....))... ( -38.20)
>consensus
AGGGCCUAGAACCCAGGAAACCAGUC____________CGAGUCCGAGUCUUAACUUUGGAACUGUGGCGGGGAUUACCGCGCCAGUGGUAAUUCAUUUGGGCCAUUACCUGCGCGGAUU
..((((((((...............................(((..(((((.......)).)))..)))..((((((((((....)))))))))).))))))))....((.....))... (-28.23 = -28.35 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:51 2006