Locus 8469

Sequence ID	3L_DroMel_CAF1
Location	22,272,852 – 22,273,012
Length	160
Max. P	0.967048

overview

Window 2

Location	22,272,852 – 22,272,972
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.04
Mean single sequence MFE	-34.95
Consensus MFE	-27.05
Energy contribution	-27.05
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-2.11
Structure conservation index	0.77
SVM decision value	0.36
SVM RNA-class probability	0.703848
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22272852 120 - 23771897
GAGCACUUUAAUGUGGCAGUGCGCUACAGUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUUCUUUCUGUCCGCCAAUUUGCAUUUUGCAUAUCGUUUAUAG
((((((((......((((((((((....)))((((....)))).(((((.....)))))......))))))).))))))))...((((..((.....(((.....)))....))..)))) ( -35.80)
>DroSec_CAF1 31258 110 - 1
GAGCACUUUAAUGUGGCA----------GUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUUCUUUCUGUCCGCCAAUUUGCAUUUUGCAUAUCGUUUAUAG
((((((((......((((----------(((((((....)))).(((((.....)))))......))))))).))))))))...((((..((.....(((.....)))....))..)))) ( -35.60)
>DroSim_CAF1 22834 110 - 1
GAGCACUUUAAUGUGGCA----------GUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUUCUUUCUGUCCGCCAAUUUGCAUUUUGCAUAUCGUUUAUAG
((((((((......((((----------(((((((....)))).(((((.....)))))......))))))).))))))))...((((..((.....(((.....)))....))..)))) ( -35.60)
>DroEre_CAF1 30084 110 - 1
GGGCACUUUAAUGUGGCA----------GUGGCACAUUGGUGCGGCAGAUGGACUUUGCAUAUGACACUGCCCAAGUGUUCUUUCUGUCCGCCAAUUUGCAUUUUGAAUAUCGUUUAUAG
.(.(((......))).).----------...(((.(((((((.((((((.(((...........(((((.....)))))))).))))))))))))).))).................... ( -32.80)
>consensus
GAGCACUUUAAUGUGGCA__________GUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUUCUUUCUGUCCGCCAAUUUGCAUUUUGCAUAUCGUUUAUAG
..(((.....(((((.((.((.....)).)).))))).((((.((((((.((((...(((........)))......))))..))))))))))....))).................... (-27.05 = -27.05 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	22,272,892 – 22,273,012
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.70
Mean single sequence MFE	-26.85
Consensus MFE	-23.75
Energy contribution	-23.56
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-2.03
Structure conservation index	0.88
SVM decision value	1.29
SVM RNA-class probability	0.938344
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22272892 120 + 23771897
AACACUUAGGCAGUGUCAUAUGCAAAAUUCAUCUGCCGCACCGAUGUGCCACUGUAGCGCACUGCCACAUUAAAGUGCUCCGAAUGCCGGCCAAAACUUCACAUUAAAUCCAGGCCACAA
........((((...((....(((.........))).((((.((((((.((.((.....)).)).))))))...))))...)).))))((((....................)))).... ( -28.55)
>DroSec_CAF1 31298 109 + 1
AACACUUAGGCAGUGUCAUAUGCAAAAUUCAUCUGCCGCACCGAUGUGCCAC----------UGCCACAUUAAAGUGCUCCGAAUGCCGGCCAAAACUUCACAUUAAAUCCAGGCCACA-
..(((((.(((((((......(((.........))).((((....)))))))----------))))......)))))...........((((....................))))...- ( -24.95)
>DroSim_CAF1 22874 109 + 1
AACACUUAGGCAGUGUCAUAUGCAAAAUUCAUCUGCCGCACCGAUGUGCCAC----------UGCCACAUUAAAGUGCUCCGAAAGCCGGCCAAAACUUCACAUUAAAUCCAGGCCACA-
........(((((((......(((.........))).((((....)))))))----------))))........(.(((.....))))((((....................))))...- ( -25.55)
>DroEre_CAF1 30124 109 + 1
AACACUUGGGCAGUGUCAUAUGCAAAGUCCAUCUGCCGCACCAAUGUGCCAC----------UGCCACAUUAAAGUGCCCCGAGUUCCGGCCAAAACUUCACAUUAAAUCCAGGCCACA-
...((((((((((((.(((((((..((.....))...)))....)))).)))----------)))(((......)))..))))))...((((....................))))...- ( -28.35)
>consensus
AACACUUAGGCAGUGUCAUAUGCAAAAUUCAUCUGCCGCACCGAUGUGCCAC__________UGCCACAUUAAAGUGCUCCGAAUGCCGGCCAAAACUUCACAUUAAAUCCAGGCCACA_
........(((((((..............)).)))))((((.((((((.((...........)).))))))...))))..........((((....................)))).... (-23.75 = -23.56 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	22,272,892 – 22,273,012
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.70
Mean single sequence MFE	-39.75
Consensus MFE	-33.97
Energy contribution	-34.35
Covariance contribution	0.38
Combinations/Pair	1.00
Mean z-score	-2.43
Structure conservation index	0.85
SVM decision value	1.60
SVM RNA-class probability	0.967048
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22272892 120 - 23771897
UUGUGGCCUGGAUUUAAUGUGAAGUUUUGGCCGGCAUUCGGAGCACUUUAAUGUGGCAGUGCGCUACAGUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUU
.(((((((..(((((......)))))..)))).))).....(((((((......((((((((((....)))((((....)))).(((((.....)))))......))))))).))))))) ( -40.40)
>DroSec_CAF1 31298 109 - 1
-UGUGGCCUGGAUUUAAUGUGAAGUUUUGGCCGGCAUUCGGAGCACUUUAAUGUGGCA----------GUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUU
-(((((((..(((((......)))))..)))).))).....(((((((......((((----------(((((((....)))).(((((.....)))))......))))))).))))))) ( -40.00)
>DroSim_CAF1 22874 109 - 1
-UGUGGCCUGGAUUUAAUGUGAAGUUUUGGCCGGCUUUCGGAGCACUUUAAUGUGGCA----------GUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUU
-..(((((..(((((......)))))..)))))........(((((((......((((----------(((((((....)))).(((((.....)))))......))))))).))))))) ( -39.60)
>DroEre_CAF1 30124 109 - 1
-UGUGGCCUGGAUUUAAUGUGAAGUUUUGGCCGGAACUCGGGGCACUUUAAUGUGGCA----------GUGGCACAUUGGUGCGGCAGAUGGACUUUGCAUAUGACACUGCCCAAGUGUU
-(.(((((..(((((......)))))..))))).)......((((((....((.((((----------(((((((....)))).(((((.....)))))......))))))))))))))) ( -39.00)
>consensus
_UGUGGCCUGGAUUUAAUGUGAAGUUUUGGCCGGCAUUCGGAGCACUUUAAUGUGGCA__________GUGGCACAUCGGUGCGGCAGAUGAAUUUUGCAUAUGACACUGCCUAAGUGUU
...(((((..(((((......)))))..))))).........(((((...(((((.((.((.....)).)).))))).))))).(((((.....)))))....((((((.....)))))) (-33.97 = -34.35 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:15 2006