Locus 1488

Sequence ID	3L_DroMel_CAF1
Location	4,328,756 – 4,328,903
Length	147
Max. P	0.965674

overview

Window 7

Location	4,328,756 – 4,328,875
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.80
Mean single sequence MFE	-31.99
Consensus MFE	-28.59
Energy contribution	-28.65
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-1.76
Structure conservation index	0.89
SVM decision value	1.41
SVM RNA-class probability	0.951427
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4328756 119 - 23771897
GAACUGCCAACAAGAAU-GCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUUUGAUUCUUUGCAUAACCGAAAUGCAAUUGGGCUUCGACUG
.............(((.-((((.(((..(((((((((((....))))).(((((......((((.(((......)))...))))...)))))))))))...)))....)))))))..... ( -31.60)
>DroSec_CAF1 15327 119 - 1
AAACCACCAACAAGAAU-GCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUUUGAUUCUUUGCAUAACCGAAAUGCAAUUGGGCUUCGAUUG
.............(((.-((((.(((..(((((((((((....))))).(((((......((((.(((......)))...))))...)))))))))))...)))....)))))))..... ( -31.60)
>DroSim_CAF1 13888 119 - 1
AAACCACCAACAAGAAU-GCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUUUGAUUCUUUGCAUAACCGAAAUGCAAUUGGGCUUCAAUUG
.............(((.-((((.(((..(((((((((((....))))).(((((......((((.(((......)))...))))...)))))))))))...)))....)))))))..... ( -31.60)
>DroEre_CAF1 15286 119 - 1
AAACCACCAACAAGAAU-GCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUUUGAUUCUUUGCAUAACCAAAAUGCAAUUGGGCUUCGACUG
.............(((.-((((.(((..(((((((((((....))))).(((((......((((.(((......)))...))))...)))))))))))...)))....)))))))..... ( -32.30)
>DroYak_CAF1 14431 119 - 1
AAACCAGCAACAAGAAU-GCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGAGAUUUGAUUCUUUGCAUAACCGAAAUGCAAUUGGGCUUCGACUG
.............(((.-((((.(((..(((((((((((....))))).(((((((((((.(((.........))).)))))))....))))))))))...)))....)))))))..... ( -31.90)
>DroAna_CAF1 15280 114 - 1
------GCAACAAGAAUCGCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUUCGAUUCUUUGCAUAACCGAAAUGCAAUUGAGCUUCGACUU
------(((.....(((((((.....)))))))((((((....)))))))))........((((..((((((.((((.((((..............)))).)))).))))))..)))).. ( -32.94)
>consensus
AAACCACCAACAAGAAU_GCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUUUGAUUCUUUGCAUAACCGAAAUGCAAUUGGGCUUCGACUG
.............(((..((((.(((..(((((((((((....))))).(((((......((((.(((......)))...))))...)))))))))))...)))....)))))))..... (-28.59 = -28.65 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	4,328,796 – 4,328,903
Length	107
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	90.32
Mean single sequence MFE	-35.58
Consensus MFE	-30.46
Energy contribution	-31.10
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.85
Structure conservation index	0.86
SVM decision value	1.58
SVM RNA-class probability	0.965674
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4328796 107 + 23771897
AAUCACAUUUAAGCGGCGACAUUUAAUUGCAAACUGGUUGUCCAGUUAACCACCUGCGGGGCAUUCUUGUUGGCAGUUCCAUUGGUUGCUUUCUGCCCCGCCGGGUA------------
.....((.(((((.(....).))))).))..((((((....))))))....((((((((((((.....(..(((((..((...)))))))..)))))))).))))).------------ ( -34.30)
>DroSec_CAF1 15367 107 + 1
AAUCACAUUUAAGCGGCGACAUUUAAUUGCAAACUGGUUGUCCAGUUAACCACCUGCGGGGCAUUCUUGUUGGUGGUUUCAUUGGUUGCUUUCAGCCCCGCCGGGUA------------
.............(((((.............((((((....))))))(((((((.(((((.....))))).))))))).....(((((....))))).)))))....------------ ( -35.40)
>DroSim_CAF1 13928 107 + 1
AAUCACAUUUAAGCGGCGACAUUUAAUUGCAAACUGGUUGUCCAGUUAACCACCUGCGGGGCAUUCUUGUUGGUGGUUUCAUUGGUUGCUUUCAGCCCCGCCGGGUA------------
.............(((((.............((((((....))))))(((((((.(((((.....))))).))))))).....(((((....))))).)))))....------------ ( -35.40)
>DroEre_CAF1 15326 113 + 1
AAUCACAUUUAAGCGGCGACAUUUAAUUGCAAACUGGUUGUCCAGUUAACCACCUGCGGGGCAUUCUUGUUGGUGGUUUCAGUGGUUGCUUUCUGCCCCACCGGGUAUGCACA------
..........(((((((.((...........((((((....))))))(((((((.(((((.....))))).)))))))...)).)))))))..(((((....)))))......------ ( -38.50)
>DroYak_CAF1 14471 119 + 1
AAUCUCAUUUAAGCGGCGACAUUUAAUUGCAAACUGGUUGUCCAGUUAACCACCUGCGGGGCAUUCUUGUUGCUGGUUUCAGUGCUUGCCUUCUGCCCCACCGGGUGUGCACACUCACA
........(((((.(....).))))).((((((((((....))))))...((((((.((((((.....((.((((....))))....))....))))))..))))))))))........ ( -34.30)
>consensus
AAUCACAUUUAAGCGGCGACAUUUAAUUGCAAACUGGUUGUCCAGUUAACCACCUGCGGGGCAUUCUUGUUGGUGGUUUCAUUGGUUGCUUUCUGCCCCGCCGGGUA____________
..............((((((...........((((((....))))))(((((((.(((((.....))))).)))))))......))))))....((((....))))............. (-30.46 = -31.10 +   0.64)

alignment

secondary structure

dotplot

Window 9

Location	4,328,796 – 4,328,903
Length	107
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	90.32
Mean single sequence MFE	-32.49
Consensus MFE	-28.17
Energy contribution	-27.97
Covariance contribution	-0.20
Combinations/Pair	1.09
Mean z-score	-1.57
Structure conservation index	0.87
SVM decision value	0.94
SVM RNA-class probability	0.886781
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4328796 107 - 23771897
------------UACCCGGCGGGGCAGAAAGCAACCAAUGGAACUGCCAACAAGAAUGCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUU
------------((((..(((((((((........)..(((.....))).......)))))))).))))((.((((((....)))))).)).............(((......)))... ( -32.40)
>DroSec_CAF1 15367 107 - 1
------------UACCCGGCGGGGCUGAAAGCAACCAAUGAAACCACCAACAAGAAUGCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUU
------------((((..(((((((................................))))))).))))((.((((((....)))))).)).............(((......)))... ( -29.05)
>DroSim_CAF1 13928 107 - 1
------------UACCCGGCGGGGCUGAAAGCAACCAAUGAAACCACCAACAAGAAUGCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUU
------------((((..(((((((................................))))))).))))((.((((((....)))))).)).............(((......)))... ( -29.05)
>DroEre_CAF1 15326 113 - 1
------UGUGCAUACCCGGUGGGGCAGAAAGCAACCACUGAAACCACCAACAAGAAUGCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUU
------.(((((((((..((((((((..............................)))))))).))).((.((((((....)))))).))......))).)))(((......)))... ( -30.91)
>DroYak_CAF1 14471 119 - 1
UGUGAGUGUGCACACCCGGUGGGGCAGAAGGCAAGCACUGAAACCAGCAACAAGAAUGCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGAGAUU
..((((((.((.((((..((((((((...........(((....))).........)))))))).))))((.((((((....)))))).))...........))))))))......... ( -41.05)
>consensus
____________UACCCGGCGGGGCAGAAAGCAACCAAUGAAACCACCAACAAGAAUGCCCCGCAGGUGGUUAACUGGACAACCAGUUUGCAAUUAAAUGUCGCCGCUUAAAUGUGAUU
............((((..(((((((................................))))))).))))((.((((((....)))))).)).............(((......)))... (-28.17 = -27.97 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:00 2006