Locus 435

Sequence ID	3L_DroMel_CAF1
Location	1,268,716 – 1,268,854
Length	138
Max. P	0.994090

overview

Window 3

Location	1,268,716 – 1,268,832
Length	116
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	87.29
Mean single sequence MFE	-42.02
Consensus MFE	-33.58
Energy contribution	-33.82
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.66
Structure conservation index	0.80
SVM decision value	2.23
SVM RNA-class probability	0.990712
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1268716 116 + 23771897
AGUGUGGCCAUGGGCCAAGUAGGCUGCCGCAUAAAUUGCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAAAAGGCAUCGCGUUCUUCCGCAAUGUUGGCAUUGCUAAGUUUGUUGC-
.(((((((....((((.....))))))))))).......((((...((((((.(((((.((((((((((.......))))))))))..)))).)..))))))...)))).......- ( -40.30)
>DroSec_CAF1 23487 107 + 1
AGUGUAGCCAUUGGCCAAGUAGGCUGCCGCAUAAAUUGCACUUUCGAGUGCAUCUUGCCAAGAAUGCGAAAAGGAAUCGCGUUCUUCCGCAUU---------GCUAAGUUUGUUUA-
.(.(((((((((.....))).)))))))(((.....((((((....))))))...(((.((((((((((.......))))))))))..))).)---------))............- ( -33.80)
>DroSim_CAF1 23906 116 + 1
AGUGUGGCCAUUGGCCAAGUAGGCUGCCGCAUAAAUUGCACUUUCGAGUGCAUCUUGCCAAGAAUGCGAAAAGGAAUCGCCUUCUUCCGCAUUGUUGGCAUUGAUAAGUUUGUUUA-
.(((((((....((((.....)))))))))))((((((((((....)))))(((.((((((.((((((((((((.....)))).)).)))))).))))))..))).))))).....- ( -44.40)
>DroEre_CAF1 23316 117 + 1
AGUGUGGCCAUUGGCCAAGUAGGCUGCCGCAUACAUUGCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAAAAGGCAUCGCGUUCUUCCGCAUUGUGGGCAUUGCAGAGGUGGCUGCA
....(((((...))))).....((.((((((.....)))((((..((((((((..(((.((((((((((.......))))))))))..)))....))))))).)..))))))).)). ( -45.90)
>DroYak_CAF1 23908 108 + 1
AGUGUGGCCAUUGGCCAAGUAGGCUGCCGCAUAAAUUGCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAGAAGGCAUCGCGUUCUUCCGCGUUGUUGGCAUUGCAGAG---------
.(((((((....((((.....))))))))))).....(((((....)))))((((((((((.((((((.(((((........))))))))))).))))))....))))--------- ( -45.70)
>consensus
AGUGUGGCCAUUGGCCAAGUAGGCUGCCGCAUAAAUUGCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAAAAGGCAUCGCGUUCUUCCGCAUUGUUGGCAUUGCUAAGUUUGUUGA_
.(((((((....((((.....))))))))))).....(((((....)))))....(((.((((((((((.......))))))))))..))).......................... (-33.58 = -33.82 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	1,268,716 – 1,268,832
Length	116
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	87.29
Mean single sequence MFE	-35.88
Consensus MFE	-28.06
Energy contribution	-29.94
Covariance contribution	1.88
Combinations/Pair	1.07
Mean z-score	-2.18
Structure conservation index	0.78
SVM decision value	1.27
SVM RNA-class probability	0.938811
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1268716 116 - 23771897
-GCAACAAACUUAGCAAUGCCAACAUUGCGGAAGAACGCGAUGCCUUUUCGCAUUCUUGGCAAGAGGCACUCGAAAGUGCAAUUUAUGCGGCAGCCUACUUGGCCCAUGGCCACACU
-(((.....(((.((((((....))))))..))).((.(((((((((((.((.......)))))))))).)))...))........)))(((.(((.....))).....)))..... ( -35.80)
>DroSec_CAF1 23487 107 - 1
-UAAACAAACUUAGC---------AAUGCGGAAGAACGCGAUUCCUUUUCGCAUUCUUGGCAAGAUGCACUCGAAAGUGCAAUUUAUGCGGCAGCCUACUUGGCCAAUGGCUACACU
-..........((((---------..(((..(((((.((((.......)))).))))).((((((((((((....))))).)))).))).)))(((.....))).....)))).... ( -30.60)
>DroSim_CAF1 23906 116 - 1
-UAAACAAACUUAUCAAUGCCAACAAUGCGGAAGAAGGCGAUUCCUUUUCGCAUUCUUGGCAAGAUGCACUCGAAAGUGCAAUUUAUGCGGCAGCCUACUUGGCCAAUGGCCACACU
-................((((((.(((((((((..(((.....)))))))))))).))))))...((((((....)))))).....((.(((.(((.....))).....))).)).. ( -37.60)
>DroEre_CAF1 23316 117 - 1
UGCAGCCACCUCUGCAAUGCCCACAAUGCGGAAGAACGCGAUGCCUUUUCGCAUUCUUGGCAAGAGGCACUCGAAAGUGCAAUGUAUGCGGCAGCCUACUUGGCCAAUGGCCACACU
.(((((((..((((((.((....)).))))))((((.((((.......)))).)))))))).....(((((....)))))......)))(((.(((.....))).....)))..... ( -39.80)
>DroYak_CAF1 23908 108 - 1
---------CUCUGCAAUGCCAACAACGCGGAAGAACGCGAUGCCUUCUCGCAUUCUUGGCAAGAGGCACUCGAAAGUGCAAUUUAUGCGGCAGCCUACUUGGCCAAUGGCCACACU
---------(((((((.((((((...((((......))))((((......))))..))))))....(((((....)))))......))))).))......(((((...))))).... ( -35.60)
>consensus
_GAAACAAACUUAGCAAUGCCAACAAUGCGGAAGAACGCGAUGCCUUUUCGCAUUCUUGGCAAGAGGCACUCGAAAGUGCAAUUUAUGCGGCAGCCUACUUGGCCAAUGGCCACACU
.............(((.((((((.((((((((((..........)))).)))))).))))))....(((((....)))))......)))(((.(((.....))).....)))..... (-28.06 = -29.94 +   1.88)

alignment

secondary structure

dotplot

Window 5

Location	1,268,753 – 1,268,854
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	68.71
Mean single sequence MFE	-31.95
Consensus MFE	-14.42
Energy contribution	-16.62
Covariance contribution	2.19
Combinations/Pair	1.05
Mean z-score	-2.51
Structure conservation index	0.45
SVM decision value	2.45
SVM RNA-class probability	0.994090
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1268753 101 + 23771897
GCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAAAAGGCAUCGCGUUCUUCCGCAAUGUUGGCAUUGCUAAGUUUGUUGC-------AAGAGUGACUAAUUCUACUCUA------------
(((((....)))))(((((((.((((((((((.......))))))))))..((((((....))))))..........))-------))))).................------------ ( -34.90)
>DroSec_CAF1 23524 92 + 1
GCACUUUCGAGUGCAUCUUGCCAAGAAUGCGAAAAGGAAUCGCGUUCUUCCGCAUU---------GCUAAGUUUGUUUA-------AAGGGUGACUAAUUCUACUCUA------------
(((((....)))))....(((.((((((((((.......))))))))))..)))..---------..............-------.((((((........)))))).------------ ( -24.90)
>DroSim_CAF1 23943 101 + 1
GCACUUUCGAGUGCAUCUUGCCAAGAAUGCGAAAAGGAAUCGCCUUCUUCCGCAUUGUUGGCAUUGAUAAGUUUGUUUA-------AAGGGUGACUAAUUCUACUCUA------------
(((((....)))))(((.((((((.((((((((((((.....)))).)).)))))).))))))..)))...........-------.((((((........)))))).------------ ( -33.40)
>DroEre_CAF1 23353 108 + 1
GCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAAAAGGCAUCGCGUUCUUCCGCAUUGUGGGCAUUGCAGAGGUGGCUGCAAUUCGCAGAAACUACUACUUCAACUCUA------------
........((((((((..(((.((((((((((.......))))))))))..)))....))))......(((((((((((.....))))......))))))).))))..------------ ( -36.20)
>DroYak_CAF1 23945 98 + 1
GCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAGAAGGCAUCGCGUUCUUCCGCGUUGUUGGCAUUGCAGAG----------UUUGCGAACAUUACCAAUUCAACUCAA------------
(((((....)))))....((((((.((((((.(((((........))))))))))).))))))((((((..----------.))))))....................------------ ( -31.70)
>DroAna_CAF1 24318 101 + 1
GCCCGGCCGAGU-------GCCAAGAAUGCGAAAAUGCAACA----CUGCCGCAUUGCUGGCAUCUCAGAGUCGGUUGU-------AGG-CCAAAACAUGCGAAUCUACGAAAACAAAUU
..((((((((((-------((((..((((((.....(((...----.)))))))))..))))).))).).)))))((((-------(((-(........))....))))))......... ( -30.60)
>consensus
GCACUUUCGAGUGCCUCUUGCCAAGAAUGCGAAAAGGCAUCGCGUUCUUCCGCAUUGUUGGCAUUGCAAAGUUUGUUGA_______AAGAGUGACUAAUUCUACUCUA____________
(((((....))))).....(((((.((((((...(((........)))..)))))).))))).......................................................... (-14.42 = -16.62 +   2.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:45 2006