Locus 1118

Sequence ID	2L_DroMel_CAF1
Location	3,020,466 – 3,020,572
Length	106
Max. P	0.806233

overview

Window 1

Location	3,020,466 – 3,020,572
Length	106
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	83.77
Mean single sequence MFE	-25.20
Consensus MFE	-15.69
Energy contribution	-15.20
Covariance contribution	-0.49
Combinations/Pair	1.43
Mean z-score	-2.85
Structure conservation index	0.62
SVM decision value	0.24
SVM RNA-class probability	0.650297
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3020466 106 + 22407834
CAACAGCAACAACAUUAGGCAAUGCUGCAGUGACCACUACAGCACCUACUUCUAGCACCCUCAUGCAGAUGCUAGCCAACAUGGCAAACUCCACAACCACAACGCU
....((((.......((((...(((((.(((....))).)))))))))..(((.(((......)))))))))).(((.....)))..................... ( -23.90)
>DroSec_CAF1 1686 106 + 1
CAACAGCAGCUACAUUAGGAAAUGCUGCAGUGACCACAACAGCACCCACUUCUAGCACCCUCAUGCAGAUGCUAGCCAAUAUGGCAAACUCUACAACCACAACGCU
....((((.((.(((.(((...(((((.((((..............))))..))))).))).))).)).)))).(((.....)))..................... ( -22.54)
>DroSim_CAF1 4254 106 + 1
CAACAGCAGCUACAUUAGGGAAUGCUGCAGUGACCACAACAGCACCCACUUCUAGCACCCUCAUGCAGAUGCUAGCCAACAUGGCAAACUCCACAACCACAACGCU
....((((.((.(((.((((..(((((.((((..............))))..))))))))).))).)).)))).(((.....)))..................... ( -25.94)
>DroEre_CAF1 7308 106 + 1
GAACAGCAUCAACAUUAGGCAAUGCUGCAGUGACCACUACAGCACCCACUUCUAGCACCCUCAUGCAGAUGAUAGCUAACAUGGCAAAUUCCACAUCUACAUCGCU
....(((((((......((...(((((.(((....))).))))).))...(((.(((......)))))))))).(((.....)))..................))) ( -20.70)
>DroYak_CAF1 13004 106 + 1
CAACCGCAGCAACAUCAGGCAAUGCUGCAGUGACCACUGCAGCACCCACUUCUAGCACCCUCAUGCAGAUGCUAGCCAACAUGGCAAACUCCACAACCGCCACCCU
.....((((((......((...(((((((((....))))))))).))...(((.(((......)))))))))).(((.....))).............))...... ( -31.00)
>DroAna_CAF1 23589 103 + 1
UA---GGAGCAACAGCAGGUAAUGUAGCCACGACUACGCCUGUCCCUACCUCCAGCACCCUAAUGCAAAUGCUGGCCAGUAUGGCCAACUCCACUACCACGACCUU
..---((((((...((((((...((((......))))))))))...........(((......)))...)))(((((.....)))))..))).............. ( -27.10)
>consensus
CAACAGCAGCAACAUUAGGCAAUGCUGCAGUGACCACUACAGCACCCACUUCUAGCACCCUCAUGCAGAUGCUAGCCAACAUGGCAAACUCCACAACCACAACGCU
.....(((((.......((...(((((.(((....))).))))).)).......(((......)))....))).(((.....)))..................)). (-15.69 = -15.20 +  -0.49)

alignment

secondary structure

dotplot

Window 2

Location	3,020,466 – 3,020,572
Length	106
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	83.77
Mean single sequence MFE	-38.92
Consensus MFE	-28.80
Energy contribution	-28.62
Covariance contribution	-0.18
Combinations/Pair	1.38
Mean z-score	-2.63
Structure conservation index	0.74
SVM decision value	0.63
SVM RNA-class probability	0.806233
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3020466 106 - 22407834
AGCGUUGUGGUUGUGGAGUUUGCCAUGUUGGCUAGCAUCUGCAUGAGGGUGCUAGAAGUAGGUGCUGUAGUGGUCACUGCAGCAUUGCCUAAUGUUGUUGCUGUUG
(((((((.(((.((((......)))).....(((((((((......))))))))).....(((((((((((....))))))))))))))))))))).......... ( -38.20)
>DroSec_CAF1 1686 106 - 1
AGCGUUGUGGUUGUAGAGUUUGCCAUAUUGGCUAGCAUCUGCAUGAGGGUGCUAGAAGUGGGUGCUGUUGUGGUCACUGCAGCAUUUCCUAAUGUAGCUGCUGUUG
(((..((((((..........))))))...)))((((.((((((.((((((((...(((((.(((....))).)))))..)))))..))).)))))).)))).... ( -37.40)
>DroSim_CAF1 4254 106 - 1
AGCGUUGUGGUUGUGGAGUUUGCCAUGUUGGCUAGCAUCUGCAUGAGGGUGCUAGAAGUGGGUGCUGUUGUGGUCACUGCAGCAUUCCCUAAUGUAGCUGCUGUUG
(((..((((((..........))))))...)))((((.((((((.((((((((...(((((.(((....))).)))))..))))..)))).)))))).)))).... ( -38.00)
>DroEre_CAF1 7308 106 - 1
AGCGAUGUAGAUGUGGAAUUUGCCAUGUUAGCUAUCAUCUGCAUGAGGGUGCUAGAAGUGGGUGCUGUAGUGGUCACUGCAGCAUUGCCUAAUGUUGAUGCUGUUC
((((((((.(((((((......))))))).)).)))(((.((((..((((((.....)).(((((((((((....))))))))))))))).)))).)))))).... ( -36.90)
>DroYak_CAF1 13004 106 - 1
AGGGUGGCGGUUGUGGAGUUUGCCAUGUUGGCUAGCAUCUGCAUGAGGGUGCUAGAAGUGGGUGCUGCAGUGGUCACUGCAGCAUUGCCUGAUGUUGCUGCGGUUG
...(..((..(...((......((((.....(((((((((......)))))))))..))))((((((((((....))))))))))..))....)..))..)..... ( -43.10)
>DroAna_CAF1 23589 103 - 1
AAGGUCGUGGUAGUGGAGUUGGCCAUACUGGCCAGCAUUUGCAUUAGGGUGCUGGAGGUAGGGACAGGCGUAGUCGUGGCUACAUUACCUGCUGUUGCUCC---UA
.(((..((..(((..(.(((..((.((((..(((((((((......))))))))).)))).))...)))(((((....))))).....)..)))..)).))---). ( -39.90)
>consensus
AGCGUUGUGGUUGUGGAGUUUGCCAUGUUGGCUAGCAUCUGCAUGAGGGUGCUAGAAGUGGGUGCUGUAGUGGUCACUGCAGCAUUGCCUAAUGUUGCUGCUGUUG
......(((((.((((......))))((((((((((((((......))))))))).....(((((((((((....)))))))))))..)))))...)))))..... (-28.80 = -28.62 +  -0.18)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:10 2006