Locus 1838

Sequence ID	2L_DroMel_CAF1
Location	5,079,729 – 5,079,839
Length	110
Max. P	0.645357

overview

Window 2

Location	5,079,729 – 5,079,839
Length	110
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	91.30
Mean single sequence MFE	-20.80
Consensus MFE	-17.76
Energy contribution	-18.07
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.51
Structure conservation index	0.85
SVM decision value	0.23
SVM RNA-class probability	0.645357
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5079729 110 + 22407834
UUUUUGUAUUAAAAUAUACAAAUGUACGGAUAAUUGCGCUCGAAUUAUUGUUGAGCUAUGAAUUCACU-CGCCUCUUAUUUGCCCAGCAAUUUAUUACCAAUUUUUUUUGC--------
..(((((((......)))))))((..(((((((..((((((((.......))))))...((......)-)))...)))))))..))((((.................))))-------- ( -17.53)
>DroSec_CAF1 9165 110 + 1
-UUUUGUAUUAAAAUAUACAAAUGUACGGAUAAUUGCGCUCGAUUUAUUGUCGAGCUAUGAAUUCACUUCGCCUCUUAUUUGCCCAGCAAUUUAUUACCAAUUUUGUUUGC--------
-.(((((((......)))))))((..(((((((..(((((((((.....)))))))...(((.....)))))...)))))))..))((((.................))))-------- ( -22.33)
>DroSim_CAF1 10975 111 + 1
UUUUUGUAUUAAAAUAUACAAAUGUACGGAUAAUUGCGCUCGAUUUAUUGUCGAGCCAUGAAUUCACUUCGCCUCUUAUUUGCCCAGCAAUUUAUUACCAAUUUUGUUUGC--------
..(((((((......)))))))((..(((((((..(((((((((.....)))))))...(((.....)))))...)))))))..))((((.................))))-------- ( -21.93)
>DroYak_CAF1 10469 119 + 1
UUUUCGUAUAAAAAUAUACAAAUAUACAGAUAAUUGCGCUCGAUUUAUUGUCGAGCUAUGAAUUCACUUCGCCUCUUAUUUGCCCAGCAAUUUAUUACCAAUUUGGUUAGCCACACACG
.....(((((....))))).........((((((((((((((((.....)))))))...(((.....)))................)))).))))).......(((....)))...... ( -21.40)
>consensus
UUUUUGUAUUAAAAUAUACAAAUGUACGGAUAAUUGCGCUCGAUUUAUUGUCGAGCUAUGAAUUCACUUCGCCUCUUAUUUGCCCAGCAAUUUAUUACCAAUUUUGUUUGC________
..(((((((......)))))))......((((((((((((((((.....)))))))..((....))....................)))).)))))....................... (-17.76 = -18.07 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	5,079,729 – 5,079,839
Length	110
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	91.30
Mean single sequence MFE	-21.70
Consensus MFE	-19.81
Energy contribution	-19.88
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.26
Structure conservation index	0.91
SVM decision value	-0.08
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5079729 110 - 22407834
--------GCAAAAAAAAUUGGUAAUAAAUUGCUGGGCAAAUAAGAGGCG-AGUGAAUUCAUAGCUCAACAAUAAUUCGAGCGCAAUUAUCCGUACAUUUGUAUAUUUUAAUACAAAAA
--------............((((((...(..((.(.(........).).-))..).......((((...........))))...))))))......(((((((......))))))).. ( -17.40)
>DroSec_CAF1 9165 110 - 1
--------GCAAACAAAAUUGGUAAUAAAUUGCUGGGCAAAUAAGAGGCGAAGUGAAUUCAUAGCUCGACAAUAAAUCGAGCGCAAUUAUCCGUACAUUUGUAUAUUUUAAUACAAAA-
--------..........(..((((....))))..)((..((((...(((((.....)))...((((((.......))))))))..))))..))...(((((((......))))))).- ( -21.50)
>DroSim_CAF1 10975 111 - 1
--------GCAAACAAAAUUGGUAAUAAAUUGCUGGGCAAAUAAGAGGCGAAGUGAAUUCAUGGCUCGACAAUAAAUCGAGCGCAAUUAUCCGUACAUUUGUAUAUUUUAAUACAAAAA
--------..........(..((((....))))..)((..((((...(((((.....)))...((((((.......))))))))..))))..))...(((((((......))))))).. ( -21.30)
>DroYak_CAF1 10469 119 - 1
CGUGUGUGGCUAACCAAAUUGGUAAUAAAUUGCUGGGCAAAUAAGAGGCGAAGUGAAUUCAUAGCUCGACAAUAAAUCGAGCGCAAUUAUCUGUAUAUUUGUAUAUUUUUAUACGAAAA
(((((((((....)))..(..((((....))))..)((((((((((.(((((.....)))...((((((.......)))))))).....)))...))))))).......)))))).... ( -26.60)
>consensus
________GCAAACAAAAUUGGUAAUAAAUUGCUGGGCAAAUAAGAGGCGAAGUGAAUUCAUAGCUCGACAAUAAAUCGAGCGCAAUUAUCCGUACAUUUGUAUAUUUUAAUACAAAAA
..................(..((((....))))..)((..((((...((...(((....))).((((((.......))))))))..))))..))...(((((((......))))))).. (-19.81 = -19.88 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:30 2006