Locus 4532

Sequence ID	X_DroMel_CAF1
Location	11,944,496 – 11,944,656
Length	160
Max. P	0.997231

overview

Window 1

Location	11,944,496 – 11,944,616
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.61
Mean single sequence MFE	-31.83
Consensus MFE	-23.00
Energy contribution	-23.62
Covariance contribution	0.62
Combinations/Pair	1.09
Mean z-score	-2.26
Structure conservation index	0.72
SVM decision value	0.74
SVM RNA-class probability	0.838710
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11944496 120 + 22224390
UACCAUGCCAUCCUUUGGCACUUCAAGUCGAUUUACAGCUACAAACGAAUGUCUCGAGGACAUUUCCAUGCCUUCAUAUCGCGAUAAUACCGAAUCGCUUAGGCAUAGAUGUCCUACACC
.....(((((.....))))).........................(((.....)))(((((((((..((((((.......(((((........)))))..)))))))))))))))..... ( -31.20)
>DroSec_CAF1 27506 120 + 1
UACCAUGCCAUCCUAUGGCACUUCAAGUCGAUUUACAGCUACAAAUGAAUGUCUCGAGGACAUUUCCAUGCCUUCAUAUCGCGAUAAUACCGGAUCGCUUAGGCAAAGAUGUCCUACACC
.....((((((...)))))).......((((...(((............))).))))((((((((...(((((.......(((((........)))))..))))).))))))))...... ( -29.00)
>DroEre_CAF1 12427 120 + 1
UACCAUGCCAUCCUUUGGCACUUCUACCUUUGGCACGGCUACCAAUGAAUGUCUCGAGGACAUUUCAAUGCCUUCAUAUCGGGAUCACACCGGAUCGCUUAGGCAUAGAUGUCCAACACC
..((.(((((......((........))..))))).))...................((((((((..((((((....(((.((......)).))).....))))))))))))))...... ( -32.60)
>DroYak_CAF1 12001 120 + 1
UGCCAUGGCAUCCUUUGGUACUUUAAGUCGACAUACAGCUACAAAUGAAUGUCUCGAGGACAUUUCAAUGCCUUCAUAUCGGGAUAAUACCGGAUCGCUGAGGCAUAGAUGUCCAACACC
(((((.((...))..))))).........(((((.((........)).)))))....((((((((..(((((((...(((.((......)).)))....)))))))))))))))...... ( -34.50)
>consensus
UACCAUGCCAUCCUUUGGCACUUCAAGUCGAUUUACAGCUACAAAUGAAUGUCUCGAGGACAUUUCAAUGCCUUCAUAUCGCGAUAAUACCGGAUCGCUUAGGCAUAGAUGUCCAACACC
.....(((((.....))))).....................................((((((((..((((((.....((((.......)))).......))))))))))))))...... (-23.00 = -23.62 +   0.62)

alignment

secondary structure

dotplot

Window 2

Location	11,944,536 – 11,944,656
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.09
Mean single sequence MFE	-28.31
Consensus MFE	-19.96
Energy contribution	-21.27
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-2.86
Structure conservation index	0.71
SVM decision value	2.82
SVM RNA-class probability	0.997231
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11944536 120 + 22224390
ACAAACGAAUGUCUCGAGGACAUUUCCAUGCCUUCAUAUCGCGAUAAUACCGAAUCGCUUAGGCAUAGAUGUCCUACACCAAUUCAGAGCUCUAGACAAGAAUGUCUGGAUGAUAUGACU
......((((......(((((((((..((((((.......(((((........)))))..)))))))))))))))......)))).....((((((((....)))))))).......... ( -36.30)
>DroSec_CAF1 27546 91 + 1
ACAAAUGAAUGUCUCGAGGACAUUUCCAUGCCUUCAUAUCGCGAUAAUACCGGAUCGCUUAGGCAAAGAUGUCCUACACCAAUUCAGAGCU-----------------------------
.....(((((......(((((((((...(((((.......(((((........)))))..))))).)))))))))......))))).....----------------------------- ( -26.50)
>DroEre_CAF1 12467 91 + 1
ACCAAUGAAUGUCUCGAGGACAUUUCAAUGCCUUCAUAUCGGGAUCACACCGGAUCGCUUAGGCAUAGAUGUCCAACACCAAUGCAGAGCU-----------------------------
..........(.(((..((((((((..((((((....(((.((......)).))).....))))))))))))))..((....))..)))).----------------------------- ( -23.50)
>DroYak_CAF1 12041 91 + 1
ACAAAUGAAUGUCUCGAGGACAUUUCAAUGCCUUCAUAUCGGGAUAAUACCGGAUCGCUGAGGCAUAGAUGUCCAACACCAAUUCAGAGCA-----------------------------
.....(((((.......((((((((..(((((((...(((.((......)).)))....))))))))))))))).......))))).....----------------------------- ( -26.94)
>consensus
ACAAAUGAAUGUCUCGAGGACAUUUCAAUGCCUUCAUAUCGCGAUAAUACCGGAUCGCUUAGGCAUAGAUGUCCAACACCAAUUCAGAGCU_____________________________
......((((......(((((((((..((((((.....((((.......)))).......)))))))))))))))......))))................................... (-19.96 = -21.27 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	11,944,536 – 11,944,656
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.09
Mean single sequence MFE	-28.38
Consensus MFE	-21.02
Energy contribution	-22.40
Covariance contribution	1.38
Combinations/Pair	1.07
Mean z-score	-1.53
Structure conservation index	0.74
SVM decision value	0.09
SVM RNA-class probability	0.578665
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11944536 120 - 22224390
AGUCAUAUCAUCCAGACAUUCUUGUCUAGAGCUCUGAAUUGGUGUAGGACAUCUAUGCCUAAGCGAUUCGGUAUUAUCGCGAUAUGAAGGCAUGGAAAUGUCCUCGAGACAUUCGUUUGU
.(((((((((..((((..((((.....)))).))))...))))))(((((((((((((((..(((((........))))).......)))))))))..))))))...))).......... ( -38.20)
>DroSec_CAF1 27546 91 - 1
-----------------------------AGCUCUGAAUUGGUGUAGGACAUCUUUGCCUAAGCGAUCCGGUAUUAUCGCGAUAUGAAGGCAUGGAAAUGUCCUCGAGACAUUCAUUUGU
-----------------------------.....(((((.(.((.(((((((((.(((((..(((((........))))).......))))).)))..))))))))...))))))..... ( -25.00)
>DroEre_CAF1 12467 91 - 1
-----------------------------AGCUCUGCAUUGGUGUUGGACAUCUAUGCCUAAGCGAUCCGGUGUGAUCCCGAUAUGAAGGCAUUGAAAUGUCCUCGAGACAUUCAUUGGU
-----------------------------.......((.((((((((((((((.((((((.....(((.((......)).)))....)))))).))..)))))....)))).))).)).. ( -23.90)
>DroYak_CAF1 12041 91 - 1
-----------------------------UGCUCUGAAUUGGUGUUGGACAUCUAUGCCUCAGCGAUCCGGUAUUAUCCCGAUAUGAAGGCAUUGAAAUGUCCUCGAGACAUUCAUUUGU
-----------------------------......((((..((((((((((((.((((((((...(((.((......)).))).)).)))))).))..)))))....)))))..)))).. ( -26.40)
>consensus
_____________________________AGCUCUGAAUUGGUGUAGGACAUCUAUGCCUAAGCGAUCCGGUAUUAUCCCGAUAUGAAGGCAUGGAAAUGUCCUCGAGACAUUCAUUUGU
...................................((((..((((.((((((((((((((.....(((.((......)).)))....)))))))))..))))).....))))..)))).. (-21.02 = -22.40 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:27 2006