Locus 4325

Sequence ID	3L_DroMel_CAF1
Location	12,709,118 – 12,709,208
Length	90
Max. P	0.941683

overview

Window 4

Location	12,709,118 – 12,709,208
Length	90
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	81.76
Mean single sequence MFE	-28.39
Consensus MFE	-20.75
Energy contribution	-21.87
Covariance contribution	1.11
Combinations/Pair	1.12
Mean z-score	-3.27
Structure conservation index	0.73
SVM decision value	1.32
SVM RNA-class probability	0.941683
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12709118 90 + 23771897
GCAUGUCGAUGCUAUUAAAUAUAAUUCUUGCAUAUAUUUUCCUUUGUGCGAUAUGUGUGCAAGGAUCUGUGAAACAAGGUAAUGUUUCAA----------------
((((....))))...........((((((((((((((..(((.....).)).))))))))))))))...(((((((......))))))).---------------- ( -24.80)
>DroPse_CAF1 554 101 + 1
GCAUGUCAAUGCUUUCAAAUAUUAUCCUUAUAUAUAUUUUUCUUUGCACAAUAUUUGUGCAUGGAUAUAAAAAGCAAGGUAACAGC--AAGCAACA---GUAUAAA
((.(((...(((((((......(((((.................((((((.....)))))).)))))......).))))))...))--).))....---....... ( -17.47)
>DroSec_CAF1 1543 106 + 1
GCAUGUCGAUGCUAUUAAAUAUUAUCCUUGCAUAUAUUUUCCUUUGUGCGAUAUGUGUGCAAGGAUCUAUGAAACAAGGUAAUGUUUCAAAUUGGACUUACCCGAA
((((....))))...........((((((((((((((..(((.....).)).))))))))))))))...(((((((......)))))))..((((......)))). ( -30.40)
>DroSim_CAF1 1518 106 + 1
GCAUGUCGAUGCUAUUAAAUAUAAUCCUUGCAUAUAUUUUCCUUUGUGCGAUAUGUGUGCAAGGAUCUAUGAAACAAGGUAAUGUUUCAAAUAGGACUUACCUGAA
((((....)))).......((((((((((((((((((..(((.....).)).)))))))))))))).)))).....((((((.((((......))))))))))... ( -30.30)
>DroEre_CAF1 1490 105 + 1
GCAUGUCGAUGCUUUUAAAUAUAAUCCUUGCAUAUAUUUUCCUUUGUGCGAUAUGUGUGCAAGGAACUGUGAAACAAGGUAAUGUUUCAA-UAGGAGUUCCUUGCA
((((((((.(((....(((((((.........)))))))......))))))))))).(((((((((((.(((((((......))))))).-....))))))))))) ( -34.10)
>DroYak_CAF1 1527 105 + 1
GCAUGUCGAUGCUUUUAAAUAUAAUCCUUGCAUAUAUUUUCCUUUGUGCGAUAUGUGUGCAAGGAACUGUGAAACAAGGUAAUGUUUCAA-UAGGAGUUUCUUGCA
(((....((.(((((((.......(((((((((((((..(((.....).)).)))))))))))))....(((((((......))))))).-))))))).)).))). ( -33.30)
>consensus
GCAUGUCGAUGCUAUUAAAUAUAAUCCUUGCAUAUAUUUUCCUUUGUGCGAUAUGUGUGCAAGGAUCUAUGAAACAAGGUAAUGUUUCAA_UAGGA_UUACCUGAA
((((....))))............(((((((((((((..((........)).)))))))))))))....(((((((......)))))))................. (-20.75 = -21.87 +   1.11)

alignment

secondary structure

dotplot

Window 5

Location	12,709,118 – 12,709,208
Length	90
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	81.76
Mean single sequence MFE	-21.00
Consensus MFE	-14.09
Energy contribution	-14.70
Covariance contribution	0.62
Combinations/Pair	1.26
Mean z-score	-2.18
Structure conservation index	0.67
SVM decision value	0.61
SVM RNA-class probability	0.798623
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12709118 90 - 23771897
----------------UUGAAACAUUACCUUGUUUCACAGAUCCUUGCACACAUAUCGCACAAAGGAAAAUAUAUGCAAGAAUUAUAUUUAAUAGCAUCGACAUGC
----------------.(((((((......)))))))....(((((((.........)))...))))(((((((.........)))))))....((((....)))) ( -14.40)
>DroPse_CAF1 554 101 - 1
UUUAUAC---UGUUGCUU--GCUGUUACCUUGCUUUUUAUAUCCAUGCACAAAUAUUGUGCAAAGAAAAAUAUAUAUAAGGAUAAUAUUUGAAAGCAUUGACAUGC
.......---........--(((((((...(((((((..(((((.((((((.....))))))........((....)).)))))......))))))).))))).)) ( -19.80)
>DroSec_CAF1 1543 106 - 1
UUCGGGUAAGUCCAAUUUGAAACAUUACCUUGUUUCAUAGAUCCUUGCACACAUAUCGCACAAAGGAAAAUAUAUGCAAGGAUAAUAUUUAAUAGCAUCGACAUGC
.....(((.(((.....(((((((......)))))))...(((((((((......((........)).......)))))))))................))).))) ( -21.82)
>DroSim_CAF1 1518 106 - 1
UUCAGGUAAGUCCUAUUUGAAACAUUACCUUGUUUCAUAGAUCCUUGCACACAUAUCGCACAAAGGAAAAUAUAUGCAAGGAUUAUAUUUAAUAGCAUCGACAUGC
.....(((.(((((((((((((((......)))))))..((((((((((......((........)).......))))))))))......)))))....))).))) ( -23.52)
>DroEre_CAF1 1490 105 - 1
UGCAAGGAACUCCUA-UUGAAACAUUACCUUGUUUCACAGUUCCUUGCACACAUAUCGCACAAAGGAAAAUAUAUGCAAGGAUUAUAUUUAAAAGCAUCGACAUGC
(((((((((((....-.(((((((......))))))).)))))))))))..(((.(((.........(((((((.........)))))))........))).))). ( -26.63)
>DroYak_CAF1 1527 105 - 1
UGCAAGAAACUCCUA-UUGAAACAUUACCUUGUUUCACAGUUCCUUGCACACAUAUCGCACAAAGGAAAAUAUAUGCAAGGAUUAUAUUUAAAAGCAUCGACAUGC
((((((.((((....-.(((((((......))))))).)))).))))))..(((.(((.........(((((((.........)))))))........))).))). ( -19.83)
>consensus
UUCAAGUAA_UCCUA_UUGAAACAUUACCUUGUUUCACAGAUCCUUGCACACAUAUCGCACAAAGGAAAAUAUAUGCAAGGAUUAUAUUUAAAAGCAUCGACAUGC
.................(((((((......)))))))..((((((((((......((........)).......))))))))))..........((((....)))) (-14.09 = -14.70 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:39 2006