Locus 2811

Sequence ID	2R_DroMel_CAF1
Location	9,797,242 – 9,797,378
Length	136
Max. P	0.932175

overview

Window 7

Location	9,797,242 – 9,797,355
Length	113
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	72.93
Mean single sequence MFE	-26.85
Consensus MFE	-11.84
Energy contribution	-13.48
Covariance contribution	1.65
Combinations/Pair	1.33
Mean z-score	-2.16
Structure conservation index	0.44
SVM decision value	1.22
SVM RNA-class probability	0.932175
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9797242 113 - 20766785
-----AUAUAUCUGAAAACUCUCAGUGAUGACCUGGUUAAGGUCAUUGCAAUAACGAACUGAGUUCACGAAUGGUUCAUCGAAUGUCGUUUGUUUGAAAAUGCCAUUUUAAAUACACU
-----.......((((....((((((((((((((.....))))))))..........)))))))))).(((((((...(((((((.....)))))))....))))))).......... ( -27.00)
>DroSec_CAF1 35350 113 - 1
-----AUGUAUCUGAAAACUCUCAGCGAUGACCCGGUUAAGGUCAUUGCAAUAACGAACUGAGUUCACGAAUGGUUCAUCAAAUGUCGCUUGUUUGAAAAUGCCAUUUUAAAUACACU
-----.(((((.(((((....((.(((((((((.......)))))))))......((((...))))..)).((((...(((((((.....)))))))....))))))))).))))).. ( -29.40)
>DroSim_CAF1 34874 113 - 1
-----AUGUAUCUGAAAACUCUCAGUGAUGACCCGGUUAAGGUCAUUGCAAUAACGAACUGAGUUCACGAAUGGUUCAUCAAAUGUCGCUUGUUUGAAAAUGCCAUUUUAAAUACACU
-----.(((((.(((((....((.(..((((((.......))))))..)......((((...))))..)).((((...(((((((.....)))))))....))))))))).))))).. ( -27.20)
>DroEre_CAF1 38324 118 - 1
GCCACCUGUAUCUGGAAAACUCCAGUGAUGACCUGAUUAAGGUCAUUGCUAUAACAAACAAAGUUCAUGAAUGGUUCAUCCAAUGUCGUUUAUAUGGAAAUGCCAUUUUAAAUACACU
......(((....(((....)))((..(((((((.....)))))))..))...)))......((....(((((((...(((((((.....))).))))...))))))).....))... ( -30.60)
>DroYak_CAF1 36956 118 - 1
ACCACUUGUUUCUGGAAAAGUCUAGUGACGACCUGACUAAGGUCAUUGCAAUAACAAACAGAGUUCAUUAAUGGUUCAUCCCAUGUCAUUUGUAUGGAAAUGCCAUUUUAAACACACU
.....(((((..((.((..(((....)))(((((.....))))).)).))..))))).....(((....((((((.....(((((.(....))))))....))))))...)))..... ( -26.40)
>DroAna_CAF1 35804 98 - 1
ACGACCUUGUUUUGUAAAGACC------UUGCCCCAUCAAGGUCAUUCAUAUAG---------CUCUCAUAUAGU-CACAUGAUGUGUUAUUUAUGAAAAUGUGAUUUUAAAUU----
..(((((((....((((.....------)))).....)))))))..((((((..---------...(((((....-(((.....))).....)))))..)))))).........---- ( -20.50)
>consensus
_____AUGUAUCUGAAAACUCCCAGUGAUGACCCGAUUAAGGUCAUUGCAAUAACGAACUGAGUUCACGAAUGGUUCAUCAAAUGUCGUUUGUAUGAAAAUGCCAUUUUAAAUACACU
......(((((.(((((.......(((((((((.......)))))))))..............(((((((((((...........))))))))..))).......))))).))))).. (-11.84 = -13.48 +   1.65)

alignment

secondary structure

dotplot

Window 8

Location	9,797,280 – 9,797,378
Length	98
Sequences	3
Columns	101
Reading direction	forward
Mean pairwise identity	92.72
Mean single sequence MFE	-23.33
Consensus MFE	-23.08
Energy contribution	-22.20
Covariance contribution	-0.88
Combinations/Pair	1.15
Mean z-score	-1.46
Structure conservation index	0.99
SVM decision value	0.44
SVM RNA-class probability	0.737989
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9797280 98 + 20766785
GAUGAACCAUUCGUGAACUCAGUUCGUUAUUGCAAUGACCUUAACCAGGUCAUCACUGAGAGUUUUCAGAUAUAUUCUGAUUAUAUUUAGGGUAUAUG---
.((((.....))))...((((((..((....)).(((((((.....))))))).)))))).........(((((((((((......))))))))))).--- ( -24.50)
>DroSec_CAF1 35388 101 + 1
GAUGAACCAUUCGUGAACUCAGUUCGUUAUUGCAAUGACCUUAACCGGGUCAUCGCUGAGAGUUUUCAGAUACAUUCUGAUCAUAUUUAGGAUACAUACCU
......((....((((.((((((..((....)).(((((((.....))))))).)))))).....(((((.....))))))))).....)).......... ( -23.40)
>DroSim_CAF1 34912 100 + 1
GAUGAACCAUUCGUGAACUCAGUUCGUUAUUGCAAUGACCUUAACCGGGUCAUCACUGAGAGUUUUCAGAUACAUUCUGGUCAUAUUUAGGAUACAUACC-
......((....((((.((((((..((....)).(((((((.....))))))).)))))).....(((((.....))))))))).....)).........- ( -22.10)
>consensus
GAUGAACCAUUCGUGAACUCAGUUCGUUAUUGCAAUGACCUUAACCGGGUCAUCACUGAGAGUUUUCAGAUACAUUCUGAUCAUAUUUAGGAUACAUACC_
......((....((((.((((((..((....)).(((((((.....))))))).)))))).....(((((.....))))))))).....)).......... (-23.08 = -22.20 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:01 2006