Locus 7315

Sequence ID	3L_DroMel_CAF1
Location	19,604,782 – 19,604,878
Length	96
Max. P	0.686967

overview

Window 4

Location	19,604,782 – 19,604,878
Length	96
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	79.38
Mean single sequence MFE	-28.55
Consensus MFE	-15.97
Energy contribution	-16.50
Covariance contribution	0.53
Combinations/Pair	1.28
Mean z-score	-1.92
Structure conservation index	0.56
SVM decision value	0.32
SVM RNA-class probability	0.686967
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19604782 96 + 23771897
UAUCGAUUAGGCGAGCAACAAUAUAAGCUUUCUGGUAAGUAGAUUAUU--UCUAAAAUCUCUGGGGAUUAUCGUUGGACUGUGGCUGCUCGCCCGCCU
........((((((((..........)))....((..(((((.((((.--((((((((((....)))))....)))))..)))))))))..))))))) ( -24.70)
>DroSec_CAF1 19764 96 + 1
UAUCGGUUAGGCGAGCAACAAAAUAAGCUUUCUGCUAAGUAGGUUAUU--CCUAAAAUCUCUGGGGAUUAUCGUUGGACUGUGGCUGCUCGCCCGCCU
....(((..((((((((.((.....(((.....))).(((.(((.(((--((((.......))))))).))).....))).))..)))))))).))). ( -30.40)
>DroSim_CAF1 19566 96 + 1
UAUCGGUUAGGCGAGCAACAAAAUAAGCUUUCUGCUAAGUAGAUUAUU--CCUAAAAUCUCUGGGGAUUAUCGUUGGACUGUGGCUGCUCGCCCGCCU
....(((..((((((((.((.....(((.....))).(((.(((.(((--((((.......))))))).))).....))).))..)))))))).))). ( -31.00)
>DroEre_CAF1 19545 96 + 1
UAUCGGUUAGGCGAGCAACAAAAUAAGCUUUUUGCUAAGUAGGUAAUU--UCUAAAAUCUCUGGGGAUUAUCGCUGGACUGCGGCUGCUCGCCCGCCU
....(((..((((((((........(((.....))).....((((((.--.(((.......)))..))))))((((.....)))))))))))).))). ( -34.40)
>DroYak_CAF1 19515 96 + 1
UAUGGGUUAGGCGAGCAACAAAAUAAGCUUUCUGCUAAAUAGGUAAUU--CCUAAAACCUCUGCGGAUUAUCGCUGGAUUGUGACUGCUCGCCCGCCU
...((((..((((((((((((....(((.....)))...((((.....--))))...((...(((......))).)).))))...)))))))).)))) ( -30.80)
>DroAna_CAF1 19858 77 + 1
UAUG---UGGGCGA--AAC----------------UCUAUAGGUCACUCUCUUAAGCUCCCUGAUGACUUUCCCCGGUCUGAGACGGCUCGCCUGCCU
...(---..(((((--..(----------------(((.((((...((......))...))))..((((......))))..))).)..)))))..).. ( -20.00)
>consensus
UAUCGGUUAGGCGAGCAACAAAAUAAGCUUUCUGCUAAGUAGGUUAUU__CCUAAAAUCUCUGGGGAUUAUCGCUGGACUGUGGCUGCUCGCCCGCCU
.........((((((((......................((((.......)))).....(((((.(.....).))))).......))))))))..... (-15.97 = -16.50 +   0.53)

alignment

secondary structure

dotplot

Window 5

Location	19,604,782 – 19,604,878
Length	96
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	79.38
Mean single sequence MFE	-25.77
Consensus MFE	-15.49
Energy contribution	-16.18
Covariance contribution	0.70
Combinations/Pair	1.21
Mean z-score	-1.63
Structure conservation index	0.60
SVM decision value	0.18
SVM RNA-class probability	0.622482
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19604782 96 - 23771897
AGGCGGGCGAGCAGCCACAGUCCAACGAUAAUCCCCAGAGAUUUUAGA--AAUAAUCUACUUACCAGAAAGCUUAUAUUGUUGCUCGCCUAAUCGAUA
....(((((((((((....(((....))).........(((((.....--...))))).....................)))))))))))........ ( -22.90)
>DroSec_CAF1 19764 96 - 1
AGGCGGGCGAGCAGCCACAGUCCAACGAUAAUCCCCAGAGAUUUUAGG--AAUAACCUACUUAGCAGAAAGCUUAUUUUGUUGCUCGCCUAACCGAUA
.((.(((((((((((.............................((((--.....))))...(((.....)))......)))))))))))..)).... ( -26.20)
>DroSim_CAF1 19566 96 - 1
AGGCGGGCGAGCAGCCACAGUCCAACGAUAAUCCCCAGAGAUUUUAGG--AAUAAUCUACUUAGCAGAAAGCUUAUUUUGUUGCUCGCCUAACCGAUA
.((.(((((((((((.....(((......((((......))))...))--)...........(((.....)))......)))))))))))..)).... ( -26.10)
>DroEre_CAF1 19545 96 - 1
AGGCGGGCGAGCAGCCGCAGUCCAGCGAUAAUCCCCAGAGAUUUUAGA--AAUUACCUACUUAGCAAAAAGCUUAUUUUGUUGCUCGCCUAACCGAUA
.((.((((((((((((((......))).....................--............(((.....)))......)))))))))))..)).... ( -27.10)
>DroYak_CAF1 19515 96 - 1
AGGCGGGCGAGCAGUCACAAUCCAGCGAUAAUCCGCAGAGGUUUUAGG--AAUUACCUAUUUAGCAGAAAGCUUAUUUUGUUGCUCGCCUAACCCAUA
.((.((((((((((.((.......(((......)))....(((.((((--.....))))...))).............))))))))))))...))... ( -28.10)
>DroAna_CAF1 19858 77 - 1
AGGCAGGCGAGCCGUCUCAGACCGGGGAAAGUCAUCAGGGAGCUUAAGAGAGUGACCUAUAGA----------------GUU--UCGCCCA---CAUA
.(((......)))..........(((((((.((...(((..((((....))))..)))...))----------------.))--)).))).---.... ( -24.20)
>consensus
AGGCGGGCGAGCAGCCACAGUCCAACGAUAAUCCCCAGAGAUUUUAGG__AAUAACCUACUUAGCAGAAAGCUUAUUUUGUUGCUCGCCUAACCGAUA
....(((((((((((..............((((......)))).((((.......))))....................)))))))))))........ (-15.49 = -16.18 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:48 2006