Locus 4958

Sequence ID	3R_DroMel_CAF1
Location	13,043,390 – 13,043,550
Length	160
Max. P	0.999943

overview

Window 2

Location	13,043,390 – 13,043,510
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-36.72
Consensus MFE	-32.60
Energy contribution	-32.60
Covariance contribution	0.00
Combinations/Pair	1.15
Mean z-score	-1.49
Structure conservation index	0.89
SVM decision value	1.11
SVM RNA-class probability	0.916688
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13043390 120 - 27905053
CACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUAACGGCAGGCACUUCCUUUGGAGUAUUCACAUUAGGAAUGUUGUUUCCAUGGGCAAACACUAUAGGCACAGCGGUC
.((((.(((((......((((((((((...((((.....)))).....))))))))))))))).))))...........((.((((((.((.((((.......)))).)).)))))).)) ( -36.80)
>DroSec_CAF1 63496 120 - 1
CACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGGAAUAUUCACAUUAGGAAUGUUGUUCCCAUGGGCAAACACAAUAGGCACAGCGGUG
((((.(....((...((((((((((((...((((.....)))).....))))))))).(((.((((((((((.......)))))))....))).)))......)))...))....))))) ( -32.80)
>DroSim_CAF1 55731 119 - 1
CACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGG-AUAUUCACAUUAGGAAUGCUGUUCCCAUGGGCAAACACAAUAGGCACAGCGGUG
(((((.(((((......((((((((((...((((.....)))).....))))))))))))))).)-)...............((((((.((..((........))...)).))))))))) ( -34.10)
>DroEre_CAF1 63958 120 - 1
CACUUAGGAGGCAUUCUGAGUGUCUGCAAUUCGAUAUCCUCGAUCACGGCAGGCACUUCUUUUGGAAUAUUCACAUUAGGCAUGCUGUUCCCAUGGGCAAAUACCAUAGGCACAGCGGUG
((((...(((..(((((((((((((((...((((.....)))).....)))))))))).....))))).)))...........(((((.((.((((.......)))).)).))))))))) ( -40.40)
>DroYak_CAF1 65314 120 - 1
CACAUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGGAAUAUUCACGUUAGGCAUGCUGUUCCCAUGGGCAAAUAGCAUAGGCACAGCGGUG
(((.(.(((((......((((((((((...((((.....)))).....))))))))))))))).)........((((..((((((((((((....))..))))))))..))..))))))) ( -39.50)
>consensus
CACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGGAAUAUUCACAUUAGGAAUGCUGUUCCCAUGGGCAAACACAAUAGGCACAGCGGUG
(((...(((((......((((((((((...((((.....)))).....)))))))))))))))...................((((((.((.((((.......)))).)).))))))))) (-32.60 = -32.60 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	13,043,430 – 13,043,550
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.75
Mean single sequence MFE	-35.78
Consensus MFE	-33.38
Energy contribution	-33.66
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.69
Structure conservation index	0.93
SVM decision value	4.72
SVM RNA-class probability	0.999943
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13043430 120 - 27905053
CCAGGGAAUUUUAGCCUUUCUUAUAGUAUUCUUACUACAGCACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUAACGGCAGGCACUUCCUUUGGAGUAUUCACAUUAGG
((((((.......(((((((...(((((....)))))........))))))).....((((((((((...((((.....)))).....)))))))))).))))))............... ( -37.60)
>DroSec_CAF1 63536 120 - 1
CCAGGGAAUUUUCGCCUUUCUUCUAGUAUUUUUACUACAGCACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGGAAUAUUCACAUUAGG
((((((.......(((((((...(((((....)))))........))))))).....((((((((((...((((.....)))).....)))))))))).))))))............... ( -37.70)
>DroSim_CAF1 55771 119 - 1
CCAGGGAAUUUUUGCCUUUCUUCUAGUAUUUCUACUACAGCACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGG-AUAUUCACAUUAGG
((((((......((((((((...(((((....)))))........))))))))....((((((((((...((((.....)))).....)))))))))).))))))-.............. ( -37.30)
>DroEre_CAF1 63998 120 - 1
CCAGGGACUUUUCGCAUUUCUGCUAGUAUUCUUACUACAGCACUUAGGAGGCAUUCUGAGUGUCUGCAAUUCGAUAUCCUCGAUCACGGCAGGCACUUCUUUUGGAAUAUUCACAUUAGG
.(((((..(((((......(((.(((((....))))))))......)))))..)))))(((((((((...((((.....)))).....))))))))).((..((((....)).))..)). ( -30.90)
>DroYak_CAF1 65354 120 - 1
CCAGGGAAUCGUUGCAUUUCUGCUAGUAUUCCUACUACAGCACAUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGGAAUAUUCACGUUAGG
(((((((((((.(((.((((((((((((....))))..))))...)))).)))...)))((((((((...((((.....)))).....)))))))))))).))))............... ( -35.40)
>consensus
CCAGGGAAUUUUCGCCUUUCUUCUAGUAUUCUUACUACAGCACUUGAGAGGCAUUUUGAGUGUCUGCAAUUCGAUAUCCUCGAUUACGGCAGGCACUUCCUUUGGAAUAUUCACAUUAGG
((((((.......(((((((...(((((....)))))........))))))).....((((((((((...((((.....)))).....)))))))))).))))))............... (-33.38 = -33.66 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:00 2006