Locus 6193

Sequence ID	3L_DroMel_CAF1
Location	16,407,908 – 16,408,040
Length	132
Max. P	0.999722

overview

Window 4

Location	16,407,908 – 16,408,009
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	85.64
Mean single sequence MFE	-23.35
Consensus MFE	-20.72
Energy contribution	-20.92
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.78
Structure conservation index	0.89
SVM decision value	3.15
SVM RNA-class probability	0.998571
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16407908 101 + 23771897
UGGCUUUCUGCAUCACUGCUUUCAUUUGCAUUCGAUAGCAGAAAUGCAACUUCCGUUGCACUGAGCGAAAAUAAUAAUAUCAUUUCAUUUUAUGCUUAAAC
....((((((((((..(((........)))...))).)))))))((((((....)))))).(((((((((((..............))))).))))))... ( -23.84)
>DroSec_CAF1 22825 101 + 1
UGGCUUUCUGCAUCACUGCUUUCAUUUGCAUUCGAUAGCAGAAAUGCAACUUCCGUUGCACUGAGCGAAAAUAAUUAUAUCAUUUUAAAUUAUGCAUAAAC
..((((((((((((..(((........)))...))).)))))..((((((....))))))..))))(...((((((.((......)))))))).)...... ( -21.90)
>DroSim_CAF1 22942 101 + 1
UGGCUUUCUGCAUCACUGCUUUCAUUUGCAUUCGAUAGCAGAAAUGCAACUUCCGUUGCACUGAGCGAAAAUAUUAAUAUAAUUUCAAAUUAUGCAUAAAC
..((((((((((((..(((........)))...))).)))))..((((((....))))))..))))((((.(((....))).))))............... ( -23.80)
>DroEre_CAF1 24215 101 + 1
UGGCUUUCUGCAUCACUGCUUUCAUUUGCAUUCGCUAGCAGAUAUGCAACUUCCGUUGCACUGAGCGAAUAUAUCAAUAGGAUUUCUUUUUAUGCUUAAGC
..((((...((((....((........))(((((((..(((...((((((....)))))))))))))))).....................))))..)))) ( -24.60)
>DroYak_CAF1 23267 83 + 1
UGGCUUUCUGCAUCACUGCUUUCAUUUGCAUUCGAUAGCAGAUAUGCAACUUCCGUUGCACUGAGCAAAAAUGUCAAUAUU------------------AC
(((((((.(((.((((((((.((..........)).)))))...((((((....)))))).)))))).))).)))).....------------------.. ( -22.60)
>consensus
UGGCUUUCUGCAUCACUGCUUUCAUUUGCAUUCGAUAGCAGAAAUGCAACUUCCGUUGCACUGAGCGAAAAUAUUAAUAUCAUUUCAAAUUAUGCAUAAAC
..((((((((((((..(((........)))...))).)))))..((((((....))))))..))))................................... (-20.72 = -20.92 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	16,407,908 – 16,408,009
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	85.64
Mean single sequence MFE	-28.06
Consensus MFE	-24.72
Energy contribution	-24.92
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.50
Structure conservation index	0.88
SVM decision value	3.95
SVM RNA-class probability	0.999722
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16407908 101 - 23771897
GUUUAAGCAUAAAAUGAAAUGAUAUUAUUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAUGCAAAUGAAAGCAGUGAUGCAGAAAGCCA
...............((((((((...)))))))).(((..(((((((....)))))))((((((.((((..(((........))).))))))))))))).. ( -27.50)
>DroSec_CAF1 22825 101 - 1
GUUUAUGCAUAAUUUAAAAUGAUAUAAUUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAUGCAAAUGAAAGCAGUGAUGCAGAAAGCCA
..((((((((........))).)))))........(((..(((((((....)))))))((((((.((((..(((........))).))))))))))))).. ( -27.70)
>DroSim_CAF1 22942 101 - 1
GUUUAUGCAUAAUUUGAAAUUAUAUUAAUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAUGCAAAUGAAAGCAGUGAUGCAGAAAGCCA
...............((((.(((....))).))))(((..(((((((....)))))))((((((.((((..(((........))).))))))))))))).. ( -28.30)
>DroEre_CAF1 24215 101 - 1
GCUUAAGCAUAAAAAGAAAUCCUAUUGAUAUAUUCGCUCAGUGCAACGGAAGUUGCAUAUCUGCUAGCGAAUGCAAAUGAAAGCAGUGAUGCAGAAAGCCA
((((..((((........(((.....)))....((((((((((((((....))))))...)))..)))))))))........(((....)))...)))).. ( -29.40)
>DroYak_CAF1 23267 83 - 1
GU------------------AAUAUUGACAUUUUUGCUCAGUGCAACGGAAGUUGCAUAUCUGCUAUCGAAUGCAAAUGAAAGCAGUGAUGCAGAAAGCCA
..------------------..........(((((((((((((((((....)))))))..(((((.(((........))).)))))))).))))))).... ( -27.40)
>consensus
GUUUAAGCAUAAAAUGAAAUGAUAUUAAUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAUGCAAAUGAAAGCAGUGAUGCAGAAAGCCA
...................................(((..(((((((....))))))).(((((.((((..(((........))).))))))))).))).. (-24.72 = -24.92 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	16,407,937 – 16,408,040
Length	103
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	76.64
Mean single sequence MFE	-20.66
Consensus MFE	-14.24
Energy contribution	-15.60
Covariance contribution	1.36
Combinations/Pair	1.05
Mean z-score	-2.19
Structure conservation index	0.69
SVM decision value	1.95
SVM RNA-class probability	0.983747
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16407937 103 - 23771897
---------ACUGUAACUCAACCAACUAUUUUAACAAAUGGUUUAAGCAUAAAAUGAAAUGAUAUUAUUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAU
---------........((....((((((((....))))))))..((((......((((((((...)))))))).....((((((((....))))))))..))))...)).. ( -20.80)
>DroSec_CAF1 22854 103 - 1
---------ACUUUAACUCAACCAACUAUGUUACCAAAUGGUUUAUGCAUAAUUUAAAAUGAUAUAAUUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAU
---------.................(((((.(((....)))....)))))....((((((((...)))))))).((..((((((((....))))))))...))........ ( -21.50)
>DroSim_CAF1 22971 103 - 1
---------ACUUUAACUCAACCAACUAUAUUACCAAAUGGUUUAUGCAUAAUUUGAAAUUAUAUUAAUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAU
---------.................((((..(((....))).))))........((((.(((....))).))))((..((((((((....))))))))...))........ ( -19.40)
>DroEre_CAF1 24244 112 - 1
AUACCGCCGACCUUAUCUCAACAAAACAUUAUACCAAAUGGCUUAAGCAUAAAAAGAAAUCCUAUUGAUAUAUUCGCUCAGUGCAACGGAAGUUGCAUAUCUGCUAGCGAAU
.............(((.((((.....((((......))))((....))................)))).)))(((((((((((((((....))))))...)))..)))))). ( -23.40)
>DroYak_CAF1 23296 81 - 1
-------------UAUCUCAACAAAGCAUUAUUCCAAAUGGU------------------AAUAUUGACAUUUUUGCUCAGUGCAACGGAAGUUGCAUAUCUGCUAUCGAAU
-------------...........((((.((((((....)).------------------)))).(((((....)).)))(((((((....)))))))...))))....... ( -18.20)
>consensus
_________ACUUUAACUCAACCAACUAUUUUACCAAAUGGUUUAAGCAUAAAAUGAAAUGAUAUUAAUAUUUUCGCUCAGUGCAACGGAAGUUGCAUUUCUGCUAUCGAAU
.................((....(((((((......)))))))................................((..((((((((....))))))))...))....)).. (-14.24 = -15.60 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:28 2006