Locus 5699

Sequence ID	X_DroMel_CAF1
Location	14,738,813 – 14,738,950
Length	137
Max. P	0.747041

overview

Window 1

Location	14,738,813 – 14,738,911
Length	98
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	79.92
Mean single sequence MFE	-33.03
Consensus MFE	-24.60
Energy contribution	-25.05
Covariance contribution	0.45
Combinations/Pair	1.13
Mean z-score	-1.27
Structure conservation index	0.74
SVM decision value	0.30
SVM RNA-class probability	0.677558
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14738813 98 + 22224390
CAUCAGCGUAUUUGCCGGACCCGCCGAACGGGCAGCGCACUGGGCGCUAAGGAACUCCAUU------GUGGUGUUCCAAA-AUGUCCUUUAGUUGUGCUAAA-------AGA
....((((((.(((..((((..(((.....)))(((((.....)))))..(((((.((...------..)).)))))...-..))))..))).))))))...-------... ( -31.70)
>DroSec_CAF1 31917 96 + 1
CAUCAGCGUAUUUGCCGGACCCGCCGAACGGGCAGCGCACUGGGCGCUAAGGAACUCCAUU------GUGGUGUUCCAAA-AUGUCCUUUAGAUGAGCUAAA-------A--
....(((.((((((..((((..(((.....)))(((((.....)))))..(((((.((...------..)).)))))...-..))))..)))))).)))...-------.-- ( -34.60)
>DroSim_CAF1 35990 96 + 1
CAUCAGCGUAUUUGCCGGACCCGCCGAACGGGCAGCGCACUGGGCGCUAAGGAACUCCAUU------GUGGUGUUCCAAA-AUGUCCUUUAGAUGAGCUAAA-------A--
....(((.((((((..((((..(((.....)))(((((.....)))))..(((((.((...------..)).)))))...-..))))..)))))).)))...-------.-- ( -34.60)
>DroEre_CAF1 28757 98 + 1
CAUCAGGGUAUUCGCCGGACCAGCCGAACGGGCGGCGCACUGGGCGCUAAGGAACUCCAUC------GUGGUGUUCCAAA-ACGUCCUUCACGUGUGCUGGA-------AAA
..((..(((....))).))(((((((((.(((((((((.....))))...(((((.((...------..)).)))))...-.))))))))....).))))).-------... ( -36.00)
>DroWil_CAF1 28906 102 + 1
CAUCAACGUGUUCGCCGGCCCCGCCGACCGUGCAGCGCACUGGGCACUGAGAAAUUCCAUGCCUUUUGUAGCUCUCCAAGAAUGCGCCGUA-AGAAGCCAAA-------C--
......(((((((((((((......).))).))((((((..(((((.((.(.....))))))))..))).)))......))))))).....-..........-------.-- ( -25.50)
>DroYak_CAF1 31472 105 + 1
CAUCAGCGUGUUCGCCGGACCCGCCGAACGGGCAGCGCACUGGGCGCUCAGGAACUCCAUU------GUGCUGUUCCAAA-AAGUCCUUGACGUGUGCUUAAAAAUAAAAAA
.....((.((((((.((....)).)))))).))(((((((.((((.....(((((..(...------..)..)))))...-..)))).....)))))))............. ( -35.80)
>consensus
CAUCAGCGUAUUCGCCGGACCCGCCGAACGGGCAGCGCACUGGGCGCUAAGGAACUCCAUU______GUGGUGUUCCAAA_AUGUCCUUUAGAUGAGCUAAA_______A__
.............(((((.....)))...(((((((((.....)))))..(((((.((((.......)))).)))))......)))).........)).............. (-24.60 = -25.05 +   0.45)

alignment

secondary structure

dotplot

Window 2

Location	14,738,853 – 14,738,950
Length	97
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	77.89
Mean single sequence MFE	-23.12
Consensus MFE	-14.89
Energy contribution	-15.70
Covariance contribution	0.81
Combinations/Pair	1.20
Mean z-score	-1.80
Structure conservation index	0.64
SVM decision value	0.46
SVM RNA-class probability	0.747041
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14738853 97 + 22224390
UGGGCGCUAAGGAACUCCAUUGUGGUGUUCCAAAAUGUCCUUUAGUUGUGCUAAA-------AGAAAAAUUGG-CCAUUAGUGCAACAGUAAAAAGAAAUAAGAG
.(((((....(((((.((.....)).)))))....)))))....((((..((((.-------...........-...))))..)))).................. ( -25.16)
>DroSec_CAF1 31957 95 + 1
UGGGCGCUAAGGAACUCCAUUGUGGUGUUCCAAAAUGUCCUUUAGAUGAGCUAAA-------A--AAAAUUGG-UCAUUAGUGUCACAGUAAAAAUAAAAAACAG
(((((((((((((((.((.....)).)))))....((.(((((((.....)))))-------.--......))-.)))))))))).))................. ( -22.91)
>DroEre_CAF1 28797 97 + 1
UGGGCGCUAAGGAACUCCAUCGUGGUGUUCCAAAACGUCCUUCACGUGUGCUGGA-------AAAAAAACUGC-UCAUUAGUAUCAUGGUAAAAAUUGAAAAAAU
.(((((....(((((.((.....)).)))))....)))))....((((((((((.-------...........-...)))))).))))................. ( -22.26)
>DroYak_CAF1 31512 105 + 1
UGGGCGCUCAGGAACUCCAUUGUGCUGUUCCAAAAAGUCCUUGACGUGUGCUUAAAAAUAAAAAAAAAAAUGCGUCAUUAGUGGCAUUGUUAAAACUGGAAAAAU
..(((((...((....))...))))).(((((....(((((((((((((....................))))))))..)).)))...((....))))))).... ( -22.15)
>consensus
UGGGCGCUAAGGAACUCCAUUGUGGUGUUCCAAAAUGUCCUUUACGUGUGCUAAA_______AAAAAAAUUGC_UCAUUAGUGUCACAGUAAAAAUAAAAAAAAG
..(((((((((((((.((.....)).))))).........(((((.....)))))......................)))))))).................... (-14.89 = -15.70 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:18 2006