Locus 5518

Sequence ID	X_DroMel_CAF1
Location	14,285,103 – 14,285,343
Length	240
Max. P	0.888505

overview

Window 3

Location	14,285,103 – 14,285,223
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.75
Mean single sequence MFE	-25.26
Consensus MFE	-21.68
Energy contribution	-21.88
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.55
Structure conservation index	0.86
SVM decision value	0.95
SVM RNA-class probability	0.888505
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14285103 120 - 22224390
CAAAAAGUAACUCAAUGGGAUUUCAGAUGGGAAACGCCUCGCGAGUGCCAUAAGCAAAAAGUUUGUAAAAUGGAAGCAUUUUGGAGCAAAAUUCAGUAAUCGAAAAAUGCAAAGAAGCAA
..............((((.((((..((.((....).).))..)))).))))..((........(.(((((((....))))))).)(((...(((.......)))...)))......)).. ( -20.50)
>DroSec_CAF1 25483 120 - 1
CAAAAAGUAACUCAAUGGGAUUUCAGAUGGGAAAUGCCUCGCGAGUGCCAUAAGCGAAAAGUUUGUAAAAUGGAAGCAUUUUGGGGCAAAAUUCAGUAAUCGAAAGAUGCAAAGAAGUAA
.........((((...((.(((((......))))).))....))))(((((((((.....))))))((((((....))))))..)))........(((.((....))))).......... ( -28.10)
>DroSim_CAF1 28782 120 - 1
CAAAAAGUAACUCAAUGGGAUUUCAGAUGGGAAAUGCCUCGCGAGUGCCAUAAGCGAAAAGUUUGUAAAAUGGAAGCAUUUUGGGGCAAAAUUCAGUAAUCGAAAGAUGCAAACAAGAAA
.........((((...((.(((((......))))).))....))))(((((((((.....))))))((((((....))))))..)))........(((.((....))))).......... ( -28.10)
>DroEre_CAF1 27304 119 - 1
CAAAAAGUAACUCAAUGGGAUUUCAGCUGGGAAAUGCCUCGCGAGUGCCAUAAGCAAAAAGUUUGUAAAGUGGCAGCAUUUUAGGGCAAAAUUCAGUAAUCGAAAAAUGCAA-GAGGAAG
..........(((....((((((..(((..(((((((..(....)((((((..((((.....))))...)))))))))))))..))).)))))).(((.........)))..-))).... ( -27.00)
>DroYak_CAF1 29103 120 - 1
CAAAAAGUAACUCAAUGGGAUUUCAGCUGGGAAAUGCCUCGCGAGUGCCAUAAGCCGAAAGUUUAUAAAGUGGAAGCAUUUCAGGGCAAAAUGUAGUAACCGAAAAAUGCAAAGCAAAAA
......(((((((...((.(((((......))))).))....))))((((((((.(....)))))).(((((....)))))...)))....................))).......... ( -22.60)
>consensus
CAAAAAGUAACUCAAUGGGAUUUCAGAUGGGAAAUGCCUCGCGAGUGCCAUAAGCAAAAAGUUUGUAAAAUGGAAGCAUUUUGGGGCAAAAUUCAGUAAUCGAAAAAUGCAAAGAAGAAA
......(((((((...((.(((((......))))).))....))))(((((((((.....))))))((((((....))))))..)))....................))).......... (-21.68 = -21.88 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	14,285,223 – 14,285,343
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.89
Mean single sequence MFE	-37.22
Consensus MFE	-24.88
Energy contribution	-24.52
Covariance contribution	-0.36
Combinations/Pair	1.10
Mean z-score	-2.60
Structure conservation index	0.67
SVM decision value	0.35
SVM RNA-class probability	0.698373
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14285223 120 + 22224390
UGGCGCACGGAUAUGCAGGCAAACUUUUCUGAGAAGAGCUCGGAUUAUUCGCAGAGUUAACUGCACAUCAGGUUGACCGAGUAUCCGAGCAUCCGAGCAUCCAAGUAUCUAAGUAUCUAA
(((.((.(((((...((((........))))......((((((((.((((((((......))))......((....))))))))))))))))))).))..)))................. ( -38.30)
>DroSec_CAF1 25603 112 + 1
UGGCACACGGAUAUGCAGGAAAACUUUUCUGAGAAGAGCUCGGAUUAUUCGCAGAGUUAACUGCACAUCAGGUUGACCGAGUAUCCGA--------GCAUCCAAGUAUCUGAGUAUCCAG
(((.((.(((((((...(((...((((.....)))).((((((((.((((((((......))))......((....))))))))))))--------)).)))..))))))).))..))). ( -40.00)
>DroSim_CAF1 28902 112 + 1
UGGCGCACGGAUAUGCAGGAAAACUUUUCUGAGAAGAGCUCGGAUUAUUCGCAGAGUUAACUGCACAUCAGGUUGACCGAGUAUCCGA--------GCAUCCAAGUAUCUGAGUAUCCAG
(((.((.(((((((...(((...((((.....)))).((((((((.((((((((......))))......((....))))))))))))--------)).)))..))))))).))..))). ( -40.30)
>DroEre_CAF1 27423 104 + 1
UGGCGCACGGAUAUGCAGCGAAACUUUUGUGAGAAGAGCUCGGAUUAUUCGCAGAGUUAACUGCACAUCAGGUUGACCGAGUAUC----------------CGAGUAUCCAAGUAUCCAA
........((((((...(.((..((((.....)))).((((((((.((((((((......))))......((....)))))))))----------------))))).)))..)))))).. ( -31.20)
>DroYak_CAF1 29223 112 + 1
UGGCGCAAGGAUAUGCAGGGAAACUUUUCGGCGAAGAGCUCGGAUUAUUCGCAGAGUUAACUGCACAUCAGGUUGACCGAGUAUCAGA--------GCAGCCAAGUAUCCAAGUAUCCAA
........((((((....(((.((((...(((.....((((.(((.((((((((......))))......((....))))))))).))--------)).))))))).)))..)))))).. ( -36.30)
>consensus
UGGCGCACGGAUAUGCAGGAAAACUUUUCUGAGAAGAGCUCGGAUUAUUCGCAGAGUUAACUGCACAUCAGGUUGACCGAGUAUCCGA________GCAUCCAAGUAUCUAAGUAUCCAA
(((.((..((((((...((....((((.....)))).((((((.......((((......)))).((......)).))))))..................))..))))))..))..))). (-24.88 = -24.52 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:54 2006