Locus 6305

Sequence ID	X_DroMel_CAF1
Location	15,969,410 – 15,969,624
Length	214
Max. P	0.954196

overview

Window 9

Location	15,969,410 – 15,969,528
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	87.61
Mean single sequence MFE	-23.38
Consensus MFE	-20.73
Energy contribution	-21.22
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.89
SVM decision value	0.74
SVM RNA-class probability	0.837246
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15969410 118 + 22224390
CCAUCUGCAUUCCCAUGGCCUUUACCUUUCCCGCUCCUGCUGACAGGUUGGCUUAUUGAGCCCGAGACAAGAUAAGUGCUUUUGUCUCUCCGCUCCUCUCCUCUCCCCCCCCCCUCCC
................((((...((((.((..((....)).)).)))).))))....((((..(((((((((.......)))))))))...))))....................... ( -27.30)
>DroSec_CAF1 37432 104 + 1
CCAUCUGCAUUCCCAUGGCCUUUACCUUUCCCGCUCCUGCUGACAGGUUGGCUUAUUGAGCCCGAGACAAGAUAAGUGCUUUUGUCUCUCC----------UCUCCCCCCC-AAU---
................((((...((((.((..((....)).)).)))).))))....(((...(((((((((.......)))))))))..)----------))........-...--- ( -24.30)
>DroSim_CAF1 28513 104 + 1
CCAUCUGCAUUCCCAUGGCCUUUACCUUUCCCGCUCCUGCUGACAGGUUGGCUUAUUGAGCCCGAGACAAGAUAAGUGCUUUUGUCUCUCC----------UCUCCCGCCC-CAU---
......((........((((...((((.((..((....)).)).)))).))))....(((...(((((((((.......)))))))))..)----------))....))..-...--- ( -25.90)
>DroEre_CAF1 36330 104 + 1
CCAUCUGCAUUCCCAUGGCCUUUACCUUUCCCGCUCCUGCUGACAGCUUGGCUUAUUGAGCCCGAGACAAGAUAAGUGCUUUUGUC-CACCCC--------CCUCCA-CAA-GCC---
................(((.............((((..((..(....)..)).....))))..(.(((((((.......)))))))-).....--------......-...-)))--- ( -16.00)
>consensus
CCAUCUGCAUUCCCAUGGCCUUUACCUUUCCCGCUCCUGCUGACAGGUUGGCUUAUUGAGCCCGAGACAAGAUAAGUGCUUUUGUCUCUCC__________UCUCCCCCCC_CAU___
.........(((....((((...((((.((..((....)).)).)))).))))....)))...(((((((((.......))))))))).............................. (-20.73 = -21.22 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	15,969,528 – 15,969,624
Length	96
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.99
Mean single sequence MFE	-35.78
Consensus MFE	-26.75
Energy contribution	-28.19
Covariance contribution	1.44
Combinations/Pair	1.04
Mean z-score	-2.34
Structure conservation index	0.75
SVM decision value	1.44
SVM RNA-class probability	0.954196
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15969528 96 - 22224390
UGUGGAUGUGAAUGUGAAUGUGAAU------------------GUGGAUGUAAACGCGCUAACAUUCGCAUCCGCGUGCAGAGCCGUAGAUCAGCAGGCAUCAAAAACGGCG------GG
.((((((((((((((....(((...------------------((........)).)))..)))))))))))))).......(((((.(((........)))....))))).------.. ( -32.70)
>DroSec_CAF1 37536 114 - 1
UGUGGAUGUGAAUGCGAGUGUGAAUGUGAGUAUGGAUGCGAGUGUGGAUGUAAACGCGCUAACAUUCGCAUCCGCGUGCAGAGCCGUAGAUCAGCAGGCAUCAAAAACGGAG------GG
.((.(((((..(((((..(((((((((..(((....))).((((((........)))))).)))))))))..)))))((.((........)).))..)))))....))....------.. ( -35.80)
>DroSim_CAF1 28617 114 - 1
UGUGGAUGUGAAUACGAGUGUGAAUGUGAGUGCGGAUGCGAGUGUGGAUGUAAACGCGCUAACAUUCGCAUCCGCGUGCAGAGCCGUAGAUCAGCAGGCAUCAAAAACGGAG------GG
.((.(((((((.((((.((.((.(((((..((((((((..((((((........))))))..))))))))..))))).))..))))))..)).....)))))....))....------.. ( -39.30)
>DroEre_CAF1 36434 105 - 1
---GGAUGUGAGUGUGGAUGUGAGUGGGG------AUGUGAGUGUGGAUGUAAACGCGCUAACAUUCGCAACCGCGUGCAGAGCCGUAGAUCAGCAGGCAUCAAAAACGAAG------GG
---.(((((...(.((.(((((..((.((------((((.((((((........)))))).)))))).))..))))).)).)((.(.....).))..))))).....(....------). ( -34.00)
>DroYak_CAF1 20324 120 - 1
UAUGGAUGUGAAUGUAGAUGUGAAUGUGGCUGUGAAUGUGAAUGUGGAUGUAAACGCGCUAACAUUCGCAUCCGCGUGCAGAGCCGUAGAUCAGCAGGCAUCAAAAACGAAAACGGAGGG
....(((((...(((.(((.((....(((((.((.(((((.((((((((((..........)))))))))).))))).)).))))))).))).))).))))).................. ( -37.10)
>consensus
UGUGGAUGUGAAUGUGAAUGUGAAUGUGA_U__G_AUGCGAGUGUGGAUGUAAACGCGCUAACAUUCGCAUCCGCGUGCAGAGCCGUAGAUCAGCAGGCAUCAAAAACGGAG______GG
...((((((((((((.........................((((((........)))))).))))))))))))((.(((.((........)).))).))..................... (-26.75 = -28.19 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:11 2006