Locus 4577

Sequence ID	2L_DroMel_CAF1
Location	13,124,370 – 13,124,557
Length	187
Max. P	0.997501

overview

Window 4

Location	13,124,370 – 13,124,478
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.83
Mean single sequence MFE	-27.28
Consensus MFE	-21.44
Energy contribution	-21.28
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.06
Structure conservation index	0.79
SVM decision value	1.07
SVM RNA-class probability	0.909732
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13124370 108 + 22407834
-------AACUA---AGAAAACAUCAGACCGACUGCAAAAAAAUAUGCUCAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAA
-------.....---.((................(((........)))....((((--((((((....)))))).....(((((((..........)))).))).......)))).)).. ( -23.70)
>DroSec_CAF1 17358 108 + 1
-------AACUA---AGAAAACAUCAGACCGACUG--AAAAAAUAUGCUCAAGAGGGGGUGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAA
-------.....---.((.....((((.....)))--)..............((((((((((((....))))))))...(((((((..........)))).))).......)))).)).. ( -25.10)
>DroSim_CAF1 18456 106 + 1
-------AACUA---AGAAAACAUCAGACCGACUG--AAAAAAUAUGCUCAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAA
-------.....---.((.....((((.....)))--)..............((((--((((((....)))))).....(((((((..........)))).))).......)))).)).. ( -25.00)
>DroEre_CAF1 18987 109 + 1
-------AACUAAGAAGAAAGCCUCAGGCCGACUG--AAAAAAUAUGCUCAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAA
-------......((.((..((((..(((.((.((--(........((.((.((((--((((((....)))))))).)))).)).))))).)))..))))(((.......))))).)).. ( -29.70)
>DroYak_CAF1 17813 113 + 1
CAUAGGAAACUA---AGAAAGCAUCAGGCCGACUG--AAAAAAUAUGCUUAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAA
..(((....)))---.(((((((((((.....)))--).......)))))..((((--((((((....)))))).....(((((((..........)))).))).......)))).)).. ( -32.91)
>consensus
_______AACUA___AGAAAACAUCAGACCGACUG__AAAAAAUAUGCUCAAGAGG__GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAA
................((......(((.....))).................((((..((((((....)))))).....(((((((..........)))).))).......)))).)).. (-21.44 = -21.28 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	13,124,400 – 13,124,518
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.13
Mean single sequence MFE	-36.08
Consensus MFE	-33.78
Energy contribution	-33.66
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-1.95
Structure conservation index	0.94
SVM decision value	2.87
SVM RNA-class probability	0.997501
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13124400 118 + 22407834
AAAUAUGCUCAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGGUCUAAGAUUGAACCAC
............((((--((((((....)))))).....(((((((..........)))).))).......)))).(((((((...((((((((.....)))))))).)))))))..... ( -38.80)
>DroSec_CAF1 17386 120 + 1
AAAUAUGCUCAAGAGGGGGUGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGGUCCAAGAUUGAACCAC
............((((((((((((....))))))))...(((((((..........)))).))).......)))).(((((((....(((((((.....)))))))..)))))))..... ( -37.20)
>DroSim_CAF1 18484 118 + 1
AAAUAUGCUCAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGUUCCAAGAUUGAACCAC
............((((--((((((....)))))).....(((((((..........)))).))).......)))).(((((((....((((.((.....))))))...)))))))..... ( -31.60)
>DroEre_CAF1 19018 118 + 1
AAAUAUGCUCAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGGCCGCCGGGGCCCAAGAUUGAACCAC
............((((--((((((....)))))).....(((((((..........)))).))).......)))).(((((((....((((((((...))))))))..)))))))..... ( -40.90)
>DroYak_CAF1 17848 118 + 1
AAAUAUGCUUAAGAGG--GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGAGCACAAGAUUGAACCAC
............((((--((((((....)))))).....(((((((..........)))).))).......)))).(((((((.....((..((.....))..))...)))))))..... ( -31.90)
>consensus
AAAUAUGCUCAAGAGG__GCGUCAAAGUUGACGCUUAUCUGCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGGUCCAAGAUUGAACCAC
............((((..((((((....)))))).....(((((((..........)))).))).......)))).(((((((....((((((((...))))))))..)))))))..... (-33.78 = -33.66 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	13,124,438 – 13,124,557
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.13
Mean single sequence MFE	-37.08
Consensus MFE	-33.94
Energy contribution	-33.98
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-1.21
Structure conservation index	0.92
SVM decision value	0.42
SVM RNA-class probability	0.728570
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13124438 119 + 22407834
GCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGGUCUAAGAUUGAACCACUGACAGCUGUCUGCAGGAGGAGCAAAUACGA-UGGAUACU
((.((((...(((....((((((.......)))...(((((((...((((((((.....)))))))).)))))))..........)))....))).)))).))........-........ ( -37.70)
>DroSec_CAF1 17426 119 + 1
GCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGGUCCAAGAUUGAACCACUGACAGCUGUCUGCAGGAGGAGCAAAUGCGA-UGGAUACU
((.((((...(((...(((((((.......((((............)))).......((((((((.((....)).))).))))).)))))))))).)))).))........-........ ( -36.90)
>DroSim_CAF1 18522 119 + 1
GCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGUUCCAAGAUUGAACCACUGACAGCUGUCUGCAGGAGGAGCAAAUGCGA-UGGAUACU
((.((((...(((...(((((((.......((((............)))).......(((.(((((.......)))))...))).)))))))))).)))).))........-........ ( -34.80)
>DroEre_CAF1 19056 117 + 1
GCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGGCCGCCGGGGCCCAAGAUUGAACCACUGACAGCUGUCCGCAGGAGGAGCAGAUGGAACUAGAU---
((.((((...(((....((((((.......)))...(((((((....((((((((...))))))))..)))))))..........)))....))).)))).))..............--- ( -39.80)
>DroYak_CAF1 17886 119 + 1
GCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGAGCACAAGAUUGAACCACUGACAGCUGUCUGCAGGAGGAGCAGAUAGCA-UGGAUGCU
((((((((...(((...)))(((.......)))...(((((((.....((..((.....))..))...))))))).....)))..(((((((((.......))))))))).-.)).))). ( -36.20)
>consensus
GCGCCUCAUUUGCCAAAGGCGGCAACAAAAGCCUCAUCAAUUUCAAAGGCCUCGACCGUCGGGGUCCAAGAUUGAACCACUGACAGCUGUCUGCAGGAGGAGCAAAUGCGA_UGGAUACU
((.((((...(((....((((((.......)))...(((((((....((((((((...))))))))..)))))))..........)))....))).)))).))................. (-33.94 = -33.98 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:31 2006