Locus 1049

Sequence ID	2L_DroMel_CAF1
Location	2,930,790 – 2,930,944
Length	154
Max. P	0.996797

overview

Window 9

Location	2,930,790 – 2,930,905
Length	115
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	84.21
Mean single sequence MFE	-43.22
Consensus MFE	-31.76
Energy contribution	-32.12
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-3.48
Structure conservation index	0.73
SVM decision value	2.75
SVM RNA-class probability	0.996797
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2930790 115 + 22407834
CAACACACCCACCCCUCCUGCAGUGAUCCC-CU---UUCAACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGGCGG
........((.((((.((.((.........-..---.......((((.(((((((((((......))))).))))))))))..(((((((........)))))))..)))).)))).)) ( -43.70)
>DroSec_CAF1 48521 109 + 1
--------CCACCCCUCCU-CAGUGAUCCC-CCCUGCUCAACCGACUUGACUGGAUGUUUGGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGGUGG
--------(((((((.((.-.((.(.....-.)))(((.....((((.(((((((((((......))))).))))))))))..(((((((........))))))).))))).))))))) ( -45.60)
>DroSim_CAF1 50104 110 + 1
--------CCACCCCUCCU-CAGUGAUCCCACCCUGCUCAACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGGUGG
--------(((((((.((.-..(((....)))...(((.....((((.(((((((((((......))))).))))))))))..(((((((........))))))).))))).))))))) ( -48.60)
>DroEre_CAF1 50190 105 + 1
CACC--AUCCACCCGACUG-CCGUGAUCCC-CU---UUCAACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGAGAAAACAUGGCCAGAAA--GGGG-----
....--...(((.......-..)))..(((-((---(((....((((.(((((((((((......))))).))))))))))...((((((.(....).))))))))))--))))----- ( -39.00)
>DroYak_CAF1 50120 107 + 1
CACC--ACCCACCCCACCA-CUGUGAUCCC-CU---UUCAACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAGAAGUGGGGG-----
..((--.(((((....(((-.(((..((((-..---.((((..((((.(((((((((((......))))).))))))))))..))))..))))..))))))......)))))))----- ( -39.20)
>consensus
CA_C__A_CCACCCCUCCU_CAGUGAUCCC_CU___UUCAACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGG_GG
........(((((..............................((((.(((((((((((......))))).))))))))))..(((((((........)))))))....)))))..... (-31.76 = -32.12 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	2,930,790 – 2,930,905
Length	115
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	84.21
Mean single sequence MFE	-46.66
Consensus MFE	-29.58
Energy contribution	-31.90
Covariance contribution	2.32
Combinations/Pair	1.03
Mean z-score	-3.01
Structure conservation index	0.63
SVM decision value	1.51
SVM RNA-class probability	0.959827
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2930790 115 - 22407834
CCGCCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUUGAA---AG-GGGAUCACUGCAGGAGGGGUGGGUGUGUUG
.(((((((((.((((((.(..((..(((((...(((.(((((((((((.((.((......)).)))))))).))))).)))..---.)-)))).))..))))))).)))))).)))... ( -50.00)
>DroSec_CAF1 48521 109 - 1
CCACCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCCAAACAUCCAGUCAAGUCGGUUGAGCAGGG-GGGAUCACUG-AGGAGGGGUGG--------
(((((((.((((.....))((((((..(((.(((((.(((((((((((.((.((......)).)))))))).))))).))).)).)))-..)).)).))-.)).)))))))-------- ( -50.40)
>DroSim_CAF1 50104 110 - 1
CCACCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUUGAGCAGGGUGGGAUCACUG-AGGAGGGGUGG--------
(((((((.((((.....))((.((..((((((((((.(((((((((((.((.((......)).)))))))).))))).))).))....)))))..))))-.)).)))))))-------- ( -46.70)
>DroEre_CAF1 50190 105 - 1
-----CCCC--UUUCUGGCCAUGUUUUCUCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUUGAA---AG-GGGAUCACGG-CAGUCGGGUGGAU--GGUG
-----((((--((((.((((..(....)..))))((.(((((((((((.((.((......)).)))))))).))))).)))))---))-)))(((((.(-(......)).).)--))). ( -39.40)
>DroYak_CAF1 50120 107 - 1
-----CCCCCACUUCUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUUGAA---AG-GGGAUCACAG-UGGUGGGGUGGGU--GGUG
-----((((((((((..(((((...(((((...(((.(((((((((((.((.((......)).)))))))).))))).)))..---.)-)))).....)-)))))))))))).--)).. ( -46.80)
>consensus
CC_CCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUUGAA___AG_GGGAUCACUG_AGGAGGGGUGG_U__G_UG
(((((((.((......((((..........))))((.(((((((((((.((.((......)).)))))))).))))).)).....................)).)))))))........ (-29.58 = -31.90 +   2.32)

alignment

secondary structure

dotplot

Window 1

Location	2,930,825 – 2,930,944
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.74
Mean single sequence MFE	-33.92
Consensus MFE	-28.48
Energy contribution	-28.24
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-2.11
Structure conservation index	0.84
SVM decision value	2.20
SVM RNA-class probability	0.990156
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2930825 119 + 22407834
AACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGGCGGUGGCAAACA-GAAGGAGAGUGGAGGGGGGGGGGGUUGGUA
.((((((((..((...(.(((..(((....((((((((...((((((((((........)))))).....)))).)))..)))))..(.-...)..)))..))).).))..)))))))). ( -39.60)
>DroSec_CAF1 48550 96 + 1
AACCGACUUGACUGGAUGUUUGGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGGUGGUGGCAAGUG-CUAGUAG-----------------------
.(((((((.(((((((((((......))))).))))))))))..(((((((........)))))))....)))....((.((((....)-))).)).----------------------- ( -34.90)
>DroSim_CAF1 50134 96 + 1
AACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGGUGGUGGCAAGUG-GUUGUAG-----------------------
((((((((.(((((((((((......))))).))))))))))(((((.(((..(...(((.((.....)).)))...)..)))))))))-)))....----------------------- ( -34.00)
>DroEre_CAF1 50222 99 + 1
AACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGAGAAAACAUGGCCAGAAA--GGGG-------ACAAAUA-GAUGGAG-------CGAGGGGG----GCAA
..((((((.(((((((((((......))))).))))))))))..(((((((.(....).)))))))...--(...-------.).....-...)).(-------(.......----)).. ( -30.00)
>DroYak_CAF1 50152 100 + 1
AACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAGAAGUGGGGG-------AGAAAUAAAAUGGAG-------CGAGGGGG------UA
.(((..((((((((((((((......))))).))))))..(((((((((((........))))))..)))))...-------...............-------.)))..))------). ( -31.10)
>consensus
AACCGACUUGACUGGAUGUUUUGCUCAAUAUGCCAGUCAGUCACUUGGCCGGGAAAACAUGGCCAAAAGCGGUGGGG_GGUGGCAAAUA_GAUGGAG________G_GGGGG_______A
..((((((.(((((((((((......))))).))))))))))..(((((((........))))))).......))............................................. (-28.48 = -28.24 +  -0.24)

alignment

secondary structure

dotplot

Window 2

Location	2,930,825 – 2,930,944
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.74
Mean single sequence MFE	-24.96
Consensus MFE	-22.72
Energy contribution	-23.12
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.91
SVM decision value	2.05
SVM RNA-class probability	0.986738
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2930825 119 - 22407834
UACCAACCCCCCCCCCCUCCACUCUCCUUC-UGUUUGCCACCGCCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUU
..............................-.....(((...((......)).(((((((..........))))))).((((((((((.((.((......)).)))))))).))))))). ( -25.60)
>DroSec_CAF1 48550 96 - 1
-----------------------CUACUAG-CACUUGCCACCACCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCCAAACAUCCAGUCAAGUCGGUU
-----------------------......(-(....)).........(((...(((((((..........))))))).((((((((((.((.((......)).)))))))).))))))). ( -26.00)
>DroSim_CAF1 50134 96 - 1
-----------------------CUACAAC-CACUUGCCACCACCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUU
-----------------------....(((-(.....................(((((((..........))))))).((((((((((.((.((......)).)))))))).)))))))) ( -26.20)
>DroEre_CAF1 50222 99 - 1
UUGC----CCCCCUCG-------CUCCAUC-UAUUUGU-------CCCC--UUUCUGGCCAUGUUUUCUCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUU
..((----(.......-------.......-.......-------....--....(((((..(....)..)))))...((((((((((.((.((......)).)))))))).))))))). ( -23.40)
>DroYak_CAF1 50152 100 - 1
UA------CCCCCUCG-------CUCCAUUUUAUUUCU-------CCCCCACUUCUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUU
.(------((......-------...............-------.....(((..(((((..........))))))))((((((((((.((.((......)).)))))))).))))))). ( -23.60)
>consensus
U_______CCCCC_C________CUCCAUC_UAUUUGCCACC_CCCCACCGCUUUUGGCCAUGUUUUCCCGGCCAAGUGACUGACUGGCAUAUUGAGCAAAACAUCCAGUCAAGUCGGUU
.............................................((......(((((((..........))))))).((((((((((.((.((......)).)))))))).)))))).. (-22.72 = -23.12 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:06 2006