Locus 4269

Sequence ID	X_DroMel_CAF1
Location	11,225,960 – 11,226,097
Length	137
Max. P	0.656479

overview

Window 2

Location	11,225,960 – 11,226,073
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	70.10
Mean single sequence MFE	-18.72
Consensus MFE	-4.10
Energy contribution	-4.34
Covariance contribution	0.24
Combinations/Pair	1.22
Mean z-score	-1.80
Structure conservation index	0.22
SVM decision value	0.26
SVM RNA-class probability	0.656479
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11225960 113 + 22224390
AACAUCUAAAUGUUAUUUAACUUAUGCAUCAAGUUGUUUAACUUGAUUUUUCCGAUCACUCGGCGGUUGGUUGUUGCAUUUUUCUCAGUGUACUUUCGCACCACAAGUUAACU
(((((....)))))..(((((((..((((((((((....)))))))).....(((....)))))((((((..((.(((((......)))))))..))).)))..))))))).. ( -23.50)
>DroSec_CAF1 13277 97 + 1
AACAUUUAAUUGUUUUUUAACUUAUGCAUCAAUUU---AAACU--AUUUUUCC-----------GUUUGGUUGUGGCAUUUUUCUCAGUGUACCUUCGCACUACAAGUUAACU
((((......))))..(((((((((((..(((((.---((((.--........-----------)))))))))..)))).......(((((......)))))..))))))).. ( -15.80)
>DroSim_CAF1 5110 97 + 1
UACAUCUCAUUGUUAUUUAACUUAUGCAUCAAGUU---AAACU--AUUUUUCC-----------GGUUGAUUGUUGCAUUUUUCUCAGUGUAAUUUCGCACUACAAGUUAACU
................((((((((((((.(((...---.((((--........-----------))))..))).))))).......(((((......)))))..))))))).. ( -16.90)
>DroEre_CAF1 12976 106 + 1
AUCAUCUAA--GUCAUAUAACUUGUGCGUUAAGUG---AAACU--AUUUUUCUAGUCAUUUGGAAGUUGGCUUCGGCAUUUUUCGAAGUGUAUUUUUGCACUACCCGUUAACU
....(((((--(((((.((((......)))).)))---).(((--(......))))..))))))(((((((.((((......))))((((((....))))))....))))))) ( -22.30)
>DroYak_CAF1 4924 88 + 1
-----------GAUAUAUAACUUCUGCAUUAAAUC---CAACU--AUUUUUCUGGACAG-------UUGGCCAUUGCUUUUUUUCCAGUGUAUUUU--CACUACACGUUAACU
-----------......((((....(((......(---(((((--.(((....))).))-------))))....)))..........(((((....--...)))))))))... ( -15.10)
>consensus
AACAUCUAA_UGUUAUUUAACUUAUGCAUCAAGUU___AAACU__AUUUUUCC___CA______GGUUGGUUGUUGCAUUUUUCUCAGUGUACUUUCGCACUACAAGUUAACU
.................((((..(((((((((..................................)))))....)))).......(((((......)))))....))))... ( -4.10 =  -4.34 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	11,225,960 – 11,226,073
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	70.10
Mean single sequence MFE	-18.72
Consensus MFE	-5.42
Energy contribution	-5.90
Covariance contribution	0.48
Combinations/Pair	1.28
Mean z-score	-1.74
Structure conservation index	0.29
SVM decision value	0.07
SVM RNA-class probability	0.567635
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11225960 113 - 22224390
AGUUAACUUGUGGUGCGAAAGUACACUGAGAAAAAUGCAACAACCAACCGCCGAGUGAUCGGAAAAAUCAAGUUAAACAACUUGAUGCAUAAGUUAAAUAACAUUUAGAUGUU
..((((((((((((((....))))..........................((((....))))....((((((((....)))))))).))))))))))..(((((....))))) ( -31.00)
>DroSec_CAF1 13277 97 - 1
AGUUAACUUGUAGUGCGAAGGUACACUGAGAAAAAUGCCACAACCAAAC-----------GGAAAAAU--AGUUU---AAAUUGAUGCAUAAGUUAAAAAACAAUUAAAUGUU
..(((((((((.((((....))))............((..(((..((((-----------........--.))))---...)))..)))))))))))................ ( -15.40)
>DroSim_CAF1 5110 97 - 1
AGUUAACUUGUAGUGCGAAAUUACACUGAGAAAAAUGCAACAAUCAACC-----------GGAAAAAU--AGUUU---AACUUGAUGCAUAAGUUAAAUAACAAUGAGAUGUA
..(((((((.(((((........)))))......(((((....((((..-----------.(((....--..)))---...))))))))))))))))................ ( -12.80)
>DroEre_CAF1 12976 106 - 1
AGUUAACGGGUAGUGCAAAAAUACACUUCGAAAAAUGCCGAAGCCAACUUCCAAAUGACUAGAAAAAU--AGUUU---CACUUAACGCACAAGUUAUAUGAC--UUAGAUGAU
............((((.........(((((........))))).............(((((......)--)))).---........))))(((((....)))--))....... ( -15.90)
>DroYak_CAF1 4924 88 - 1
AGUUAACGUGUAGUG--AAAAUACACUGGAAAAAAAGCAAUGGCCAA-------CUGUCCAGAAAAAU--AGUUG---GAUUUAAUGCAGAAGUUAUAUAUC-----------
...(((((((((...--....)))))..........(((.((.((((-------((((........))--)))))---)...)).)))....))))......----------- ( -18.50)
>consensus
AGUUAACUUGUAGUGCGAAAAUACACUGAGAAAAAUGCAACAACCAACC______UG___GGAAAAAU__AGUUU___AACUUGAUGCAUAAGUUAAAUAACA_UUAGAUGUU
...((((((((((((........)))).........(((.(((......................................))).)))))))))))................. ( -5.42 =  -5.90 +   0.48)

alignment

secondary structure

dotplot

Window 4

Location	11,226,000 – 11,226,097
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	77.16
Mean single sequence MFE	-19.33
Consensus MFE	-12.96
Energy contribution	-14.20
Covariance contribution	1.24
Combinations/Pair	1.20
Mean z-score	-1.41
Structure conservation index	0.67
SVM decision value	-0.04
SVM RNA-class probability	0.511634
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11226000 97 + 22224390
ACUUGAUUUUUCCGAUCACUCGGCGGUUGGUUGUUGCAUUUUUCUCAGUGUACUUUCGCACCACAAGUUAACUGCAGAAUGCCAACAAAGUUUUCGA
((((.......((((....))))..((((((..(((((.((..((..((((......))))....))..)).)))))...)))))).))))...... ( -22.00)
>DroSec_CAF1 13314 84 + 1
ACU--AUUUUUCC-----------GUUUGGUUGUGGCAUUUUUCUCAGUGUACCUUCGCACUACAAGUUAACUGCAGAAUGCCAACAAAGUUUUCGA
...--.......(-----------(.....((((((((((((....(((((......)))))....((.....)))))))))).))))......)). ( -17.20)
>DroSim_CAF1 5147 84 + 1
ACU--AUUUUUCC-----------GGUUGAUUGUUGCAUUUUUCUCAGUGUAAUUUCGCACUACAAGUUAACUGCAGAAUGCCAACAAAGUUUUCGA
...--.......(-----------((....((((((((((((...((((.((((((........)))))))))).)))))).)))))).....))). ( -15.20)
>DroEre_CAF1 13011 95 + 1
ACU--AUUUUUCUAGUCAUUUGGAAGUUGGCUUCGGCAUUUUUCGAAGUGUAUUUUUGCACUACCCGUUAACUGCAAUAUGCCAACAGAGUUUUCGA
...--....((((((....))))))((((((....(((.((..((.((((((....))))))...))..)).))).....))))))........... ( -24.50)
>DroYak_CAF1 4950 86 + 1
ACU--AUUUUUCUGGACAG-------UUGGCCAUUGCUUUUUUUCCAGUGUAUUUU--CACUACACGUUAACUGCAAUAUGCCAACAGAGCUUUCGA
...--.............(-------(((((.(((((..........(((((....--...))))).......)))))..))))))........... ( -17.73)
>consensus
ACU__AUUUUUCC___CA______GGUUGGUUGUUGCAUUUUUCUCAGUGUACUUUCGCACUACAAGUUAACUGCAGAAUGCCAACAAAGUUUUCGA
.........................((((((..(((((.((..((.(((((......)))))...))..)).)))))...))))))........... (-12.96 = -14.20 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:45 2006