Locus 3852

Sequence ID	2R_DroMel_CAF1
Location	12,738,975 – 12,739,102
Length	127
Max. P	0.818702

overview

Window 5

Location	12,738,975 – 12,739,067
Length	92
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	81.68
Mean single sequence MFE	-40.64
Consensus MFE	-25.82
Energy contribution	-27.77
Covariance contribution	1.95
Combinations/Pair	1.12
Mean z-score	-2.35
Structure conservation index	0.64
SVM decision value	0.63
SVM RNA-class probability	0.804947
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12738975 92 + 20766785
-CGCCACCAGUCGCGUGAGUUCGCGUCAGUUGGCAACAG---CAGUUUGGUGGCAGUGGCAGCCCGGCUAACAUGCCAGACCGCUGCC-ACG-CCC-------C-C
-.((((((((.((((......)))).).((((....)))---)....))))))).(((((((((.(((......))).)...))))))-)).-...-------.-. ( -47.80)
>DroSec_CAF1 85296 93 + 1
-CGGCACCAGUCGCGUGAGUUCGCGUCAGUUGGCAACAG---CAGUUUGGUGGCAGUGGCAGCCCGGCUAACAUGCCAGACCGCUGCC-ACG-CCC-------CCC
-.(.((((((.((((......)))).).((((....)))---)....))))).).(((((((((.(((......))).)...))))))-)).-...-------... ( -43.20)
>DroEre_CAF1 86063 92 + 1
-CGCCACCAGUCGCGUGAGUUCGCGUCAGUUGGCAACAG---CAGUUUGGUGGCAGUGGCAGCCGGGCUAACAUGCCAGACCGCUGCC-ACG-CCC-------C-C
-.((((((((.((((......)))).).((((....)))---)....))))))).((((((((..(((......))).....))))))-)).-...-------.-. ( -48.80)
>DroYak_CAF1 92963 97 + 1
-CGCCACCAGUCGCGUGAGUUCGCGUCAGUUGGCAACAGCAGCAGUUUGGUGGCAGUGGCAGCCCGGCUAACAUGCCAGACCGCUGCC-ACG-CCCCC-----C-C
-.((((((((.((((......)))).).((((....)))).......))))))).(((((((((.(((......))).)...))))))-)).-.....-----.-. ( -47.80)
>DroAna_CAF1 79395 82 + 1
-UGCCACCAGUCGCAUGAGUUCGCGUCAGUUGGCAACAG---C-----------AGUGGCAGCCUGGCCAACAUGUCUGACCGCCGCC-ACG-CCU-------UCC
-((((((..(.(((........))).).((((....)))---)-----------.))))))((.((((.................)))-).)-)..-------... ( -26.43)
>DroPer_CAF1 75051 101 + 1
CUGCCACCAGUCACAUCAGUUCGCGUCAGUUGGCAACAG---CAAC--GGCAGCAGCAGCAGCUUGGCCAACAUGCCAGACCGCUAUCCGCAGCCCUCUGCAGCCC
(((((....((.((....))..))....((((....)))---)...--)))))..(((((.(..((((......))))..).)))....((((....)))).)).. ( -29.80)
>consensus
_CGCCACCAGUCGCGUGAGUUCGCGUCAGUUGGCAACAG___CAGUUUGGUGGCAGUGGCAGCCCGGCUAACAUGCCAGACCGCUGCC_ACG_CCC_______C_C
..((((((.(.((((......)))).)...((....))..........)))))).((((((((..(((......))).....)))))).))............... (-25.82 = -27.77 +   1.95)

alignment

secondary structure

dotplot

Window 6

Location	12,739,011 – 12,739,102
Length	91
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	80.77
Mean single sequence MFE	-42.18
Consensus MFE	-28.17
Energy contribution	-28.87
Covariance contribution	0.70
Combinations/Pair	1.18
Mean z-score	-1.97
Structure conservation index	0.67
SVM decision value	0.67
SVM RNA-class probability	0.818702
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12739011 91 - 20766785
AACGAAAGGACCCUGGCCAAGAGGGCGUCGAAAUGG-G--GGGCGUGGCAGCGGUCUGGCAUGUUAGCCGGGCUGCCACUGCCACCAAACUG---CU
..(....)((((((........))).)))....(((-.--.(((((((((((...(((((......))))))))))))).))).))).....---.. ( -40.40)
>DroSec_CAF1 85332 92 - 1
AACGAAAGGACCCUGGCCAAGAGGGCGUUGGAAGGGGG--GGGCGUGGCAGCGGUCUGGCAUGUUAGCCGGGCUGCCACUGCCACCAAACUG---CU
..(....)..((((..((((.......))))..))))(--((((((((((((...(((((......))))))))))))).))).))......---.. ( -44.30)
>DroSim_CAF1 92586 90 - 1
AGCGAAAGGACCCUGGCCAAGAGGGCGUCGGAAGGG----GGGCGUGGCAGCGGUCUGGCAUGUUAGCCGGGCUGCCACUGCCACCAAACUG---CU
((((...((.(((..(((.....)))..(....)))----)(((((((((((...(((((......))))))))))))).))).))....))---)) ( -42.20)
>DroEre_CAF1 86099 90 - 1
-GCGAAAGGACCCUGGCCAAGGGGGCGUCGGAAUGG-G--GGGCGUGGCAGCGGUCUGGCAUGUUAGCCCGGCUGCCACUGCCACCAAACUG---CU
-.(((.....((((.....))))....)))...(((-.--.(((((((((((((.((((....)))).)).)))))))).))).))).....---.. ( -39.90)
>DroYak_CAF1 92999 96 - 1
AGCGAAAGGACCCUGGCCAAGGGGGCGUCGGAAUGG-GGGGGGCGUGGCAGCGGUCUGGCAUGUUAGCCGGGCUGCCACUGCCACCAAACUGCUGCU
..(....)..((((.....))))((((.(((..(((-....(((((((((((...(((((......))))))))))))).))).)))..))).)))) ( -45.80)
>DroAna_CAF1 79431 76 - 1
G--GUCCGGACUCCCGACUCCGGAC---CGGAGGCGGA--AGGCGUGGCGGCGGUCAGACAUGUUGGCCAGGCUGCCACU-----------G---CU
(--(((((((........)))))))---)...(.(...--.).)((((((((((((((.....))))))..)))))))).-----------.---.. ( -40.50)
>consensus
AGCGAAAGGACCCUGGCCAAGAGGGCGUCGGAAGGG_G__GGGCGUGGCAGCGGUCUGGCAUGUUAGCCGGGCUGCCACUGCCACCAAACUG___CU
.......((.((((.......))))................(((((((((((...(((((......))))))))))))).))).))........... (-28.17 = -28.87 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:39 2006