Locus 5452

Sequence ID	2R_DroMel_CAF1
Location	17,548,997 – 17,549,118
Length	121
Max. P	0.938585

overview

Window 4

Location	17,548,997 – 17,549,089
Length	92
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	80.22
Mean single sequence MFE	-31.40
Consensus MFE	-21.01
Energy contribution	-21.98
Covariance contribution	0.98
Combinations/Pair	1.24
Mean z-score	-2.58
Structure conservation index	0.67
SVM decision value	1.29
SVM RNA-class probability	0.938585
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17548997 92 + 20766785
CU--------------CCG--GGCCACCGGCUUCUCCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUU
..--------------(((--(....))))..(((.((..(((((((((((.......(((.((.((((.....)))).)))))..))))))))))))).)))..... ( -33.80)
>DroSec_CAF1 55477 92 + 1
CU--------------CUG--GGCCACCGGCUUCUCCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUU
..--------------(((--(....))))..(((.((..(((((((((((.......(((.((.((((.....)))).)))))..))))))))))))).)))..... ( -31.60)
>DroEre_CAF1 63487 92 + 1
CU--------------CUG--CGCCACCGGCUUCUCCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUU
.(--------------(((--((((...)))........((((((((((((.......(((.((.((((.....)))).)))))..)))))))))))))))))..... ( -32.70)
>DroYak_CAF1 58549 92 + 1
CU--------------CUG--GGCCACCGGCUUCUCCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUU
..--------------(((--(....))))..(((.((..(((((((((((.......(((.((.((((.....)))).)))))..))))))))))))).)))..... ( -31.60)
>DroAna_CAF1 57893 103 + 1
CUUCUGCCUCCUCCGCCAG--GACCACCCACGUC---CCUGGGCCACAUUUAAAUAUUUGCGCUUGGAAUUAUUUUCGCCGGCAUAAAGUGUGGCCAGGUAGACAUUU
..(((((((.......(((--(..(......)..---))))((((((((((.......(((...(((((....)))))...)))..)))))))))))))))))..... ( -32.90)
>DroPer_CAF1 72790 85 + 1
---------------GGAGGGUGGCACGCG-------CCUCAGCCGCAUUUAAAUAUUUGCGCAUGGAAUUAUUUUCUCUG-CGAAAAUGGCGGCCAGGCAGACGUUU
---------------..........(((((-------(((..(((((.......(((((.((((.((((.....)))).))-)).)))))))))).)))).).))).. ( -25.81)
>consensus
CU______________CUG__GGCCACCGGCUUCUCCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUU
......................(((..(((......)))..((((((((((.......(((.((.((((.....)))).)))))..)))))))))).)))........ (-21.01 = -21.98 +   0.98)

alignment

secondary structure

dotplot

Window 5

Location	17,548,997 – 17,549,089
Length	92
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	80.22
Mean single sequence MFE	-30.62
Consensus MFE	-19.53
Energy contribution	-21.20
Covariance contribution	1.67
Combinations/Pair	1.14
Mean z-score	-2.32
Structure conservation index	0.64
SVM decision value	1.02
SVM RNA-class probability	0.901532
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17548997 92 - 20766785
AAACGUCUACCUGGCCACACUUUAUGCCAGGGAAAAUAAUUCCGUGCGCAAAUAUUUAAAUGUGGCCAACGGGAGAAGCCGGUGGCC--CGG--------------AG
.....(((.((((((((((.(((((((((.((((.....)))).)).)))......))))))))))))..)).)))..((((....)--)))--------------.. ( -32.50)
>DroSec_CAF1 55477 92 - 1
AAACGUCUACCUGGCCACACUUUAUGCCAGGGAAAAUAAUUCCGUGCGCAAAUAUUUAAAUGUGGCCAACGGGAGAAGCCGGUGGCC--CAG--------------AG
....(.(((((((((((((.(((((((((.((((.....)))).)).)))......))))))))))))..((......)))))))).--...--------------.. ( -30.80)
>DroEre_CAF1 63487 92 - 1
AAACGUCUACCUGGCCACACUUUAUGCCAGGGAAAAUAAUUCCGUGCGCAAAUAUUUAAAUGUGGCCAACGGGAGAAGCCGGUGGCG--CAG--------------AG
...((.(((((((((((((.(((((((((.((((.....)))).)).)))......))))))))))))..((......)))))))))--...--------------.. ( -33.00)
>DroYak_CAF1 58549 92 - 1
AAACGUCUACCUGGCCACACUUUAUGCCAGGGAAAAUAAUUCCGUGCGCAAAUAUUUAAAUGUGGCCAACGGGAGAAGCCGGUGGCC--CAG--------------AG
....(.(((((((((((((.(((((((((.((((.....)))).)).)))......))))))))))))..((......)))))))).--...--------------.. ( -30.80)
>DroAna_CAF1 57893 103 - 1
AAAUGUCUACCUGGCCACACUUUAUGCCGGCGAAAAUAAUUCCAAGCGCAAAUAUUUAAAUGUGGCCCAGG---GACGUGGGUGGUC--CUGGCGGAGGAGGCAGAAG
...(((((.((((((((((.((((.....(((..............))).......)))))))))))((((---..((....))..)--)))....)))))))).... ( -30.84)
>DroPer_CAF1 72790 85 - 1
AAACGUCUGCCUGGCCGCCAUUUUCG-CAGAGAAAAUAAUUCCAUGCGCAAAUAUUUAAAUGCGGCUGAGG-------CGCGUGCCACCCUCC---------------
..((((..((((((((((.((((.((-((..(((.....)))..)))).........)))))))))).)))-------)))))..........--------------- ( -25.80)
>consensus
AAACGUCUACCUGGCCACACUUUAUGCCAGGGAAAAUAAUUCCGUGCGCAAAUAUUUAAAUGUGGCCAACGGGAGAAGCCGGUGGCC__CAG______________AG
......(((((((((((((.(((((((((.((((.....)))).)).)))......))))))))))))..((......)))))))....................... (-19.53 = -21.20 +   1.67)

alignment

secondary structure

dotplot

Window 6

Location	17,549,016 – 17,549,118
Length	102
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	84.30
Mean single sequence MFE	-27.30
Consensus MFE	-20.23
Energy contribution	-21.07
Covariance contribution	0.84
Combinations/Pair	1.17
Mean z-score	-1.98
Structure conservation index	0.74
SVM decision value	0.13
SVM RNA-class probability	0.597666
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17549016 102 + 20766785
CCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUUUACAAAGUCAAACAAAAGCUACCACCUCC-----
.....(((((((((((.......(((.((.((((.....)))).)))))..)))))))))))(((((..((((.((...)).)))).....)))))......----- ( -31.40)
>DroPse_CAF1 67858 104 + 1
--CCUCAGCCGCAUUUAAAUAUUUGCGCAUGGAAUUAUUUUCUCUG-CGAAAAUUGCGGCCAGGCAGACGUUUUACAAAGUCAAACAAAAGUUACCAACGUUAUUUG
--(((..((((((.......((((.((((.((((.....)))).))-)).)))))))))).)))..((((((..((..............))....))))))..... ( -23.35)
>DroEre_CAF1 63506 102 + 1
CCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUUUACAAAGUCAAACAAAAGCUGCCACCGCC-----
.....(((((((((((.......(((.((.((((.....)))).)))))..)))))))))))(((((..((((.((...)).)))).....)))))......----- ( -31.40)
>DroYak_CAF1 58568 102 + 1
CCCGUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUUUACAAAGUCAAACAAAAGCUGCCACCGCC-----
.....(((((((((((.......(((.((.((((.....)))).)))))..)))))))))))(((((..((((.((...)).)))).....)))))......----- ( -31.40)
>DroAna_CAF1 57925 104 + 1
--CCUGGGCCACAUUUAAAUAUUUGCGCUUGGAAUUAUUUUCGCCGGCAUAAAGUGUGGCCAGGUAGACAUUUAACAAAGUCAAACAGAAGUUGCCACCGCUUGUU-
--(((((.((((((((.......(((...(((((....)))))...)))..)))))))))))))..((((.....(((..((.....))..)))........))))- ( -23.52)
>DroPer_CAF1 72805 104 + 1
--CCUCAGCCGCAUUUAAAUAUUUGCGCAUGGAAUUAUUUUCUCUG-CGAAAAUGGCGGCCAGGCAGACGUUUUACAAAGUCAAACAAAAGUUACCAACGUUAUUUG
--(((..(((((.......(((((.((((.((((.....)))).))-)).)))))))))).)))..((((((..((..............))....))))))..... ( -22.75)
>consensus
__CCUUGGCCACAUUUAAAUAUUUGCGCACGGAAUUAUUUUCCCUGGCAUAAAGUGUGGCCAGGUAGACGUUUUACAAAGUCAAACAAAAGCUACCACCGCC_____
......((((((((((.......(((.((.((((.....)))).)))))..)))))))))).(((((..((((.((...)).)))).....)))))........... (-20.23 = -21.07 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:19 2006