Locus 6771

Sequence ID	2L_DroMel_CAF1
Location	18,925,497 – 18,925,620
Length	123
Max. P	0.643433

overview

Window 2

Location	18,925,497 – 18,925,592
Length	95
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	80.11
Mean single sequence MFE	-27.70
Consensus MFE	-20.39
Energy contribution	-19.58
Covariance contribution	-0.80
Combinations/Pair	1.25
Mean z-score	-1.13
Structure conservation index	0.74
SVM decision value	0.07
SVM RNA-class probability	0.571014
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18925497 95 - 22407834
UAUUAUAUGCACUUUUCUUCUACAAAAUGGCGGCAAACGUCGCCGCACGGUCCUGUU-------CGGGGUCCUUCUAUGGCUCUGGGACGGAUCUUA--AGGAG--
................(((((.......((((((....))))))....(((((.(((-------(.((..((......))..)).)))))))))...--)))))-- ( -30.90)
>DroPse_CAF1 51872 87 - 1
UAUUAUAUGCACUUUUCUUUUACAAAAUGGCGGCAAACGUCGCCUCACGGUCCUGUU-------CAGGGUCU----------CGGUGCGGGAUUUUC--AGGAGUU
.......((((((...............((((((....))))))....(..(((...-------.)))..).----------.))))))........--....... ( -23.90)
>DroEre_CAF1 49168 95 - 1
UAUUAUAUGCACUUUUCUUCUACAAAAUGGCGGCAAACGUCGCCGCACGGUCCUGUU-------CAGGGUCCUGCUAUGGCUCUGGGACGGAUCUUA--AGAAG--
................(((((.......((((((....))))))....(((((..((-------(((((.((......)))))))))..)))))...--)))))-- ( -31.80)
>DroYak_CAF1 49756 95 - 1
UAUUAUAUGCACUUUUCUUCUACAAAAUGGCGGCAAACGUCGCCGCACGGUCCUGUU-------CGGGGUCCUUCUCCGGCUCUGGGACGGAUCUUA--AGAAG--
................(((((.......((((((....))))))....(((((.(((-------(.((..((......))..)).)))))))))...--)))))-- ( -30.80)
>DroAna_CAF1 33697 97 - 1
UAUUAUAUGCACUUUUCUUCUACAAAAUGGCGGCAAACGUCGCCGCACGGUCCUGCUCCAGCUCCAGGGUCCUUCUAUAGCCCC-------AUCGUGGCAGGGG--
.......(((..................((((((....)))))).((((((...((....))....((((.........)))).-------)))))))))....-- ( -24.90)
>DroPer_CAF1 53972 87 - 1
UAUUAUAUGCACUUUUCUUUUACAAAAUGGCGGCAAACGUCGCCUCACGGUCCUGUU-------CAGGGUCU----------CGGUGCGGGAUUUUC--AGGAGUU
.......((((((...............((((((....))))))....(..(((...-------.)))..).----------.))))))........--....... ( -23.90)
>consensus
UAUUAUAUGCACUUUUCUUCUACAAAAUGGCGGCAAACGUCGCCGCACGGUCCUGUU_______CAGGGUCCUUCUAUGGCUCUGGGACGGAUCUUA__AGGAG__
................(((((.......((((((....))))))....(..((((.........))))..)............................))))).. (-20.39 = -19.58 +  -0.80)

alignment

secondary structure

dotplot

Window 3

Location	18,925,523 – 18,925,620
Length	97
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	77.26
Mean single sequence MFE	-20.11
Consensus MFE	-11.13
Energy contribution	-11.90
Covariance contribution	0.76
Combinations/Pair	1.17
Mean z-score	-1.71
Structure conservation index	0.55
SVM decision value	0.23
SVM RNA-class probability	0.643433
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18925523 97 - 22407834
UUUUGUUG---GCCGUGUUGCUAUUUUAUUUUAUUAUAUGCACUUUUCUUCUACAAAAUGGCGGCAAACGUCGCCG-CACGGUCCUGUU-------CGGGGUCCUUCU
........---(((((((((((((..((...))..))).))).................((((((....)))))))-))))))(((...-------.)))........ ( -24.10)
>DroVir_CAF1 45202 87 - 1
UUUUGCUGUUUUUGUUGUUGCUGUUUUAUAUUAUUAUAUGCACUUUUCUUUUACAAAAUGGCGGCGAACGUCGCCAACAUC---CUGAU-------C-----------
.........((((((.(....(((..((((....)))).))).....)....))))))(((((((....))))))).....---.....-------.----------- ( -15.10)
>DroPse_CAF1 51894 93 - 1
UUUUGUUG---UUCUUGUUGCUAUUUUAUUUUAUUAUAUGCACUUUUCUUUUACAAAAUGGCGGCAAACGUCGCCU-CACGGUCCUGUU-------CAGGGUCU----
((((((..---.......((((((..((...))..))).)))..........)))))).((((((....)))))).-...(..(((...-------.)))..).---- ( -20.01)
>DroWil_CAF1 17756 89 - 1
UCGCAUUG------UUGUUGCUAUUUUAUUUUAUUAUAUGCACUUUUCUUUUACAAAAUGGCGGCAAACGUCC--U-CCUGG---UGUU-------GGGGACCCUUCU
........------(((((((((((((...........................)))))))))))))..((((--.-((...---....-------))))))...... ( -18.83)
>DroAna_CAF1 33718 97 - 1
UU----------CCUUGUUGCUAUUUUAUUUUAUUAUAUGCACUUUUCUUCUACAAAAUGGCGGCAAACGUCGCCG-CACGGUCCUGCUCCAGCUCCAGGGUCCUUCU
..----------(((((..(((.....................................((((((....))))))(-((......)))...)))..)))))....... ( -22.60)
>DroPer_CAF1 53994 93 - 1
UUUUGUUG---UUCUUGUUGCUAUUUUAUUUUAUUAUAUGCACUUUUCUUUUACAAAAUGGCGGCAAACGUCGCCU-CACGGUCCUGUU-------CAGGGUCU----
((((((..---.......((((((..((...))..))).)))..........)))))).((((((....)))))).-...(..(((...-------.)))..).---- ( -20.01)
>consensus
UUUUGUUG___UUCUUGUUGCUAUUUUAUUUUAUUAUAUGCACUUUUCUUUUACAAAAUGGCGGCAAACGUCGCCU_CACGGUCCUGUU_______CAGGGUCC____
..............(((((((((((((...........................))))))))))))).............(..((((.........))))..)..... (-11.13 = -11.90 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:36 2006