Locus 4017

Sequence ID	X_DroMel_CAF1
Location	10,631,509 – 10,631,610
Length	101
Max. P	0.925260

overview

Window 0

Location	10,631,509 – 10,631,610
Length	101
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	81.54
Mean single sequence MFE	-31.98
Consensus MFE	-20.54
Energy contribution	-20.77
Covariance contribution	0.22
Combinations/Pair	1.05
Mean z-score	-2.37
Structure conservation index	0.64
SVM decision value	0.71
SVM RNA-class probability	0.828825
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10631509 101 + 22224390
GGCCUGCCAACUCGUUGCUA-UUGCAUAAGUUGGCAGUUCCAGCGUGGUUGCA-------A---AUUGGAAGGAAAUAGAUGG--GAAAAAGAUCCAGCGUGGCUUCU-UCCAUU
((.(((((((((...(((..-..)))..)))))))))..)).(((....))).-------.---..((((((((..(((...(--((......)))..).))..))))-)))).. ( -34.40)
>DroPse_CAF1 14169 111 + 1
GCACUGCCAACUCACCGA-AAUUGCAUAAGUUGGCAGUUCCAGCGUGGUUGCAAAAAAAAAAAAACUAAAACCAAAUGUAUG--AAAAAAUGAUCCAGCGUGGCUGGAAUA-GUU
..((((((((((......-.........))))))))))((((((.(((((...................))))).((((..(--(........))..)))).))))))...-... ( -27.87)
>DroSec_CAF1 13093 110 + 1
GGCCUGCCAACUCGUUGCUAAUUGCAUAAGUUGGCAGUUCCAGCGUGGUUGCAAAAAAAAA---AUUGGAAGGAAAAAGAUGG-GGAAAAAGAUCCAGCGUGGCUUCU-UCCAUU
((.(((((((((...(((.....)))..)))))))))..)).(((....))).........---..((((((((......(((-(........)))).......))))-)))).. ( -34.62)
>DroSim_CAF1 13191 110 + 1
GGCCUGCCAACUCGUUGCUAAUUGCAUAAGUUGGCAGUUCCAGCGUGGUUGCAAAAAAAAA---AUUGGAAGGAAAAAGAUGG-GGAAAAAGAUCCAGCGUGGCUUCU-UCCAUU
((.(((((((((...(((.....)))..)))))))))..)).(((....))).........---..((((((((......(((-(........)))).......))))-)))).. ( -34.62)
>DroEre_CAF1 12978 111 + 1
GGCCUGCCAACUCGUUGCCAAUUGCAUAAGUUGGCAGUUCCAGCGUGGUUGCAAAAAAAAA---A-UGAAGGAAAAAAGAUGGGGGAAAAUGAUCCAGCGUGGCUUCUAUCAAUU
...(((((((((...(((.....)))..)))))))))((((..(((..((.......))..---)-))..))))....((((((((...(((......)))..)))))))).... ( -32.70)
>DroYak_CAF1 13838 97 + 1
GGCCUGCCAACUCGUUGCCAGUUGCGUAAGUUGGCAGUUCCAGCGUGGUUGCAAAAAAAAA---A---------------UGGGAGAAAAUGAUCCAGCGUGGCUUCUAUAAAUU
((.(((((((((...(((.....)))..)))))))))..)).(((....))).........---(---------------((((((...(((......)))..)))))))..... ( -27.70)
>consensus
GGCCUGCCAACUCGUUGCUAAUUGCAUAAGUUGGCAGUUCCAGCGUGGUUGCAAAAAAAAA___AUUGGAAGGAAAAAGAUGG_GGAAAAAGAUCCAGCGUGGCUUCU_UCCAUU
...(((((((((...(((.....)))..)))))))))..(((((.(((..............................................))))).)))............ (-20.54 = -20.77 +   0.22)

alignment

secondary structure

dotplot

Window 1

Location	10,631,509 – 10,631,610
Length	101
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	81.54
Mean single sequence MFE	-29.67
Consensus MFE	-21.79
Energy contribution	-22.02
Covariance contribution	0.22
Combinations/Pair	1.05
Mean z-score	-2.76
Structure conservation index	0.73
SVM decision value	1.17
SVM RNA-class probability	0.925260
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10631509 101 - 22224390
AAUGGA-AGAAGCCACGCUGGAUCUUUUUC--CCAUCUAUUUCCUUCCAAU---U-------UGCAACCACGCUGGAACUGCCAACUUAUGCAA-UAGCAACGAGUUGGCAGGCC
...(((-(((((((.....))..)))))))--)...........(((((..---.-------.((......)))))))((((((((((.(((..-..)))..))))))))))... ( -32.20)
>DroPse_CAF1 14169 111 - 1
AAC-UAUUCCAGCCACGCUGGAUCAUUUUUU--CAUACAUUUGGUUUUAGUUUUUUUUUUUUUGCAACCACGCUGGAACUGCCAACUUAUGCAAUU-UCGGUGAGUUGGCAGUGC
...-...((((((.....((((.......))--))......(((((.(((...........))).))))).))))))(((((((((((((......-...))))))))))))).. ( -32.20)
>DroSec_CAF1 13093 110 - 1
AAUGGA-AGAAGCCACGCUGGAUCUUUUUCC-CCAUCUUUUUCCUUCCAAU---UUUUUUUUUGCAACCACGCUGGAACUGCCAACUUAUGCAAUUAGCAACGAGUUGGCAGGCC
..((((-((.(((...)))(((......)))-...........))))))..---.........((..((.....))..((((((((((.(((.....)))..)))))))))))). ( -32.10)
>DroSim_CAF1 13191 110 - 1
AAUGGA-AGAAGCCACGCUGGAUCUUUUUCC-CCAUCUUUUUCCUUCCAAU---UUUUUUUUUGCAACCACGCUGGAACUGCCAACUUAUGCAAUUAGCAACGAGUUGGCAGGCC
..((((-((.(((...)))(((......)))-...........))))))..---.........((..((.....))..((((((((((.(((.....)))..)))))))))))). ( -32.10)
>DroEre_CAF1 12978 111 - 1
AAUUGAUAGAAGCCACGCUGGAUCAUUUUCCCCCAUCUUUUUUCCUUCA-U---UUUUUUUUUGCAACCACGCUGGAACUGCCAACUUAUGCAAUUGGCAACGAGUUGGCAGGCC
...(((..(((((...)))(((......)))...........))..)))-.---.........((..((.....))..((((((((((.(((.....)))..)))))))))))). ( -26.10)
>DroYak_CAF1 13838 97 - 1
AAUUUAUAGAAGCCACGCUGGAUCAUUUUCUCCCA---------------U---UUUUUUUUUGCAACCACGCUGGAACUGCCAACUUACGCAACUGGCAACGAGUUGGCAGGCC
............(((.(((((..((..........---------------.---........))...))).)))))..((((((((((..((.....))...))))))))))... ( -23.31)
>consensus
AAUGGA_AGAAGCCACGCUGGAUCAUUUUCC_CCAUCUUUUUCCUUCCAAU___UUUUUUUUUGCAACCACGCUGGAACUGCCAACUUAUGCAAUUAGCAACGAGUUGGCAGGCC
............(((.(((((..............................................))).)))))..((((((((((.(((.....)))..))))))))))... (-21.79 = -22.02 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:18 2006