Locus 4584

Sequence ID	2R_DroMel_CAF1
Location	14,969,374 – 14,969,568
Length	194
Max. P	0.937703

overview

Window 4

Location	14,969,374 – 14,969,491
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.96
Mean single sequence MFE	-44.52
Consensus MFE	-36.36
Energy contribution	-35.56
Covariance contribution	-0.80
Combinations/Pair	1.24
Mean z-score	-1.63
Structure conservation index	0.82
SVM decision value	0.70
SVM RNA-class probability	0.827056
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14969374 117 - 20766785
UCGCCGGCUGGACACGCGGGGCAACCACUGUAGAGGCAUCUCCAUAGUUCGAGGACCAAGC---CUGCUGUUCCAUCCGUUGCUUCGACAGAUGCAACGAGUCCAGGGACAGCAAAGAAG
.....((((((.(...((((....))(((((.(((....))).))))).))..).)).)))---)(((((((((..(((((((.((....)).)))))).)....)))))))))...... ( -44.60)
>DroSec_CAF1 8955 117 - 1
UCGCCGGCUGGACUCGCGGUGCAACCACUGUAGAGGCAUCACCAUAGUUCGAAGACCAAGC---CUGCUGUUCCAACCGUUGCUUCGACAGAUGCAACGAGUCCAGGGACAGCACAGAAG
.....((((((.(((((((((....)))))).)))...((..........))...)).)))---)(((((((((.((((((((.((....)).)))))).))...)))))))))...... ( -41.50)
>DroSim_CAF1 9688 117 - 1
UCGCCGGCUGGACUCGCGGUGCAACCACUGUAGAGGCAUCACCAUAGUUCGAAGACCAAGC---CUGCUGUUCCAUCCGUUGCUUCGACAGAUGCAACGAGUCCAGGGACAGCAGAGAAG
.....((((((.(((((((((....)))))).)))...((..........))...)).)))---)(((((((((..(((((((.((....)).)))))).)....)))))))))...... ( -40.70)
>DroEre_CAF1 9095 117 - 1
UCGCUGGCUGGACUCGCGGAGCAACCACAGUAGAGGCACCUGCAUAGUCCGAGGACCAAGC---CUGCUGUUCCCUCCGUUGCUUUGACAGAUGCAACGAGUCCAGGGACAGCAGAGAGG
..((((.((((((((..((((.....(((((((..((....))...(((....))).....---)))))))...))))(((((..........)))))))))))))...))))....... ( -46.90)
>DroYak_CAF1 9382 120 - 1
UCGCUGGCUGGGCUCGCGGGGCAAUCACUGUAGAGGCACCUCCAUAGUUUGAAGACCAAGCCGCCUGCUGUUCCAUCCGUUGCUUCGACAGAUGCAACGAGUCCAGGGACAGCAGAGAAG
..((.(((((((((.....)))....(((((.(((....))).))))).......)).))))))((((((((((..(((((((.((....)).)))))).)....))))))))))..... ( -48.90)
>consensus
UCGCCGGCUGGACUCGCGGGGCAACCACUGUAGAGGCAUCUCCAUAGUUCGAAGACCAAGC___CUGCUGUUCCAUCCGUUGCUUCGACAGAUGCAACGAGUCCAGGGACAGCAGAGAAG
.....(((((((((...((((...((........))...))))..)))))..)).)).......((((((((((..(((((((.((....)).)))))).)....))))))))))..... (-36.36 = -35.56 +  -0.80)

alignment

secondary structure

dotplot

Window 5

Location	14,969,451 – 14,969,568
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.66
Mean single sequence MFE	-39.45
Consensus MFE	-31.26
Energy contribution	-31.14
Covariance contribution	-0.12
Combinations/Pair	1.16
Mean z-score	-1.66
Structure conservation index	0.79
SVM decision value	0.46
SVM RNA-class probability	0.746341
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14969451 117 + 20766785
GAUGCCUCUACAGUGGUUGCCCCGCGUGUCCAGCCGGCGAUGAUGUUUCAACAGAAACCCAUGAGA---CCAUUAGAGUCCCAAUGGUAUCGCCAUGGACAAAGUAACCUGGCCCAAGGC
...((((.......((((((......((((((...(((((((..(((((....)))))((((..((---((....).)))...))))))))))).))))))..)))))).......)))) ( -39.84)
>DroSec_CAF1 9032 120 + 1
GAUGCCUCUACAGUGGUUGCACCGCGAGUCCAGCCGGCGAUGACGUUUCAACAGAAACACAUGAGAAACCCAUUAGAGUCCCAAUGGUAUCGCCAUGGACAAAGUAACCUGGCACAAGGC
..((((..(((.((((.....))))..(((((...(((((((..(((((....)))))...........(((((.(....).)))))))))))).)))))...)))....))))...... ( -38.80)
>DroSim_CAF1 9765 120 + 1
GAUGCCUCUACAGUGGUUGCACCGCGAGUCCAGCCGGCGAUGAUGUUUCAACAGAAACACAUGAGAAACCCAUUGGAGUCGCAAUGGCAUCGCCAUGGACAAAGUAACCUGGCACAAGGC
..((((..(((.((((.....))))..(((((...(((((((.((((((....))))))..........((((((......))))))))))))).)))))...)))....))))...... ( -44.20)
>DroEre_CAF1 9172 117 + 1
GGUGCCUCUACUGUGGUUGCUCCGCGAGUCCAGCCAGCGAUGGUGUUUCAACAGAAACCCAUGAGG---CCAUUAGAGUCCCAAUGGUAUCGUAAUGGACAAAAUAACCUAGCCCAAAGC
((.((......(((((.....))))).(((((....(((((((.(((((....))))))).....(---(((((.(....).)))))))))))..)))))...........))))..... ( -34.10)
>DroYak_CAF1 9462 117 + 1
GGUGCCUCUACAGUGAUUGCCCCGCGAGCCCAGCCAGCGAUGAUGUUCCAACAGAAGCCCAUGAGG---CCAUUAGAGUCACAAUGGUAUCGCCAUGGGCCAAGUAAUCUGGCCCAAGGC
((((((......((((((....(((..((...))..))).((((((((.....)))(((.....))---)))))).))))))...))))))(((.(((((((.......))))))).))) ( -40.30)
>consensus
GAUGCCUCUACAGUGGUUGCACCGCGAGUCCAGCCGGCGAUGAUGUUUCAACAGAAACCCAUGAGA___CCAUUAGAGUCCCAAUGGUAUCGCCAUGGACAAAGUAACCUGGCCCAAGGC
...((((.......((((((.......(((((...(((((((..(((((....)))))...........(((((........)))))))))))).)))))...)))))).......)))) (-31.26 = -31.14 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	14,969,451 – 14,969,568
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.66
Mean single sequence MFE	-44.36
Consensus MFE	-36.16
Energy contribution	-35.92
Covariance contribution	-0.24
Combinations/Pair	1.17
Mean z-score	-1.97
Structure conservation index	0.82
SVM decision value	1.26
SVM RNA-class probability	0.937703
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14969451 117 - 20766785
GCCUUGGGCCAGGUUACUUUGUCCAUGGCGAUACCAUUGGGACUCUAAUGG---UCUCAUGGGUUUCUGUUGAAACAUCAUCGCCGGCUGGACACGCGGGGCAACCACUGUAGAGGCAUC
(((((....(((.......(((((((((((((.((((.((((((.....))---))))))))(((((....)))))...)))))))..))))))....((....)).)))..)))))... ( -49.10)
>DroSec_CAF1 9032 120 - 1
GCCUUGUGCCAGGUUACUUUGUCCAUGGCGAUACCAUUGGGACUCUAAUGGGUUUCUCAUGUGUUUCUGUUGAAACGUCAUCGCCGGCUGGACUCGCGGUGCAACCACUGUAGAGGCAUC
(((((...............((((((((((((.(((((((....))))))).........(((((((....)))))).))))))))..)))))..((((((....)))))).)))))... ( -43.40)
>DroSim_CAF1 9765 120 - 1
GCCUUGUGCCAGGUUACUUUGUCCAUGGCGAUGCCAUUGCGACUCCAAUGGGUUUCUCAUGUGUUUCUGUUGAAACAUCAUCGCCGGCUGGACUCGCGGUGCAACCACUGUAGAGGCAUC
(((((...............(((((((((((((((((((......)))))).........(((((((....)))))))))))))))..)))))..((((((....)))))).)))))... ( -45.40)
>DroEre_CAF1 9172 117 - 1
GCUUUGGGCUAGGUUAUUUUGUCCAUUACGAUACCAUUGGGACUCUAAUGG---CCUCAUGGGUUUCUGUUGAAACACCAUCGCUGGCUGGACUCGCGGAGCAACCACAGUAGAGGCACC
(((((..(((.((((.....(((((.........((((((....))))))(---((..(((((((((....))))).))))....))))))))..((...))))))..))).)))))... ( -35.70)
>DroYak_CAF1 9462 117 - 1
GCCUUGGGCCAGAUUACUUGGCCCAUGGCGAUACCAUUGUGACUCUAAUGG---CCUCAUGGGCUUCUGUUGGAACAUCAUCGCUGGCUGGGCUCGCGGGGCAAUCACUGUAGAGGCACC
(((.((((((((.....)))))))).))).........(((.(((((...(---((((.(((((((..((..(..........)..)).))))))).)))))........))))).))). ( -48.20)
>consensus
GCCUUGGGCCAGGUUACUUUGUCCAUGGCGAUACCAUUGGGACUCUAAUGG___UCUCAUGGGUUUCUGUUGAAACAUCAUCGCCGGCUGGACUCGCGGGGCAACCACUGUAGAGGCAUC
(((((......((((.....((((((((((((.(((((((....)))))))...........(((((....)))))...)))))))..)))))..((...))))))......)))))... (-36.16 = -35.92 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:50 2006