Locus 4057

Sequence ID	X_DroMel_CAF1
Location	10,754,575 – 10,754,812
Length	237
Max. P	0.801779

overview

Window 6

Location	10,754,575 – 10,754,676
Length	101
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	80.36
Mean single sequence MFE	-32.98
Consensus MFE	-19.66
Energy contribution	-21.18
Covariance contribution	1.52
Combinations/Pair	1.04
Mean z-score	-2.04
Structure conservation index	0.60
SVM decision value	0.62
SVM RNA-class probability	0.801779
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10754575 101 + 22224390
CAUUUCCUUU-----CCGGACAACCAGUCCGA------UUCCGAGUAUAAGCCGAUUAGCUGUCUCCCACCUCGUCGAGUUCGAGUUGCUUAGCUGGGCUUGGACUUGGAAU
..........-----.(((((.....)))))(------((((((((.((((((...((((((.....((.((((.......)))).))..)))))))))))).))))))))) ( -36.90)
>DroSec_CAF1 4110 96 + 1
CAUUUCCCUUCCAGUCCGGACAAGCAGUCCGA------UUCCAAGUAUAAGCCGAUUAGCUGGCUCCCACCUCGUCGAGUUCGAGUUGCUUAGCUGGGCUUG----------
............(((((((..((((((..(((------............((((((.((.(((...))).)).)))).)))))..))))))..)))))))..---------- ( -27.70)
>DroSim_CAF1 1577 96 + 1
CAUUUCCUUUUCAGUCCGGACAAGCAGUCCGA------UUCCCAGUAUAAGCCGAUUAGCUGUCUCCCACCUCGUCGAGUUCGAGUUGCUUAGCUGGGCUUG----------
................(((((.....))))).------..((((((.(((((.(((.....)))......((((.......))))..)))))))))))....---------- ( -26.00)
>DroEre_CAF1 3391 101 + 1
CACCUCCUCU-----CCGGACAACCAGUCCGA------UUCCGAGUAUAAGCUGAUUAGCUGUCUCCCUCCUCGCCGAGUUCCAGUUGCUCAGCGGGGCUGGGACUGGGAAU
..........-----.(((((.....)))))(------((((.(((...((((....))))....(((.((((((.((((.......)))).))))))..)))))).))))) ( -39.70)
>DroYak_CAF1 4766 102 + 1
CACUUCCUUC-----CCGGACAACCAGUCCGAUUCCGAUUCCGAGUAUAAGCUGAUUAGCUGUCUCCUUCCUCGCCGAGUUCCAGUUGCUUGGCGGUGCUUGGACUU-----
..........-----.(((((.....)))))........(((((((((.((((....))))...........((((((((.......)))))))))))))))))...----- ( -34.60)
>consensus
CAUUUCCUUU_____CCGGACAACCAGUCCGA______UUCCGAGUAUAAGCCGAUUAGCUGUCUCCCACCUCGUCGAGUUCGAGUUGCUUAGCUGGGCUUGGACU______
................(((((.....)))))........(((((((...(((..(.(((((..(((..........)))....))))).)..)))..)))))))........ (-19.66 = -21.18 +   1.52)

alignment

secondary structure

dotplot

Window 7

Location	10,754,676 – 10,754,784
Length	108
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	76.47
Mean single sequence MFE	-41.70
Consensus MFE	-22.84
Energy contribution	-24.77
Covariance contribution	1.94
Combinations/Pair	1.17
Mean z-score	-1.95
Structure conservation index	0.55
SVM decision value	0.23
SVM RNA-class probability	0.644786
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10754676 108 + 22224390
GGACGUGGGUUUGGGUUUGAGUUUCGAUCCGGUUGCUGUAGCUAGUGGUGGU---------GGUGGUCUGGGCCAUCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUC
......(((((((((.(((.....))).))(((((((.(((((((.((..((---------((((((....)))))))..)..))))))))).....))))))).....))))))). ( -42.70)
>DroSec_CAF1 4206 109 + 1
-------GGUUUGGGUUUGGGUUUCGAUCUGG-UGCCGUAGCUAGUGGUGGUGGUGUUGGUGGUGGUCUGGGCCACCGUUUUGCCUUGCCUAAUGAGGGCAACCUGAAACGGACCUC
-------((((((..((..((((.....(..(-..(((..((.....))..)))..)..).((((((....)))))).....(((((........)))))))))..)).)))))).. ( -41.80)
>DroSim_CAF1 1673 100 + 1
-------GGUUUGGGCUUGGGUUUCGAUCUGG-UGCCGUAGCUAGUGGUGGU---------GGUGGUCUGGGCCACCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUC
-------((((((((((..(((....)))..)-.))).(((((((.((..((---------((((((....)))))))..)..))))))))).(.(((....))).)..)))))).. ( -44.00)
>DroEre_CAF1 3492 95 + 1
GGGUUG------GGGCUUGGGCUUGGGUGUCG-AACUGGUGGUGCUGC---------------CGGUCUGGGCCACCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUC
(((((.------(((((.((((.(((..(((.-(((((((......))---------------)))).).)))..)))....)))).))))..(.(((....))).)..).))))). ( -38.30)
>consensus
_______GGUUUGGGCUUGGGUUUCGAUCUGG_UGCCGUAGCUAGUGGUGGU_________GGUGGUCUGGGCCACCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUC
.......((((((((((.((((............(((((.....)))))............((((((....)))))).....)))).))))..(.(((....))).)..)))))).. (-22.84 = -24.77 +   1.94)

alignment

secondary structure

dotplot

Window 8

Location	10,754,716 – 10,754,812
Length	96
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	87.06
Mean single sequence MFE	-35.10
Consensus MFE	-22.99
Energy contribution	-24.93
Covariance contribution	1.94
Combinations/Pair	1.07
Mean z-score	-1.69
Structure conservation index	0.65
SVM decision value	0.01
SVM RNA-class probability	0.538847
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10754716 96 + 22224390
GCUAGUGGUGGU---------GGUGGUCUGGGCCAUCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUCGGUCUUUUAGCUAUCCCAUUUCACUGGG
.((((((((((.---------((((((..(((((..((((((((....)).....(((....)))))))))(....))))))....))))))))))..)))))). ( -35.90)
>DroSec_CAF1 4238 105 + 1
GCUAGUGGUGGUGGUGUUGGUGGUGGUCUGGGCCACCGUUUUGCCUUGCCUAAUGAGGGCAACCUGAAACGGACCUCGGUCUUUUAACUAUCCCAUUUCACUGGG
.(((((((.(((((.(.((((((((((....))))))((((((..((((((.....))))))..))))))((((....))))....)))).))))))))))))). ( -42.40)
>DroSim_CAF1 1705 96 + 1
GCUAGUGGUGGU---------GGUGGUCUGGGCCACCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUCGGUCUUUUAACUAUCCCAUUUCACUGGG
.((((((((((.---------((((((..(((((.(((((((((....)).....(((....)))))))))).....)))))....))))))))))..)))))). ( -37.90)
>DroEre_CAF1 3525 88 + 1
GGUGCUGC---------------CGGUCUGGGCCACCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUCUG-CUUUUAACUAUCCCAUUUCACUGG-
((.....)---------------)(((((((((((..(.....)..)))))..(.(((....))).)..))))))....-............(((......)))- ( -24.20)
>consensus
GCUAGUGGUGGU_________GGUGGUCUGGGCCACCGUUUUGCCUUGGCUAAUGAGGGCAACCUGAAACGGACCUCGGUCUUUUAACUAUCCCAUUUCACUGGG
.((((((((((.............(((((((((((..(.....)..)))))..(.(((....))).)..))))))..(((......)))...))))..)))))). (-22.99 = -24.93 +   1.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:18 2006