Locus 3238

Sequence ID	3R_DroMel_CAF1
Location	8,649,524 – 8,649,632
Length	108
Max. P	0.925883

overview

Window 6

Location	8,649,524 – 8,649,632
Length	108
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.71
Mean single sequence MFE	-25.15
Consensus MFE	-13.25
Energy contribution	-13.83
Covariance contribution	0.59
Combinations/Pair	1.19
Mean z-score	-2.39
Structure conservation index	0.53
SVM decision value	0.71
SVM RNA-class probability	0.831023
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8649524 108 + 27905053
AUUGCAAAAAUUGAGCGGGGAGAAAAUUGUUAACAAUUAGUCAACGCUGUUCGCAACAAUGGCAAAUAAUUAAUUUUAAUUGUAUGCCAUGCAUAAC------AGCACAGGAAU
..(((.......(((((((..((.(((((....)))))..))..).))))))(((....(((((.(((((((....))))))).)))))))).....------.)))....... ( -27.50)
>DroPse_CAF1 87471 103 + 1
-------AA----AGGGGGGGAAAAUUUGUUAACAAUUAGUCAACUGAGCCCGCAACAAUGGCAAAUAAUUAAUUUUAAUUGUAUGCCACGCAUAGCUGCAUCUGCAUAGGAAU
-------..----.((((..((....(((....)))....))..)....)))(((....(((((.(((((((....))))))).))))).(((....)))...)))........ ( -22.60)
>DroSec_CAF1 76382 108 + 1
AUUGCAAAAAUUGAGUGGGGAGAAAAUUGUUAACAAUUAGUCAACGCUAUUCGCAACAAUGGCAAAUAAUUAAUUUUAAUUGUAUGCCAUGCAUAAC------UGCACAGGAAU
..((((......(((((((..((.(((((....)))))..))..).))))))(((....(((((.(((((((....))))))).)))))))).....------))))....... ( -26.60)
>DroEre_CAF1 89518 108 + 1
AUUGCAAAAAUUGGGCUGGGAGAAAAUUGUUAACAAUUAGUCAACGGUGCUCGCAACAAUGGCAAAUAAUUAAUUUUAAUUGUAUGUCGUGCAUAAC------UGCACAGGAAU
.........((((...((.(((...((((((.((.....)).)))))).))).)).))))((((.(((((((....))))))).))))(((((....------)))))...... ( -26.10)
>DroAna_CAF1 71205 95 + 1
-------------AGCGGGGAGAAAAUUGUUAACAAUUAGUCAACUGAGCCAGCAACAAUGGCAAAUAAUUAAUUUUAAUUGUAUGCCACGCAUAAG------UGCGCUGAAAC
-------------.((.((..((.(((((....)))))..))..))..))((((.....(((((.(((((((....))))))).))))).(((....------))))))).... ( -25.50)
>DroPer_CAF1 83586 102 + 1
-------AG----AGGG-GGGAAAAUUUGUUAACAAUUAGUCAACUGAGCCCGCAACAAUGGCAAAUAAUUAAUUUUAAUUGUAUGCCACGCAUAGAUGCAUCUGCAUAGGAAU
-------..----.(((-........(((....)))((((....)))).)))(((....(((((.(((((((....))))))).))))).(((....)))...)))........ ( -22.60)
>consensus
_______AA____AGCGGGGAGAAAAUUGUUAACAAUUAGUCAACGGAGCCCGCAACAAUGGCAAAUAAUUAAUUUUAAUUGUAUGCCACGCAUAAC______UGCACAGGAAU
..............(((((.....(((((....))))).(....)....))))).....(((((.(((((((....))))))).))))).(((..........)))........ (-13.25 = -13.83 +   0.59)

alignment

secondary structure

dotplot

Window 7

Location	8,649,524 – 8,649,632
Length	108
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.71
Mean single sequence MFE	-22.67
Consensus MFE	-15.28
Energy contribution	-14.87
Covariance contribution	-0.42
Combinations/Pair	1.20
Mean z-score	-2.23
Structure conservation index	0.67
SVM decision value	1.17
SVM RNA-class probability	0.925883
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8649524 108 - 27905053
AUUCCUGUGCU------GUUAUGCAUGGCAUACAAUUAAAAUUAAUUAUUUGCCAUUGUUGCGAACAGCGUUGACUAAUUGUUAACAAUUUUCUCCCCGCUCAAUUUUUGCAAU
........(((------(((.(((((((((...(((((....)))))...)))))....))))))))))((((((.....))))))............((.........))... ( -26.30)
>DroPse_CAF1 87471 103 - 1
AUUCCUAUGCAGAUGCAGCUAUGCGUGGCAUACAAUUAAAAUUAAUUAUUUGCCAUUGUUGCGGGCUCAGUUGACUAAUUGUUAACAAAUUUUCCCCCCCU----UU-------
........((...((((((.....((((((...(((((....)))))...)))))).)))))).))...((((((.....))))))...............----..------- ( -23.80)
>DroSec_CAF1 76382 108 - 1
AUUCCUGUGCA------GUUAUGCAUGGCAUACAAUUAAAAUUAAUUAUUUGCCAUUGUUGCGAAUAGCGUUGACUAAUUGUUAACAAUUUUCUCCCCACUCAAUUUUUGCAAU
.......((((------(((((((((((((...(((((....)))))...)))))....)))..)))))((((((.....))))))......................)))).. ( -22.10)
>DroEre_CAF1 89518 108 - 1
AUUCCUGUGCA------GUUAUGCACGACAUACAAUUAAAAUUAAUUAUUUGCCAUUGUUGCGAGCACCGUUGACUAAUUGUUAACAAUUUUCUCCCAGCCCAAUUUUUGCAAU
.......((((------(...(((.((.((.(((((..((((.....))))...))))))))).)))..((((((.....)))))).....................))))).. ( -18.80)
>DroAna_CAF1 71205 95 - 1
GUUUCAGCGCA------CUUAUGCGUGGCAUACAAUUAAAAUUAAUUAUUUGCCAUUGUUGCUGGCUCAGUUGACUAAUUGUUAACAAUUUUCUCCCCGCU-------------
(..((((((((------....)))((((((...(((((....)))))...))))))....)))))..).((((((.....))))))...............------------- ( -23.40)
>DroPer_CAF1 83586 102 - 1
AUUCCUAUGCAGAUGCAUCUAUGCGUGGCAUACAAUUAAAAUUAAUUAUUUGCCAUUGUUGCGGGCUCAGUUGACUAAUUGUUAACAAAUUUUCCC-CCCU----CU-------
........((((..(((....)))((((((...(((((....)))))...))))))..))))(((....((((((.....)))))).......)))-....----..------- ( -21.60)
>consensus
AUUCCUGUGCA______GUUAUGCAUGGCAUACAAUUAAAAUUAAUUAUUUGCCAUUGUUGCGAGCACAGUUGACUAAUUGUUAACAAUUUUCUCCCCGCU____UU_______
......(((((..........)))))((((...(((((....)))))...))))...............((((((.....))))))............................ (-15.28 = -14.87 +  -0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:24 2006