Locus 5960

Sequence ID	3L_DroMel_CAF1
Location	15,972,302 – 15,972,443
Length	141
Max. P	0.793023

overview

Window 8

Location	15,972,302 – 15,972,418
Length	116
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.55
Mean single sequence MFE	-40.39
Consensus MFE	-26.60
Energy contribution	-26.58
Covariance contribution	-0.02
Combinations/Pair	1.36
Mean z-score	-1.70
Structure conservation index	0.66
SVM decision value	0.59
SVM RNA-class probability	0.793023
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15972302 116 - 23771897
CCUCCGGCCAUAGCGUGGCCAUGAACAACACCGUGGUUACUCCAGUGGCGGGCAGCAGCAAUCAGUUGAAUAGCCAGAAUAAUCUCCUGGCCGCUGCAGCAGCCUCUUCGAAUGUC
....(((((((.(.(((((((((........))))))))).)..)))))((((.(((((..((....))...(((((.........))))).)))))....))))...))...... ( -39.90)
>DroVir_CAF1 50658 113 - 1
CUUCCGGUCAUAGCGUGGCCAUGAAUAACACGGUGGUCACCCCAGUGGCUGGCAGCAGCAACCAAUUGAAUAGCCAGAAUAAUUUAUUAGCUGCUGCGGCAGC---GGCGAAUGCU
....(((((((.(.((((((((..........)))))))).)..)))))))((((((((......(((......)))((((...)))).))))))))((((..---......)))) ( -35.70)
>DroGri_CAF1 53268 113 - 1
CUUCAGGCCAUAGUGUGGCGAUGAACAACACGGUCGUCACUCCUGUGGCUGGUAGCAGCAAUCAGUUGAACAGCCAGAAUAAUCUAUUAGCCGCUGCGGCAGC---UGCAAAUGCC
.....((((((((.((((((((..........))))))))..))))))))(((((((((..((....))...((((((....)))....((....))))).))---)))...)))) ( -39.30)
>DroMoj_CAF1 58009 113 - 1
CCUCUGGCCAUAGCGUGGCCAUGAAUAACACGGUGGUCACUCCAGUGGCUGGCAGCAGCAAUCAGUUGAAUAGCCAGAACAACAUAUUAAAUGCGGCAGCAGC---UGCAAAUCUC
((.(((((....))((((((((..........))))))))..))).))(((((..((((.....))))....)))))..............((((((....))---))))...... ( -36.40)
>DroAna_CAF1 1681 116 - 1
CCUCCGGCCAUAGUGUGGCCAUGAACAAUACGGUGGUGACUCCGGUGGCGGGCAGUAGCAAUCAGUUGAACAGCCAGAACAAUCUCCUGGCCGCUGCUUCGGUCGCCUCGAAUGUC
.....((((((...))))))..........(((.(((((((..((..((((.(((.((.......(((......)))......)).))).))))..))..))))))))))...... ( -43.02)
>DroPer_CAF1 7443 110 - 1
CCUCUGGCCACAGCGUAGCCAUGAACAACACGGUGGUGACGCCUGUGGCAGGCAGCAGCAAUCAGUUGAAUAGCCAAAACAAUCUGCUGGUCGCUGCUGCGGCUGCUUC------C
...(((....))).((((((........(((((((....)))).)))....((((((((.((((((.((.............)).)))))).))))))))))))))...------. ( -48.02)
>consensus
CCUCCGGCCAUAGCGUGGCCAUGAACAACACGGUGGUCACUCCAGUGGCUGGCAGCAGCAAUCAGUUGAAUAGCCAGAACAAUCUACUAGCCGCUGCAGCAGC___UGCGAAUGUC
......(((((...((((((((..........))))))))....))))).(((..((((.....))))....)))..............(((((....)))))............. (-26.60 = -26.58 +  -0.02)

alignment

secondary structure

dotplot

Window 9

Location	15,972,339 – 15,972,443
Length	104
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	80.34
Mean single sequence MFE	-32.10
Consensus MFE	-22.91
Energy contribution	-22.55
Covariance contribution	-0.36
Combinations/Pair	1.25
Mean z-score	-1.15
Structure conservation index	0.71
SVM decision value	0.01
SVM RNA-class probability	0.539499
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15972339 104 - 23771897
GCAGCAGCGGCAGCUUGUGCCAAUGCCUCCGGCCAUAGCGUGGCCAUGAACAACACCGUGGUUACUCCAGUGGCGGGCAGCAGCAAUCAGUUGAAUAGCCAGAA
((..((((((((.....))))..(((..((.(((((.(.(((((((((........))))))))).)..))))).))..))).......))))....))..... ( -37.50)
>DroVir_CAF1 50692 95 - 1
-------C--CGCCAUGUGUAAACACUUCCGGUCAUAGCGUGGCCAUGAAUAACACGGUGGUCACCCCAGUGGCUGGCAGCAGCAACCAAUUGAAUAGCCAGAA
-------(--((((..(((....)))....((((((...))))))...........)))))((((....))))(((((.....(((....)))....))))).. ( -26.20)
>DroPse_CAF1 7456 103 - 1
-CAUCGGCCAUACCAUGCGUGAACACCUCUGGCCACAGCGUAGCCAUGAACAACACGGUGGUGACGCCCGUGGCAGGCAGCAGCAAUCAGUUGAAUAGCCAAAA
-....(((....(((((((((..((....))..))).)))).((((((........((((....)))))))))).))...((((.....))))....))).... ( -31.90)
>DroGri_CAF1 53302 95 - 1
-------C--CGUCCUGUGUCAACACUUCAGGCCAUAGUGUGGCGAUGAACAACACGGUCGUCACUCCUGUGGCUGGUAGCAGCAAUCAGUUGAACAGCCAGAA
-------.--....((((.(((((......((((((((.((((((((..........))))))))..))))))))(((.......))).)))))))))...... ( -30.80)
>DroMoj_CAF1 58043 95 - 1
-------C--CGGCGUGCGUGAACACCUCUGGCCAUAGCGUGGCCAUGAAUAACACGGUGGUCACUCCAGUGGCUGGCAGCAGCAAUCAGUUGAAUAGCCAGAA
-------(--((.((((.(....)...(((((((((...))))))).))....)))).)))((((....))))(((((..((((.....))))....))))).. ( -33.10)
>DroPer_CAF1 7474 103 - 1
-CAUCGGCCAUACCAUGCGUGAACACCUCUGGCCACAGCGUAGCCAUGAACAACACGGUGGUGACGCCUGUGGCAGGCAGCAGCAAUCAGUUGAAUAGCCAAAA
-....(((.......((((....)....(((.(((((((((.(((((..........))))).))).)))))))))))).((((.....))))....))).... ( -33.10)
>consensus
_______C__CACCAUGCGUGAACACCUCUGGCCAUAGCGUGGCCAUGAACAACACGGUGGUCACUCCAGUGGCUGGCAGCAGCAAUCAGUUGAAUAGCCAGAA
...............................(((((...((((((((..........))))))))....))))).(((..((((.....))))....))).... (-22.91 = -22.55 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:11 2006