Locus 1079

Sequence ID	2R_DroMel_CAF1
Location	4,372,300 – 4,372,460
Length	160
Max. P	0.840588

overview

Window 4

Location	4,372,300 – 4,372,396
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	94.79
Mean single sequence MFE	-37.45
Consensus MFE	-33.13
Energy contribution	-33.17
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.20
Structure conservation index	0.88
SVM decision value	0.11
SVM RNA-class probability	0.587512
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372300 96 - 20766785
GGAGCCCAACUCCGCCACGUGCUCGUUGAGGGCGCGUGGAAAUAGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACCCGUUUCGAGGGUCUGCC
(((((.........((((((((((.....)))))))))).........)))))((..(((.....)))........((((.......))))..)). ( -36.27)
>DroSec_CAF1 42962 96 - 1
GGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAAUGGGCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACCCGUUUCGAGGGUCUGCC
((((((((......((((((((((.....))))))))))...)))))..........(((.....))).....)))((((.......))))..... ( -38.50)
>DroSim_CAF1 43195 96 - 1
GGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAAUGGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACCCGUUUCGAGGGUCUGCC
((((((((......((((((((((.....))))))))))...)))...)))))((..(((.....)))........((((.......))))..)). ( -37.00)
>DroEre_CAF1 39476 95 - 1
GGAGCCCUACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAGUGGCCAGCUCUGGCAUGGAUUUUUCACGUUUUCCACCCGUUUCGAGGGGCU-CC
(((((((((((...((((((((((.....)))))))))).))).((((....)))).((((............))))..........))))))-)) ( -43.90)
>DroYak_CAF1 41386 96 - 1
GGAGCCCAACUCCGCCACGUGCUCCUUGAGGGCGCGUGAAAAUGGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACCCGUUUCGAGGGUCUGCC
((((.....))))..(((((((((.....)))))))))...(((((.......)))))(((............)))((((.......))))..... ( -31.60)
>consensus
GGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAAUGGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACCCGUUUCGAGGGUCUGCC
(((((.........((((((((((.....)))))))))).........)))))....((((............))))(((.......)))...... (-33.13 = -33.17 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	4,372,317 – 4,372,420
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	92.91
Mean single sequence MFE	-34.39
Consensus MFE	-29.50
Energy contribution	-30.14
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.36
Structure conservation index	0.86
SVM decision value	0.43
SVM RNA-class probability	0.734850
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372317 103 - 20766785
GAACACCACCACAAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUUGAGGGCGCGUGGAAAUAGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACC
((((....................(((((.........((((((((((.....)))))))))).........)))))....(((.....))).))))...... ( -31.97)
>DroSec_CAF1 42979 103 - 1
GCACACCACCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAAUGGGCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACC
((...(((..((........)).))).(((((......((((((((((.....))))))))))...))))).)).......((((............)))).. ( -34.80)
>DroSim_CAF1 43212 103 - 1
GCACACCACCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAAUGGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACC
..........(((((((.......((((.....)))).((((((((((.....)))))))))))))))))...........((((............)))).. ( -34.50)
>DroEre_CAF1 39492 103 - 1
GCACAACACCGCCAUUUUCGCCCUGGAGCCCUACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAGUGGCCAGCUCUGGCAUGGAUUUUUCACGUUUUCCACC
((........)).......(((..(((((.(((((...((((((((((.....)))))))))).)))))...)))))))).((((............)))).. ( -37.90)
>DroYak_CAF1 41403 102 - 1
GCACA-CGCCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCCUUGAGGGCGCGUGAAAAUGGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACC
.....-.((.(((((((((.....((((.....))))...((((((((.....)))))))))))))))))..)).......((((............)))).. ( -32.80)
>consensus
GCACACCACCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGAAAUGGCCAGCUCCGCCAUGGAUUUUCCACGUUUUCCACC
..........(((((((.......((((.....)))).((((((((((.....)))))))))))))))))...........((((............)))).. (-29.50 = -30.14 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	4,372,356 – 4,372,460
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	94.13
Mean single sequence MFE	-32.40
Consensus MFE	-28.42
Energy contribution	-29.82
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.88
SVM decision value	0.75
SVM RNA-class probability	0.840588
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372356 104 - 20766785
UCGAAUCGUCGGAAUUAUAAUUGCAAAUCUUAUGCAACGCGAACACCACCACAAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUUGAGGGCGCGUGGA
.......(.(((((......(((((.......))))).(.(........).)....))))).).((((.....)))).((((((((((.....)))))))))). ( -31.10)
>DroSec_CAF1 43018 104 - 1
UCGAAUCGUCGGAAUUAUAAUUGCAAAUCUUAUGCAACGCGCACACCACCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGA
.......(.(((((......(((((.......))))).(((........)))....))))).).((((.....)))).((((((((((.....)))))))))). ( -34.80)
>DroSim_CAF1 43251 104 - 1
UCGAAUCGUCGGAAUUAUAAUUGCAAAUCUUAUGCAACGCGCACACCACCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGA
.......(.(((((......(((((.......))))).(((........)))....))))).).((((.....)))).((((((((((.....)))))))))). ( -34.80)
>DroEre_CAF1 39531 104 - 1
UCGAAUCGUCGGAAUUAUAAUUGCAAAUCUUAUGCAACGCGCACAACACCGCCAUUUUCGCCCUGGAGCCCUACUCCGCCACGUGCUCGUCGAGGGCGCGUGGA
.......(.(((((......(((((.......))))).(((........)))...))))))...((((.....)))).((((((((((.....)))))))))). ( -31.50)
>DroYak_CAF1 41442 103 - 1
UCGAAUCGUAAGAUUUAUAAUUGCAAAUCUUAUGCAACGCGCACA-CGCCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCCUUGAGGGCGCGUGAA
..(((((....)))))....(((((.......))))).(((....-)))...............((((.....))))..(((((((((.....))))))))).. ( -29.80)
>consensus
UCGAAUCGUCGGAAUUAUAAUUGCAAAUCUUAUGCAACGCGCACACCACCGCCAUUUUCCGCCUGGAGCCCAACUCCGCCACGUGCUCGUCGAGGGCGCGUGGA
.......(.(((((......(((((.......))))).(((........)))....))))).).((((.....)))).((((((((((.....)))))))))). (-28.42 = -29.82 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:54 2006