Locus 6505

Sequence ID	3L_DroMel_CAF1
Location	17,263,887 – 17,264,075
Length	188
Max. P	0.994906

overview

Window 0

Location	17,263,887 – 17,263,998
Length	111
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	98.65
Mean single sequence MFE	-33.45
Consensus MFE	-33.83
Energy contribution	-33.45
Covariance contribution	-0.38
Combinations/Pair	1.07
Mean z-score	-1.74
Structure conservation index	1.01
SVM decision value	0.28
SVM RNA-class probability	0.665290
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17263887 111 - 23771897
GGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACAACGGCAAACACCCGAAAGACUCAAAAGCGAGCGCGGCUAA
((((....))))(((((..(((((((......(((.......((((..(............)..))))....(((.......)))...))).....)).))))).))))). ( -32.80)
>DroSec_CAF1 147431 111 - 1
GGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACAACGGCAAACACCCGAAAGACUCAAAAGCGAGCGCGGCUAA
((((....))))(((((..(((((((......(((.......((((..(............)..))))....(((.......)))...))).....)).))))).))))). ( -32.80)
>DroSim_CAF1 142455 111 - 1
GGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACAACGGCAAACACCCGAAAGACUCAAAAGCGAGCGCGGCUAA
((((....))))(((((..(((((((......(((.......((((..(............)..))))....(((.......)))...))).....)).))))).))))). ( -32.80)
>DroEre_CAF1 150586 111 - 1
GGGCGAUAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACAACGGCAAACACCCGAAAGACUCAAAAGCGAGCGCGGCCAA
((((....))))(((((..(((((((......(((.......((((..(............)..))))....(((.......)))...))).....)).))))).))))). ( -35.40)
>consensus
GGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACAACGGCAAACACCCGAAAGACUCAAAAGCGAGCGCGGCUAA
((((....))))(((((..(((((((......(((.......((((..(............)..))))....(((.......)))...))).....)).))))).))))). (-33.83 = -33.45 +  -0.38)

alignment

secondary structure

dotplot

Window 1

Location	17,263,927 – 17,264,035
Length	108
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	95.22
Mean single sequence MFE	-38.28
Consensus MFE	-36.00
Energy contribution	-35.62
Covariance contribution	-0.38
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.94
SVM decision value	1.12
SVM RNA-class probability	0.917676
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17263927 108 - 23771897
AGCGAAAAGACUGGCCUUUGGAUGGGGCUGGAGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACA
(((((.....(..(((((.....)))))..).(((..((((....))))..))).)))))..((((...(((((....))))).......(((.....)))))))... ( -39.60)
>DroSec_CAF1 147471 107 - 1
AGCGAAAAGACUGGCCUU-UGGUGGGGCUCGGGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACA
(((((.....((((((((-....))))).)))(((..((((....))))..))).)))))..((((...(((((....))))).......(((.....)))))))... ( -38.40)
>DroSim_CAF1 142495 108 - 1
AGCGAAAAGACUGGCCUUUUGAUGGGGCUCGGGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACA
(((((.....((((((((.....))))).)))(((..((((....))))..))).)))))..((((...(((((....))))).......(((.....)))))))... ( -38.40)
>DroEre_CAF1 150626 107 - 1
AGCGGAAAGACUGGCCUUUGGAUGGGGUU-GAGGUUGGGGCGAUAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACA
...........(((((((((...(((((.-(((((..((((....))))..))).))))))).......(((((....)))))..))))..((.....)))))))... ( -36.70)
>consensus
AGCGAAAAGACUGGCCUUUGGAUGGGGCUCGAGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAAUGUCAUCAAAGUGGCUACGAAAUGCAUAAAGCGGCCAACA
...........(((((.......(((((....(((..((((....))))..)))...)))))..(((..(((((....)))))))).....((.....)))))))... (-36.00 = -35.62 +  -0.38)

alignment

secondary structure

dotplot

Window 2

Location	17,263,967 – 17,264,075
Length	108
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	95.22
Mean single sequence MFE	-29.91
Consensus MFE	-27.63
Energy contribution	-27.88
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.92
SVM decision value	0.93
SVM RNA-class probability	0.884738
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17263967 108 + 23771897
UUACCAGGAGCGAUGGCCAGAGCUUUCACCCCAACCUCCAGCCCCAUCCAAAGGCCAGUCUUUUCGCUCCGUCAUGGCUUAAUGGCAUUACGCCCAAGGCCCCACAUU
......(((((((.(((..(((.((.......)).)))..)))......(((((....))))))))))))((...(((((...(((.....)))..)))))..))... ( -29.90)
>DroSec_CAF1 147511 107 + 1
UUACCAGGAGCGAUGGCCAGAGCUUUCACCCCAACCCCGAGCCCCACCA-AAGGCCAGUCUUUUCGCUCCGUCAUGGCUUAAUGGCAUUACGCCCAAGGCCCCACAUU
......((((((((((((.(.((((.............)))).).....-..)))))......)))))))((...(((((...(((.....)))..)))))..))... ( -29.32)
>DroSim_CAF1 142535 108 + 1
UUACCAGGAGCGAUGGCCAGAGCUUUCACCCCAACCCCGAGCCCCAUCAAAAGGCCAGUCUUUUCGCUCCGUCAUGGCUUAAUGGCAUUACGCCCAAGGCCCCACAUU
......((((((((((((.(......)...........((......))....)))))......)))))))((...(((((...(((.....)))..)))))..))... ( -30.80)
>DroEre_CAF1 150666 107 + 1
UUACCAGGAGCGAUGGCCAGAGCUAUCGCCCCAACCUC-AACCCCAUCCAAAGGCCAGUCUUUCCGCUCCGUCAUGGCUUAAUGGCAUUACGCCCAAGGCCCCACAUU
......(((((((((((....))))))(((........-.............)))..........)))))((...(((((...(((.....)))..)))))..))... ( -29.60)
>consensus
UUACCAGGAGCGAUGGCCAGAGCUUUCACCCCAACCCCGAGCCCCAUCAAAAGGCCAGUCUUUUCGCUCCGUCAUGGCUUAAUGGCAUUACGCCCAAGGCCCCACAUU
......((((((((((((..................................)))))......)))))))((...(((((...(((.....)))..)))))..))... (-27.63 = -27.88 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	17,263,967 – 17,264,075
Length	108
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	95.22
Mean single sequence MFE	-45.80
Consensus MFE	-44.39
Energy contribution	-43.82
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-3.08
Structure conservation index	0.97
SVM decision value	2.52
SVM RNA-class probability	0.994906
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17263967 108 - 23771897
AAUGUGGGGCCUUGGGCGUAAUGCCAUUAAGCCAUGACGGAGCGAAAAGACUGGCCUUUGGAUGGGGCUGGAGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAA
...((.((((....(((.....))).....))).).))(((((((.....(..(((((.....)))))..).(((..((((....))))..))).)))))))...... ( -48.00)
>DroSec_CAF1 147511 107 - 1
AAUGUGGGGCCUUGGGCGUAAUGCCAUUAAGCCAUGACGGAGCGAAAAGACUGGCCUU-UGGUGGGGCUCGGGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAA
...((.((((....(((.....))).....))).).))(((((((.....((((((((-....))))).)))(((..((((....))))..))).)))))))...... ( -46.80)
>DroSim_CAF1 142535 108 - 1
AAUGUGGGGCCUUGGGCGUAAUGCCAUUAAGCCAUGACGGAGCGAAAAGACUGGCCUUUUGAUGGGGCUCGGGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAA
...((.((((....(((.....))).....))).).))(((((((.....((((((((.....))))).)))(((..((((....))))..))).)))))))...... ( -46.80)
>DroEre_CAF1 150666 107 - 1
AAUGUGGGGCCUUGGGCGUAAUGCCAUUAAGCCAUGACGGAGCGGAAAGACUGGCCUUUGGAUGGGGUU-GAGGUUGGGGCGAUAGCUCUGGCCAUCGCUCCUGGUAA
...((.((((....(((.....))).....))).).))(((((((.......((((((.....))))))-..(((..((((....))))..))).)))))))...... ( -41.60)
>consensus
AAUGUGGGGCCUUGGGCGUAAUGCCAUUAAGCCAUGACGGAGCGAAAAGACUGGCCUUUGGAUGGGGCUCGAGGUUGGGGUGAAAGCUCUGGCCAUCGCUCCUGGUAA
...((.((((....(((.....))).....))).).))(((((((.....(.((((((.....)))))).).(((..((((....))))..))).)))))))...... (-44.39 = -43.82 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:51 2006