Locus 1916

Sequence ID	2L_DroMel_CAF1
Location	5,226,602 – 5,226,908
Length	306
Max. P	0.909389

overview

Window 2

Location	5,226,602 – 5,226,722
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.72
Mean single sequence MFE	-40.17
Consensus MFE	-31.39
Energy contribution	-31.32
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.13
Structure conservation index	0.78
SVM decision value	1.06
SVM RNA-class probability	0.909389
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5226602 120 - 22407834
CGAAACGCACUCUGUUCGCAAAACAAUGGUGAUUUUACAGUCGCUCGUUGUUGCGCUACAGUGACGCAACAGUGCGUUAACAGUGGGCGUCGAAUGCUACCGAGAGUUCACUGUACCAGC
...((((((((((((.((((..(((((((((((......))))).))))))))))..)))).........)))))))).(((((((((.(((........)))..)))))))))...... ( -44.10)
>DroSec_CAF1 4064 107 - 1
CGAAACGCACUCA-CUCGCAAAACAAUGGCGAUUUUACAG------------GCGCUACAGUGACGCAACAGUGCGUUAACAGUGGGCGUUGGAUGCUACCGAGAGUUCACUGUAGCAGG
...((((((((..-.((((.........))))........------------((((......).)))...)))))))).(((((((((.((((......))))..)))))))))...... ( -34.00)
>DroSim_CAF1 4941 108 - 1
CGAAACGCACUCUGGUCGCAAAACAAUGGCGAUUUUACAG------------GCGCUACAGUGACGCAACAGUGCGUUAACAGUGGGCGUCGGAUGCUACCGAGAGUUCACUGUAGCAGC
...((((((((((((((((.........)))))....)))------------((((......).)))...)))))))).(((((((((.((((......))))..)))))))))...... ( -38.80)
>DroYak_CAF1 5113 120 - 1
CAAAACGCACUCUGGUCGCACAACAAUGGCGAUUUCACAGUCGCUCGAUGUUGAGCUACAGUGACGCAACAGUGCGUUAACAGUGGCCGUCGGAUGCUACUGAGAGUUCACUGUACCAGC
...........((((..((.(((((.(((((((......))))).)).))))).))((((((((((((....))))....(((((((........))))))).....)))))))))))). ( -43.80)
>consensus
CGAAACGCACUCUGGUCGCAAAACAAUGGCGAUUUUACAG____________GCGCUACAGUGACGCAACAGUGCGUUAACAGUGGGCGUCGGAUGCUACCGAGAGUUCACUGUACCAGC
...((((((((....((((.........))))....................((((......).)))...)))))))).((((((..(.((((......))))..)..))))))...... (-31.39 = -31.32 +  -0.06)

alignment

secondary structure

dotplot

Window 3

Location	5,226,642 – 5,226,762
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.41
Mean single sequence MFE	-31.73
Consensus MFE	-24.27
Energy contribution	-24.15
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-2.08
Structure conservation index	0.77
SVM decision value	0.76
SVM RNA-class probability	0.842321
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5226642 120 + 22407834
UUAACGCACUGUUGCGUCACUGUAGCGCAACAACGAGCGACUGUAAAAUCACCAUUGUUUUGCGAACAGAGUGCGUUUCGCUUUGCAUAAAUGCAUUUUACAAGCGUUUAAUUGACUUUC
..(((((((((((((((.......)))))))..........((((((((.......)))))))).....)))))))).(((((((((....))))......))))).............. ( -30.50)
>DroSec_CAF1 4104 107 + 1
UUAACGCACUGUUGCGUCACUGUAGCGC------------CUGUAAAAUCGCCAUUGUUUUGCGAG-UGAGUGCGUUUCGCUUUGCAUAAAUGCAUUUUACAAGCGUUUAAUUGACUUUC
.....(((....)))((((....(((((------------.((((((((.((.(((....((((((-((((.....))))).)))))..))))))))))))).)))))....)))).... ( -32.80)
>DroSim_CAF1 4981 108 + 1
UUAACGCACUGUUGCGUCACUGUAGCGC------------CUGUAAAAUCGCCAUUGUUUUGCGACCAGAGUGCGUUUCGCUUUGCAUAAAUGCAUUUUACAAGCGUUUAAUUGACUUUC
.....(((....)))((((....(((((------------.((((((((.((.(((....(((((...(((.....)))...)))))..))))))))))))).)))))....)))).... ( -29.00)
>DroYak_CAF1 5153 120 + 1
UUAACGCACUGUUGCGUCACUGUAGCUCAACAUCGAGCGACUGUGAAAUCGCCAUUGUUGUGCGACCAGAGUGCGUUUUGCUUUGCAUAAAUGCAUUUUACAAGCGUUUAAUUGACUUUC
..(((((.(((.....((((.((.((((......)))).)).))))..((((((....)).)))).)))((((((((((((...))).)))))))))......)))))............ ( -34.60)
>consensus
UUAACGCACUGUUGCGUCACUGUAGCGC____________CUGUAAAAUCGCCAUUGUUUUGCGACCAGAGUGCGUUUCGCUUUGCAUAAAUGCAUUUUACAAGCGUUUAAUUGACUUUC
..((((((((((((((....))))))...............((((((((.......)))))))).....)))))))).(((((((((....))))......))))).............. (-24.27 = -24.15 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	5,226,642 – 5,226,762
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.41
Mean single sequence MFE	-32.23
Consensus MFE	-22.21
Energy contribution	-22.52
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.64
Structure conservation index	0.69
SVM decision value	0.57
SVM RNA-class probability	0.784935
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5226642 120 - 22407834
GAAAGUCAAUUAAACGCUUGUAAAAUGCAUUUAUGCAAAGCGAAACGCACUCUGUUCGCAAAACAAUGGUGAUUUUACAGUCGCUCGUUGUUGCGCUACAGUGACGCAACAGUGCGUUAA
..............(((((......((((....))))))))).((((((((((((.((((..(((((((((((......))))).))))))))))..)))).........)))))))).. ( -36.60)
>DroSec_CAF1 4104 107 - 1
GAAAGUCAAUUAAACGCUUGUAAAAUGCAUUUAUGCAAAGCGAAACGCACUCA-CUCGCAAAACAAUGGCGAUUUUACAG------------GCGCUACAGUGACGCAACAGUGCGUUAA
....((((......(((((((((((((((....))))..(((...))).....-.((((.........))))))))))))------------)))......))))(((....)))..... ( -29.00)
>DroSim_CAF1 4981 108 - 1
GAAAGUCAAUUAAACGCUUGUAAAAUGCAUUUAUGCAAAGCGAAACGCACUCUGGUCGCAAAACAAUGGCGAUUUUACAG------------GCGCUACAGUGACGCAACAGUGCGUUAA
....((((......((((((((((.((((....))))..(((...)))......(((((.........))))))))))))------------)))......))))(((....)))..... ( -29.40)
>DroYak_CAF1 5153 120 - 1
GAAAGUCAAUUAAACGCUUGUAAAAUGCAUUUAUGCAAAGCAAAACGCACUCUGGUCGCACAACAAUGGCGAUUUCACAGUCGCUCGAUGUUGAGCUACAGUGACGCAACAGUGCGUUAA
...............((((......((((....))))))))..((((((((.(((((((.(((((.(((((((......))))).)).))))).(...).))))).))..)))))))).. ( -33.90)
>consensus
GAAAGUCAAUUAAACGCUUGUAAAAUGCAUUUAUGCAAAGCGAAACGCACUCUGGUCGCAAAACAAUGGCGAUUUUACAG____________GCGCUACAGUGACGCAACAGUGCGUUAA
..............(((((......((((....))))))))).((((((((....((((.........))))....................((((......).)))...)))))))).. (-22.21 = -22.52 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	5,226,762 – 5,226,868
Length	106
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.27
Mean single sequence MFE	-33.80
Consensus MFE	-26.83
Energy contribution	-26.82
Covariance contribution	-0.00
Combinations/Pair	1.07
Mean z-score	-2.07
Structure conservation index	0.79
SVM decision value	0.84
SVM RNA-class probability	0.864560
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5226762 106 + 22407834
AAAACGUGUCACAGGCAAUACAAACAUGUUUUUGCUGUUAGCCAGCAGCUGUAAGCGGCAUGAAUGG-------CCAACUGGCUAUGGCUUCGGUUUU-------UGCCUUCCGAUAAAU
......((((..((((((.(((....)))....((((..((((....((((....))))....((((-------((....)))))))))).))))..)-------)))))...))))... ( -31.30)
>DroSec_CAF1 4211 106 + 1
AAAACGUGUCACAGGCAAUAAAAACAUGUUUUUGCUGUUAGCCAGCAGCUGUAAGCGGCAUGAAUGG-------CCAACUGGCUUCGGCUUCGGUUUU-------UGCCUUCCGAUAAAU
......((((..((((((...((((.((.....((((..((((((..((.....))(((.......)-------))..)))))).))))..)))))))-------)))))...))))... ( -31.10)
>DroSim_CAF1 5089 106 + 1
AAAACGUGUCACAGGCAAUACAAACAUGUUUUUGCUGUUAGCCAGCAGCUGUAAGCGGCAUGAAUGG-------CCAACUGGCUUCGGCUUCGGUUUU-------UGCCUUCCGAUAAAU
......((((..((((((...((((.((.....((((..((((((..((.....))(((.......)-------))..)))))).))))..)))))))-------)))))...))))... ( -31.10)
>DroYak_CAF1 5273 120 + 1
AAAACGUGUCACAGGCAAUACAAACAUGUUUUUGCUGUUAGCCAGCAGCUGUAAGCCGCAUGAAUGGCCAAUGGCCAACUGGCUCUGGCUUUGGCUAUUGCCUAUUGCCUUCCGAUAAAU
......((((..((((((((....(((((...(((((.....)))))((.....)).)))))...(((.(((((((((..(((....)))))))))))))))))))))))...))))... ( -41.70)
>consensus
AAAACGUGUCACAGGCAAUACAAACAUGUUUUUGCUGUUAGCCAGCAGCUGUAAGCGGCAUGAAUGG_______CCAACUGGCUUCGGCUUCGGUUUU_______UGCCUUCCGAUAAAU
......((((..(((((..........(((...((((..((((((..((((....)))).....((((.....)))).)))))).))))...)))..........)))))...))))... (-26.83 = -26.82 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	5,226,802 – 5,226,908
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.68
Mean single sequence MFE	-37.70
Consensus MFE	-31.72
Energy contribution	-32.41
Covariance contribution	0.69
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.84
SVM decision value	0.95
SVM RNA-class probability	0.887371
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5226802 106 - 22407834
UGAGCAAUCGCGGCAUGGGAAAUAACUGGUUGCUUAGCUGAUUUAUCGGAAGGCA-------AAAACCGAAGCCAUAGCCAGUUGG-------CCAUUCAUGCCGCUUACAGCUGCUGGC
..(((....((((((((((...((((((((((.....((((....))))..(((.-------.........))).)))))))))).-------...)))))))))).....)))...... ( -36.90)
>DroSec_CAF1 4251 106 - 1
UGAGCAAACGCGGCAUGGGAAAUAACUGGUUGCUUAGCUGAUUUAUCGGAAGGCA-------AAAACCGAAGCCGAAGCCAGUUGG-------CCAUUCAUGCCGCUUACAGCUGCUGGC
..(((....((((((((((...(((((((((((...)).......((((..((..-------....))....))))))))))))).-------...)))))))))).....)))...... ( -36.40)
>DroSim_CAF1 5129 106 - 1
UGAGCAAACGCGGCAUGGGAAAUAACUGGUUGCUUAGCUGAUUUAUCGGAAGGCA-------AAAACCGAAGCCGAAGCCAGUUGG-------CCAUUCAUGCCGCUUACAGCUGCUGGC
..(((....((((((((((...(((((((((((...)).......((((..((..-------....))....))))))))))))).-------...)))))))))).....)))...... ( -36.40)
>DroYak_CAF1 5313 120 - 1
UGAGCAAUCUCGGCAUGGGAAAUAACUGGUUGCUUAGCUGAUUUAUCGGAAGGCAAUAGGCAAUAGCCAAAGCCAGAGCCAGUUGGCCAUUGGCCAUUCAUGCGGCUUACAGCUGCUGGC
.(((....)))(((...((...(((((((((((((..((((....)))).))))....(((....)))........))))))))).))....)))..(((.(((((.....)))))))). ( -41.10)
>consensus
UGAGCAAACGCGGCAUGGGAAAUAACUGGUUGCUUAGCUGAUUUAUCGGAAGGCA_______AAAACCGAAGCCAAAGCCAGUUGG_______CCAUUCAUGCCGCUUACAGCUGCUGGC
..(((....((((((((((....((((((((......((((....))))..(((.................)))..))))))))(((.....))).)))))))))).....)))...... (-31.72 = -32.41 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:39 2006