Locus 4179

Sequence ID	3R_DroMel_CAF1
Location	11,337,419 – 11,337,673
Length	254
Max. P	0.999789

overview

Window 1

Location	11,337,419 – 11,337,539
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-39.06
Consensus MFE	-38.46
Energy contribution	-38.74
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-2.51
Structure conservation index	0.98
SVM decision value	4.08
SVM RNA-class probability	0.999789
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11337419 120 + 27905053
GCUUUUGUAGCUGCAAGGAUAUUGCAGCUGCAACGUGUUGAAGUGGCGCCUCGGUAAAAUUGUGUCAAACUGUGAUUGCAUUUUUGUGACUGGCAUUCAAUUGCUAUGGUGUUUGGCUUU
....((((((((((((.....))))))))))))......(((((((((((..(((((....((((((.((.(((....)))....))...))))))....)))))..))))))..))))) ( -38.90)
>DroSec_CAF1 76243 120 + 1
GCUUUUGUAGCUGCAAGGAUAUUGCAGCUGCAACGUGUUGAAGUGGCGCCUCGGUAAAAUUGUGUCAAACUGUGAUUGCAUUUUUGUGACUGGCAUUCAAUUGCUGUGGUGUUUGGCUUU
....((((((((((((.....))))))))))))......(((((((((((.((((((....((((((.((.(((....)))....))...))))))....)))))).))))))..))))) ( -41.80)
>DroSim_CAF1 74841 120 + 1
GCUUUUGUAGCUGCAAGGAUAUUGCAGCUGCAACGUGUUGAAGUGGCGCCUCGGUAAAAUUGUGUCAAACUGUGAUUGCAUUUUUGUGACUGGCAUUCAAUUGCUGUGGUGUUUGGCUUU
....((((((((((((.....))))))))))))......(((((((((((.((((((....((((((.((.(((....)))....))...))))))....)))))).))))))..))))) ( -41.80)
>DroEre_CAF1 72132 120 + 1
GCUCUUGUAACUGCAAGGAUAUUGCAGCUGCAACGUGUUGAAGUGGCGCCUCGGUGAAAUUGUGUCAAACUGUGAUUGCAUUUUUGUGACUGGCAUUCAAUUGCUGUGGUGUUUGGCUUU
((.((((((.((((((.....)))))).))))).).)).(((((((((((.(((..(....((((((.((.(((....)))....))...))))))....)..))).))))))..))))) ( -35.20)
>DroYak_CAF1 73854 120 + 1
GCUUUUGUAGCUGUAAGGAUAUUGCAGCUGCAACGUGUUGAAGUGGCGCCUCGGUAAAAUUGUGUCAAACUGUGAUUGCAUUUUUGUGACUGCCAUUCAAUUGCUGUGGUGUUUGGCUUU
....((((((((((((.....))))))))))))......(((((((((((.(((((((((.((((((....(((....))).....)))).)).)))...)))))).))))))..))))) ( -37.60)
>consensus
GCUUUUGUAGCUGCAAGGAUAUUGCAGCUGCAACGUGUUGAAGUGGCGCCUCGGUAAAAUUGUGUCAAACUGUGAUUGCAUUUUUGUGACUGGCAUUCAAUUGCUGUGGUGUUUGGCUUU
....((((((((((((.....))))))))))))......(((((((((((.((((((....((((((.((.(((....)))....))...))))))....)))))).))))))..))))) (-38.46 = -38.74 +   0.28)

alignment

secondary structure

dotplot

Window 2

Location	11,337,419 – 11,337,539
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-22.32
Consensus MFE	-20.60
Energy contribution	-20.84
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	0.92
SVM decision value	0.33
SVM RNA-class probability	0.689869
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11337419 120 - 27905053
AAAGCCAAACACCAUAGCAAUUGAAUGCCAGUCACAAAAAUGCAAUCACAGUUUGACACAAUUUUACCGAGGCGCCACUUCAACACGUUGCAGCUGCAAUAUCCUUGCAGCUACAAAAGC
...(((..........(((......)))..((((.((...((......)).)))))).............)))((.((........)).))((((((((.....))))))))........ ( -23.40)
>DroSec_CAF1 76243 120 - 1
AAAGCCAAACACCACAGCAAUUGAAUGCCAGUCACAAAAAUGCAAUCACAGUUUGACACAAUUUUACCGAGGCGCCACUUCAACACGUUGCAGCUGCAAUAUCCUUGCAGCUACAAAAGC
...(((..........(((......)))..((((.((...((......)).)))))).............)))((.((........)).))((((((((.....))))))))........ ( -23.40)
>DroSim_CAF1 74841 120 - 1
AAAGCCAAACACCACAGCAAUUGAAUGCCAGUCACAAAAAUGCAAUCACAGUUUGACACAAUUUUACCGAGGCGCCACUUCAACACGUUGCAGCUGCAAUAUCCUUGCAGCUACAAAAGC
...(((..........(((......)))..((((.((...((......)).)))))).............)))((.((........)).))((((((((.....))))))))........ ( -23.40)
>DroEre_CAF1 72132 120 - 1
AAAGCCAAACACCACAGCAAUUGAAUGCCAGUCACAAAAAUGCAAUCACAGUUUGACACAAUUUCACCGAGGCGCCACUUCAACACGUUGCAGCUGCAAUAUCCUUGCAGUUACAAGAGC
...(((..........(((......)))..((((.((...((......)).)))))).............)))((.((........)).))((((((((.....))))))))........ ( -21.00)
>DroYak_CAF1 73854 120 - 1
AAAGCCAAACACCACAGCAAUUGAAUGGCAGUCACAAAAAUGCAAUCACAGUUUGACACAAUUUUACCGAGGCGCCACUUCAACACGUUGCAGCUGCAAUAUCCUUACAGCUACAAAAGC
................(((((((((((((.(((.(.(((((....(((.....)))....)))))...).))))))).))))....)))))(((((...........)))))........ ( -20.40)
>consensus
AAAGCCAAACACCACAGCAAUUGAAUGCCAGUCACAAAAAUGCAAUCACAGUUUGACACAAUUUUACCGAGGCGCCACUUCAACACGUUGCAGCUGCAAUAUCCUUGCAGCUACAAAAGC
...(((..........(((......)))..((((.((...((......)).)))))).............)))((.((........)).))((((((((.....))))))))........ (-20.60 = -20.84 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	11,337,539 – 11,337,633
Length	94
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-32.90
Consensus MFE	-24.96
Energy contribution	-24.64
Covariance contribution	-0.32
Combinations/Pair	1.17
Mean z-score	-2.01
Structure conservation index	0.76
SVM decision value	1.16
SVM RNA-class probability	0.923926
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11337539 94 + 27905053
GGCAACUCUGCCCAUGUCCUUAACUCCCUUUACC----------------------CGCCCACUUGG----GCAUGUGGGCGUGGUCCGAUUUGGGCACUAACACUUGUCGCCUUCAGAU
(((.....((((((.(((.............(((----------------------(((((((....----....))))))).)))..))).))))))...((....)).)))....... ( -31.46)
>DroSec_CAF1 76363 94 + 1
GGCAACUCUGCCCAUGUCCUCAACUCCCUUUACC----------------------CGCCCACUUGG----GCAUGUGGGCGUGGUCCGAUUUAGGCACUAACACUUGUCGCCUUCAGAU
((((....))))...................(((----------------------(((((((....----....))))))).)))..((...((((((........)).)))))).... ( -28.30)
>DroSim_CAF1 74961 94 + 1
GGCAACUCUGCCCAUGUCCUCAACUCCCUUUACC----------------------CGCCCACUUGG----GCAUGUGGGCGUGGUCCGAUUUGGGCCCUAACACUUGUCGCCUUCAGAU
(((......(((((.(((.............(((----------------------(((((((....----....))))))).)))..))).)))))....((....)).)))....... ( -30.06)
>DroEre_CAF1 72252 120 + 1
GGCAACCCUGCCCAAGUGCUCAACUCCCUUUUCCCAGAAUACCUACACUCCACUGCCACCCACUUGGGCGGCCAUGUGGGCGUGGUCCGAUUUGGGCACUAACACUUGUCGCCCUUGGAC
((((....)))).................................((((((((.(((.(((....))).)))...))))).)))((((((...((((((........)).)))))))))) ( -39.70)
>DroYak_CAF1 73974 87 + 1
GGCAACCCUGCCCAUGUCCUCCACUCC-----------------------------CGCCCACUUGG----UCAUGUGGGCGUGGUCCGAAGUGGGCACUAACACUUGUCGCCUUCGGAC
((((....)))).............((-----------------------------(((((((....----....))))))).))(((((((..((((........))))..))))))). ( -35.00)
>consensus
GGCAACUCUGCCCAUGUCCUCAACUCCCUUUACC______________________CGCCCACUUGG____GCAUGUGGGCGUGGUCCGAUUUGGGCACUAACACUUGUCGCCUUCAGAU
((((....))))............................................(((((((.((......)).)))))))..(((.((...((((((........)).)))))).))) (-24.96 = -24.64 +  -0.32)

alignment

secondary structure

dotplot

Window 4

Location	11,337,539 – 11,337,633
Length	94
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.46
Mean single sequence MFE	-39.08
Consensus MFE	-28.06
Energy contribution	-27.94
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-2.27
Structure conservation index	0.72
SVM decision value	1.53
SVM RNA-class probability	0.961635
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11337539 94 - 27905053
AUCUGAAGGCGACAAGUGUUAGUGCCCAAAUCGGACCACGCCCACAUGC----CCAAGUGGGCG----------------------GGUAAAGGGAGUUAAGGACAUGGGCAGAGUUGCC
.......((((((.........((((((..((..(((.(((((((....----....)))))))----------------------)))...))..(((...))).))))))..)))))) ( -33.80)
>DroSec_CAF1 76363 94 - 1
AUCUGAAGGCGACAAGUGUUAGUGCCUAAAUCGGACCACGCCCACAUGC----CCAAGUGGGCG----------------------GGUAAAGGGAGUUGAGGACAUGGGCAGAGUUGCC
.......((((((...(((..((((((...((..(((.(((((((....----....)))))))----------------------)))...))......))).)))..)))..)))))) ( -36.40)
>DroSim_CAF1 74961 94 - 1
AUCUGAAGGCGACAAGUGUUAGGGCCCAAAUCGGACCACGCCCACAUGC----CCAAGUGGGCG----------------------GGUAAAGGGAGUUGAGGACAUGGGCAGAGUUGCC
.......((((((...((((...((((((.((..(((.(((((((....----....)))))))----------------------)))...))...))).)).)...))))..)))))) ( -35.20)
>DroEre_CAF1 72252 120 - 1
GUCCAAGGGCGACAAGUGUUAGUGCCCAAAUCGGACCACGCCCACAUGGCCGCCCAAGUGGGUGGCAGUGGAGUGUAGGUAUUCUGGGAAAAGGGAGUUGAGCACUUGGGCAGGGUUGCC
(((....)))..((((((((....(((...(((((((((((((((...(((((((....))))))).)))).)))).))...))))).....))).....))))))))(((......))) ( -53.00)
>DroYak_CAF1 73974 87 - 1
GUCCGAAGGCGACAAGUGUUAGUGCCCACUUCGGACCACGCCCACAUGA----CCAAGUGGGCG-----------------------------GGAGUGGAGGACAUGGGCAGGGUUGCC
.......((((((.........(((((((((((..((.(((((((....----....)))))))-----------------------------))..)))))....))))))..)))))) ( -37.00)
>consensus
AUCUGAAGGCGACAAGUGUUAGUGCCCAAAUCGGACCACGCCCACAUGC____CCAAGUGGGCG______________________GGUAAAGGGAGUUGAGGACAUGGGCAGAGUUGCC
.......((((((.........((((((..........(((((((.((......)).)))))))................................((.....)).))))))..)))))) (-28.06 = -27.94 +  -0.12)

alignment

secondary structure

dotplot

Window 5

Location	11,337,573 – 11,337,673
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.35
Mean single sequence MFE	-41.54
Consensus MFE	-28.62
Energy contribution	-29.94
Covariance contribution	1.32
Combinations/Pair	1.21
Mean z-score	-1.70
Structure conservation index	0.69
SVM decision value	0.46
SVM RNA-class probability	0.743754
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11337573 100 + 27905053
----------------CGCCCACUUGG----GCAUGUGGGCGUGGUCCGAUUUGGGCACUAACACUUGUCGCCUUCAGAUGACCGAUUGCAACGUGGCUUUUGGACAGAGAUCGCUCAGG
----------------.((((((....----....))))))(((((((.((((((((((........)).)))..)))))..((((..((......))..))))...).))))))..... ( -33.60)
>DroSec_CAF1 76397 100 + 1
----------------CGCCCACUUGG----GCAUGUGGGCGUGGUCCGAUUUAGGCACUAACACUUGUCGCCUUCAGAUGACCGAUUGCGACGGGGUUGCUAGAUGGAGAUCGCUCAUG
----------------.((((((....----....))))))(((((((.((((((....((((.((((((((..((........))..)))))))))))))))))).).))))))..... ( -41.50)
>DroSim_CAF1 74995 100 + 1
----------------CGCCCACUUGG----GCAUGUGGGCGUGGUCCGAUUUGGGCCCUAACACUUGUCGCCUUCAGAUGACCGAUUGCGACGGUGUUGCUAGAUAGAGAUCGCUCAUG
----------------.((((....))----))..(((((((.(((((.....))))).(((((((.(((((..((........))..))))))))))))............))))))). ( -40.40)
>DroEre_CAF1 72292 120 + 1
ACCUACACUCCACUGCCACCCACUUGGGCGGCCAUGUGGGCGUGGUCCGAUUUGGGCACUAACACUUGUCGCCCUUGGACGACCGAUGGCGACGAGCAUGUUGGACAGAGAUCGCUCCUG
.....((((((((.(((.(((....))).)))...))))).)))((((.....)))).(((((((((((((((.((((....)))).)))))))))..)))))).(((.((....))))) ( -52.70)
>DroYak_CAF1 74001 100 + 1
----------------CGCCCACUUGG----UCAUGUGGGCGUGGUCCGAAGUGGGCACUAACACUUGUCGCCUUCGGACGAACGCUGGCGAAGAGCAUGUUGCACAGAGAACACUCCUG
----------------.((((((....----....))))))(((((((((((..((((........))))..))))))))...(.(((((((........)))).))).)..)))..... ( -39.50)
>consensus
________________CGCCCACUUGG____GCAUGUGGGCGUGGUCCGAUUUGGGCACUAACACUUGUCGCCUUCAGAUGACCGAUUGCGACGAGGAUGUUGGACAGAGAUCGCUCAUG
.................((((((.((......)).))))))((((((...((((....((((((((((((((..((........))..))))))))..)))))).))))))))))..... (-28.62 = -29.94 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:32 2006