Locus 4826

Sequence ID	2R_DroMel_CAF1
Location	15,848,927 – 15,849,129
Length	202
Max. P	0.963058

overview

Window 1

Location	15,848,927 – 15,849,035
Length	108
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	78.95
Mean single sequence MFE	-21.87
Consensus MFE	-12.68
Energy contribution	-12.60
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-1.84
Structure conservation index	0.58
SVM decision value	0.29
SVM RNA-class probability	0.668515
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15848927 108 + 20766785
CUUCCCCUCCACCCCCCGC----CAAUUUUCC--GCCAACUCUCAACACAUUUUGGCCUGCCCCACCCACUUU-UCUUAGUCCGGGGGCGUUGGCAGAUAACGGUUUACUUUCUU
.................((----(.....((.--((((((..((((......))))...(((((....(((..-....)))...))))))))))).))....))).......... ( -25.40)
>DroSec_CAF1 6146 101 + 1
CUCCCCCUGCA-------A----AAAUUUUUU--ACCAACUCUCACCACAUUUUGGCCGGCCCCACCCACUUU-UCUUAGCCCGGGGGCGUUGGCAGAUAACGGUUUACUUUCUU
...........-------.----.........--..........(((....((((.((((((((.((..((..-....))...))))).)))))))))....))).......... ( -18.50)
>DroSim_CAF1 6065 96 + 1
CUCCCCCUGCA-------A----CAAUUUUC-------ACUCUUACCACAUUUUGGCCUGCCCCACCCACUUU-UCUUAGCCCGGGGGCGUUGGCAGAUAACGGUUUACUUUCUU
......(((((-------(----(.......-------.......(((.....)))...(((((.....((..-....))....)))))))).)))).................. ( -19.40)
>DroEre_CAF1 7506 103 + 1
CCUCCCCCCCA-------C----CGACCUUCCGACCCCCCUCGCGCCACAUUUUGGAUUGCCCCACCCACUUCUUCUUAGCCCGGGGGCGUUGGCA-AUAACGGUUUACUUUCUU
..........(-------(----((.....((((((((((..((.........(((..........)))..........))..))))).)))))..-....)))).......... ( -24.61)
>DroYak_CAF1 7186 103 + 1
CCGCCCCCUCA-------GUUUUCCGCCUUC---CCCCCCUCACAUCACAUUCUGGAUUGCCCCGCCCACUUC-UCUUAGCCCGGGGGCGUUGGCA-AUAACGGUUUACUUUCUU
..........(-------((...(((.....---....((..............))((((((.(((((.((..-.........)))))))..))))-))..)))...)))..... ( -21.44)
>consensus
CUCCCCCUCCA_______A____CAAUUUUC___CCCAACUCUCACCACAUUUUGGCCUGCCCCACCCACUUU_UCUUAGCCCGGGGGCGUUGGCAGAUAACGGUUUACUUUCUU
............................................(((............(((((.....((.......))....)))))((((.....))))))).......... (-12.68 = -12.60 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	15,848,927 – 15,849,035
Length	108
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	78.95
Mean single sequence MFE	-30.38
Consensus MFE	-15.50
Energy contribution	-16.34
Covariance contribution	0.84
Combinations/Pair	1.14
Mean z-score	-1.88
Structure conservation index	0.51
SVM decision value	0.06
SVM RNA-class probability	0.562373
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15848927 108 - 20766785
AAGAAAGUAAACCGUUAUCUGCCAACGCCCCCGGACUAAGA-AAAGUGGGUGGGGCAGGCCAAAAUGUGUUGAGAGUUGGC--GGAAAAUUG----GCGGGGGGUGGAGGGGAAG
...........(((((((((((((((((((((..(((....-..)))..).)))))....(((......)))...))))))--)))....))----))))............... ( -34.40)
>DroSec_CAF1 6146 101 - 1
AAGAAAGUAAACCGUUAUCUGCCAACGCCCCCGGGCUAAGA-AAAGUGGGUGGGGCCGGCCAAAAUGUGGUGAGAGUUGGU--AAAAAAUUU----U-------UGCAGGGGGAG
......(((((..(((.(.(((((((((((((..(((....-..)))..).)))))..((((.....))))....))))))--).).))).)----)-------)))........ ( -27.40)
>DroSim_CAF1 6065 96 - 1
AAGAAAGUAAACCGUUAUCUGCCAACGCCCCCGGGCUAAGA-AAAGUGGGUGGGGCAGGCCAAAAUGUGGUAAGAGU-------GAAAAUUG----U-------UGCAGGGGGAG
...........((....(((((.(((((((((..(((....-..)))..).)))))..((((.....))))......-------.......)----)-------)))))).)).. ( -26.20)
>DroEre_CAF1 7506 103 - 1
AAGAAAGUAAACCGUUAU-UGCCAACGCCCCCGGGCUAAGAAGAAGUGGGUGGGGCAAUCCAAAAUGUGGCGCGAGGGGGGUCGGAAGGUCG----G-------UGGGGGGGAGG
...........((.((.(-..((....((((((.((((........(((((......))))).....)))).)).))))(..(....)..))----)-------..))).))... ( -35.42)
>DroYak_CAF1 7186 103 - 1
AAGAAAGUAAACCGUUAU-UGCCAACGCCCCCGGGCUAAGA-GAAGUGGGCGGGGCAAUCCAGAAUGUGAUGUGAGGGGGG---GAAGGCGGAAAAC-------UGAGGGGGCGG
......((...((.((((-((((..(.(((((..(((....-......)))(((....)))..............))))).---)..))))).....-------))).)).)).. ( -28.50)
>consensus
AAGAAAGUAAACCGUUAUCUGCCAACGCCCCCGGGCUAAGA_AAAGUGGGUGGGGCAGGCCAAAAUGUGGUGAGAGUGGGG___GAAAAUUG____G_______UGCAGGGGAAG
...........((.((..(((((..(((((....(((.......)))))))).)))))((((.....))))....................................)).))... (-15.50 = -16.34 +   0.84)

alignment

secondary structure

dotplot

Window 3

Location	15,849,035 – 15,849,129
Length	94
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	79.07
Mean single sequence MFE	-23.19
Consensus MFE	-11.27
Energy contribution	-12.34
Covariance contribution	1.07
Combinations/Pair	1.06
Mean z-score	-3.02
Structure conservation index	0.49
SVM decision value	1.55
SVM RNA-class probability	0.963058
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15849035 94 + 20766785
AAUCUCCGUACAUAAUUUUUGCGACUUCAUGUUACGCAAUGUAUGUA----UGGCGCAUUCUUUCCGCUUCUGCGAAAUAACAUACGAUCUUCU-------UCAU
.(((.(((((((((....(((((((.....))..)))))..))))))----)))...........(((....)))...........))).....-------.... ( -20.00)
>DroVir_CAF1 9809 78 + 1
AAUCUUUGUACAUAAUUUUUGCAACCUCAUGUUACGCAA--------UUUCGGGG---UUGUUGCCGCAUCCGUGUG---------GCUGUACU-------CUAU
.......(((((........((((((((..(((....))--------)...))))---)))).((((((....))))---------))))))).-------.... ( -22.60)
>DroSec_CAF1 6247 94 + 1
AAUCUCUGUACAUAAUUUUUGCGACUUCAUGUUACGCAAUGUAUGUA----UGGCGCAUUCUUUCCGCUUCUGCGGAAUAACACACGCUCUUCU-------CCAU
.......(((((((....(((((((.....))..)))))..))))))----)((((......((((((....)))))).......)))).....-------.... ( -24.52)
>DroSim_CAF1 6161 94 + 1
AAUCUCCGUACAUAAUUUUUGCGACUUCAUGUUACGCAAUGUAUGUA----UGGCGCAUUCUUUCCGCUUCUGCGGAAUAACACACGCUCUUCU-------CCAU
......((((((((....(((((((.....))..)))))..))))))----))(((......((((((....)))))).......)))......-------.... ( -26.42)
>DroEre_CAF1 7609 97 + 1
AAUCUCUGUACAUAAUUUUUGCGACUUCAUGUUACGCAAUGU----A----UGGCGCAUUCUUUCCGCUUCUGCGGAAUAACAUACGCUCUUCUUUAGCUGCCAU
.......((((((......((((((.....))..))))))))----)----)(((.......((((((....))))))........(((.......))).))).. ( -22.00)
>DroYak_CAF1 7289 97 + 1
AAUCUCCGUACAUAAUUUUUGCGACUUCAUGUUACGCAAUGU----A----UGGCGCAUUCUUUCCGCUUCUGCGGAAUAAAAUACGCUUAUCUUCAGCUGCCAU
.....((((((((......((((((.....))..))))))))----)----))).(((....((((((....))))))........(((.......))))))... ( -23.60)
>consensus
AAUCUCCGUACAUAAUUUUUGCGACUUCAUGUUACGCAAUGU____A____UGGCGCAUUCUUUCCGCUUCUGCGGAAUAACAUACGCUCUUCU_______CCAU
..................(((((((.....))..))))).............((((......((((((....)))))).......))))................ (-11.27 = -12.34 +   1.07)

alignment

secondary structure

dotplot

Window 4

Location	15,849,035 – 15,849,129
Length	94
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	79.07
Mean single sequence MFE	-23.58
Consensus MFE	-13.91
Energy contribution	-14.78
Covariance contribution	0.88
Combinations/Pair	1.18
Mean z-score	-2.20
Structure conservation index	0.59
SVM decision value	0.98
SVM RNA-class probability	0.893791
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15849035 94 - 20766785
AUGA-------AGAAGAUCGUAUGUUAUUUCGCAGAAGCGGAAAGAAUGCGCCA----UACAUACAUUGCGUAACAUGAAGUCGCAAAAAUUAUGUACGGAGAUU
....-------....((((((((....((((((....))))))...)))).((.----((((((..(((((...........)))))....)))))).)).)))) ( -21.70)
>DroVir_CAF1 9809 78 - 1
AUAG-------AGUACAGC---------CACACGGAUGCGGCAACAA---CCCCGAAA--------UUGCGUAACAUGAGGUUGCAAAAAUUAUGUACAAAGAUU
....-------.(((((((---------(.((....)).))).....---........--------....(((((.....)))))........)))))....... ( -15.70)
>DroSec_CAF1 6247 94 - 1
AUGG-------AGAAGAGCGUGUGUUAUUCCGCAGAAGCGGAAAGAAUGCGCCA----UACAUACAUUGCGUAACAUGAAGUCGCAAAAAUUAUGUACAGAGAUU
....-------....(.((((((....((((((....))))))...))))))).----((((((..(((((...........)))))....))))))........ ( -23.70)
>DroSim_CAF1 6161 94 - 1
AUGG-------AGAAGAGCGUGUGUUAUUCCGCAGAAGCGGAAAGAAUGCGCCA----UACAUACAUUGCGUAACAUGAAGUCGCAAAAAUUAUGUACGGAGAUU
....-------....(.((((((....((((((....))))))...))))))).----((((((..(((((...........)))))....))))))........ ( -23.70)
>DroEre_CAF1 7609 97 - 1
AUGGCAGCUAAAGAAGAGCGUAUGUUAUUCCGCAGAAGCGGAAAGAAUGCGCCA----U----ACAUUGCGUAACAUGAAGUCGCAAAAAUUAUGUACAGAGAUU
(((((.(((.......)))((((....((((((....))))))...))))))))----)----...(((((...........))))).................. ( -25.80)
>DroYak_CAF1 7289 97 - 1
AUGGCAGCUGAAGAUAAGCGUAUUUUAUUCCGCAGAAGCGGAAAGAAUGCGCCA----U----ACAUUGCGUAACAUGAAGUCGCAAAAAUUAUGUACGGAGAUU
(((((.(((.......)))(((((((.((((((....)))))))))))))))))----)----...((.((((.(((((...........))))))))).))... ( -30.90)
>consensus
AUGG_______AGAAGAGCGUAUGUUAUUCCGCAGAAGCGGAAAGAAUGCGCCA____U____ACAUUGCGUAACAUGAAGUCGCAAAAAUUAUGUACAGAGAUU
.................((((((....((((((....))))))...))))))..............(((((...........))))).................. (-13.91 = -14.78 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:12 2006