Locus 6139

Sequence ID	2L_DroMel_CAF1
Location	17,134,874 – 17,135,062
Length	188
Max. P	0.999904

overview

Window 9

Location	17,134,874 – 17,134,986
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.72
Mean single sequence MFE	-33.60
Consensus MFE	-23.49
Energy contribution	-25.17
Covariance contribution	1.68
Combinations/Pair	1.07
Mean z-score	-2.89
Structure conservation index	0.70
SVM decision value	1.08
SVM RNA-class probability	0.911310
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17134874 112 + 22407834
GGAAGAAAGCACUUGAUUAGGAGAAAGAGCAGGCAACCGAAAGUAAAGGCUUGGGACUUUCGGACGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAU
........((((((..((.(..(((((..(((((...(....).....)))))...)))))...).))..))))))(((((((.(.((.......)).).)))))--------))..... ( -34.10)
>DroSec_CAF1 103285 112 + 1
GGAAGAAAGCACUUGAUUAGGAGAAAGAGCAGGCAAGCGAAAGGAAAGGCUUGGGACUUCCGGGCGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAU
(((((...((.(((..........))).))...(((((..........)))))...)))))............((((((((((.(.((.......)).).)))))--------))))).. ( -34.70)
>DroSim_CAF1 115478 112 + 1
GGAAGAAAGCACUUGAUUAGGAGAAAGAGCAGGCAAGCGAAAGUAAAGGCUUGGGACUUCCGGACGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAU
(((((......(((......)))......(((((..((....))....)))))...)))))............((((((((((.(.((.......)).).)))))--------))))).. ( -35.90)
>DroEre_CAF1 100774 101 + 1
GGAUGAAAGCACUUGAUUAGCAGUAAGAGCAGGCAAGCGAAAGUAAAGGCUUCGGACUUCCGGAC-----------GGGCGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAU
........((.((((........)))).))..((..((....))....))(((((....))))).-----------.((.((((((((.........))))))))--------))..... ( -26.80)
>DroYak_CAF1 103164 120 + 1
GGUAAAAAGCACUUGAUUAGGAGAAAGAGCAGGCAAGCGAAAGUAAAGGCUUGGGACUUCCGGACAGAGAAAGUGUGGCUGUGUGAGUAAAUAAGACGCUCACACCCACACACCCACAAU
(((........(((.....((((......(((((..((....))....)))))....)))).....)))...((((((..((((((((.........)))))))))))))))))...... ( -36.50)
>consensus
GGAAGAAAGCACUUGAUUAGGAGAAAGAGCAGGCAAGCGAAAGUAAAGGCUUGGGACUUCCGGACGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC________CCACAAU
(((((...((.(((..........))).))((((..((....))....))))....)))))((.........((((((((((.(.........).))))))))))........))..... (-23.49 = -25.17 +   1.68)

alignment

secondary structure

dotplot

Window 0

Location	17,134,914 – 17,135,026
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.10
Mean single sequence MFE	-42.08
Consensus MFE	-31.11
Energy contribution	-31.83
Covariance contribution	0.72
Combinations/Pair	1.06
Mean z-score	-3.16
Structure conservation index	0.74
SVM decision value	1.77
SVM RNA-class probability	0.976390
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17134914 112 + 22407834
AAGUAAAGGCUUGGGACUUUCGGACGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCG
.......((((((.(...(((((.(((((.((.((((((((((.(.((.......)).).)))))--------))))).))....))))).)))))...).))))))(((......))). ( -44.50)
>DroSec_CAF1 103325 112 + 1
AAGGAAAGGCUUGGGACUUCCGGGCGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCG
.......((((((.((((..(((.(((((.((.((((((((((.(.((.......)).).)))))--------))))).))....))))).)))))))...))))))(((......))). ( -45.20)
>DroSim_CAF1 115518 112 + 1
AAGUAAAGGCUUGGGACUUCCGGACGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCG
.......((((((.((((..(((.(((((.((.((((((((((.(.((.......)).).)))))--------))))).))....))))).)))))))...))))))(((......))). ( -42.70)
>DroEre_CAF1 100814 101 + 1
AAGUAAAGGCUUCGGACUUCCGGAC-----------GGGCGUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCCUCGGCUGAGUCCUGUAAGCCGCUCACCAAAGCG
.......((((((((....))((((-----------.((.((((((((.........))))))))--------))........(((....)))..)))).).)))))(((......))). ( -35.40)
>DroYak_CAF1 103204 120 + 1
AAGUAAAGGCUUGGGACUUCCGGACAGAGAAAGUGUGGCUGUGUGAGUAAAUAAGACGCUCACACCCACACACCCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCG
.......((((((((..((((.....).))).((((((..((((((((.........)))))))))))))).)))(((..(..(((....)))..)...))))))))(((......))). ( -42.60)
>consensus
AAGUAAAGGCUUGGGACUUCCGGACGGAGAGAGUGUGGGUGUGUGAGUAAAUAAGACGCUCACAC________CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCG
.......((((((.((((((((((.........(((((..((((((((.........))))))))........)))))........)))))..)))))...))))))(((......))). (-31.11 = -31.83 +   0.72)

alignment

secondary structure

dotplot

Window 1

Location	17,134,914 – 17,135,026
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.10
Mean single sequence MFE	-39.68
Consensus MFE	-28.34
Energy contribution	-29.26
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-2.82
Structure conservation index	0.71
SVM decision value	1.02
SVM RNA-class probability	0.901043
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17134914 112 - 22407834
CGCUUUGGUGAGCGGCUUACACGACUCAGCCGAAGCUUUGAUUGUGG--------GUGUGAGCGUCUUAUUUACUCACACACCCACACUCUCUCCGUCCGAAAGUCCCAAGCCUUUACUU
.(((((((((((((.......)).)))).)))))))...((.(((((--------(((((.(.((.......)).).)))))))))).)).....(..(....)..)............. ( -38.50)
>DroSec_CAF1 103325 112 - 1
CGCUUUGGUGAGCGGCUUACACGACUCAGCCGAAGCUUUGAUUGUGG--------GUGUGAGCGUCUUAUUUACUCACACACCCACACUCUCUCCGCCCGGAAGUCCCAAGCCUUUCCUU
.(((((((((((((.......)).)))).)))))))...((.(((((--------(((((.(.((.......)).).)))))))))).)).........(((((.........))))).. ( -39.40)
>DroSim_CAF1 115518 112 - 1
CGCUUUGGUGAGCGGCUUACACGACUCAGCCGAAGCUUUGAUUGUGG--------GUGUGAGCGUCUUAUUUACUCACACACCCACACUCUCUCCGUCCGGAAGUCCCAAGCCUUUACUU
.(((((((((((((.......)).)))).)))))))...((.(((((--------(((((.(.((.......)).).)))))))))).))..(((....))).................. ( -39.30)
>DroEre_CAF1 100814 101 - 1
CGCUUUGGUGAGCGGCUUACAGGACUCAGCCGAGGCUUUGAUUGUGG--------GUGUGAGCGUCUUAUUUACUCACACGCCC-----------GUCCGGAAGUCCGAAGCCUUUACUU
.((((....))))(((((...(((((...(((.(((.........((--------(((((.(.((.......)).).)))))))-----------)))))).))))).)))))....... ( -36.80)
>DroYak_CAF1 103204 120 - 1
CGCUUUGGUGAGCGGCUUACACGACUCAGCCGAAGCUUUGAUUGUGGGUGUGUGGGUGUGAGCGUCUUAUUUACUCACACAGCCACACUUUCUCUGUCCGGAAGUCCCAAGCCUUUACUU
.(((((((((((((.......)).)))).)))))))((((...((((.((((((((((((((...)))))..))))))))).))))((((((.......))))))..))))......... ( -44.40)
>consensus
CGCUUUGGUGAGCGGCUUACACGACUCAGCCGAAGCUUUGAUUGUGG________GUGUGAGCGUCUUAUUUACUCACACACCCACACUCUCUCCGUCCGGAAGUCCCAAGCCUUUACUU
.(((((((((((((.......)).)))).)))))))...((.(((((........(((((((...........)))))))..))))).)).....(..(....)..)............. (-28.34 = -29.26 +   0.92)

alignment

secondary structure

dotplot

Window 2

Location	17,134,954 – 17,135,062
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-28.54
Consensus MFE	-27.36
Energy contribution	-27.20
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.37
Structure conservation index	0.96
SVM decision value	4.47
SVM RNA-class probability	0.999904
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17134954 108 + 22407834
GUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCGUAAAGACAAUUCAAUCGAUGGCAAAUACCCAUACAA----
((((((((.........))))))))--------...........((((((..(((((.((.(....((((......))))...).)).)))))..))).)))..............---- ( -27.40)
>DroSec_CAF1 103365 108 + 1
GUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCGUAAAGACAAUUCAAUCGAUGGCAAAUACCCAUACAA----
((((((((.........))))))))--------...........((((((..(((((.((.(....((((......))))...).)).)))))..))).)))..............---- ( -27.40)
>DroSim_CAF1 115558 108 + 1
GUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCGUAAAGACAAUUCAAUCGAUGGCAAAUACCCAUACAA----
((((((((.........))))))))--------...........((((((..(((((.((.(....((((......))))...).)).)))))..))).)))..............---- ( -27.40)
>DroEre_CAF1 100843 112 + 1
GUGUGAGUAAAUAAGACGCUCACAC--------CCACAAUCAAAGCCUCGGCUGAGUCCUGUAAGCCGCUCACCAAAGCGUAAAGACAAUUCAAUCGAUGGCGAAUACUCAUACAAUCGC
(((((((((.....(.....)....--------...........((((((..(((((..(((....((((......)))).....))))))))..))).)))...)))))))))...... ( -30.50)
>DroYak_CAF1 103244 120 + 1
GUGUGAGUAAAUAAGACGCUCACACCCACACACCCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCGUAAAGACAAUUCAAUCGAUGGCGAAUACUCAUACAAUCGC
(((((((((......(((((.......................(((....)))((((.((....)).)))).....))))).............(((....))).)))))))))...... ( -30.00)
>consensus
GUGUGAGUAAAUAAGACGCUCACAC________CCACAAUCAAAGCUUCGGCUGAGUCGUGUAAGCCGCUCACCAAAGCGUAAAGACAAUUCAAUCGAUGGCAAAUACCCAUACAA____
((((((((.........))))))))...................((((((..(((((..(((....((((......)))).....))))))))..))).))).................. (-27.36 = -27.20 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:19 2006