Locus 4700

Sequence ID	3L_DroMel_CAF1
Location	13,249,611 – 13,249,772
Length	161
Max. P	0.935790

overview

Window 8

Location	13,249,611 – 13,249,714
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.24
Mean single sequence MFE	-34.88
Consensus MFE	-22.98
Energy contribution	-22.78
Covariance contribution	-0.19
Combinations/Pair	1.17
Mean z-score	-1.61
Structure conservation index	0.66
SVM decision value	0.01
SVM RNA-class probability	0.540122
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13249611 103 - 23771897
GGCACAGGCACAGGC------AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUGCUCAUUACACGCUCACUG---UCUUUUG-----GCU---C
(((.(((((...(((------....)))....))))))))(((((((.((((..(((((..(((....))).)))))..))))............)))---))))...-----...---. ( -35.62)
>DroSec_CAF1 12388 93 - 1
----------CAGGC------AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUGCUCAUUACACGCUCACUG---UCUUUUG-----GCU---C
----------(((((------...........)))))((((((((((.((((..(((((..(((....))).)))))..))))............)))---)))..))-----)).---. ( -31.42)
>DroSim_CAF1 12890 93 - 1
----------CAGGC------AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUGCUCAUUACACGCUCACUG---UCUUUUG-----GCU---C
----------(((((------...........)))))((((((((((.((((..(((((..(((....))).)))))..))))............)))---)))..))-----)).---. ( -31.42)
>DroEre_CAF1 11659 104 - 1
----------CAGGCAAAGGCUAAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUGCUCAUUACACGCUCGCUG---UCUUUUGGCUUGGCU---U
----------(((((...(((((.(((.....))))))))(((((((.(((((((((((..(((....))).))))).))..........)))).)))---))))...)))))...---. ( -39.50)
>DroYak_CAF1 12585 99 - 1
----------CAGGCCCAUGCACAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUGCUCAUUACACGCUCACUG---UCUUUUG-----GCU---U
----------.(((((...((.(((((.....))))))).(((((((.((((..(((((..(((....))).)))))..))))............)))---))))..)-----)))---) ( -35.02)
>DroAna_CAF1 4426 96 - 1
----------CAGG---------AGGCCCAGGGUCUGGCCAAGGAGAUUGGCGAACGACAUGGUAAUUGCCAGUCGUCCGCUCAUUACCCACUCACUGGCUUCUUUUG-----GCUGGCU
----------.((.---------.((((.((((...(((((..(((..(((((.(((((.((((....))))))))).))).)).......)))..))))).)))).)-----)))..)) ( -36.30)
>consensus
__________CAGGC______AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUGCUCAUUACACGCUCACUG___UCUUUUG_____GCU___C
..........(((...........(((((......)))))..((((((.((...(((((..(((....))).))))))).)))))).........)))...................... (-22.98 = -22.78 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	13,249,640 – 13,249,738
Length	98
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	82.19
Mean single sequence MFE	-32.13
Consensus MFE	-21.24
Energy contribution	-21.80
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-2.12
Structure conservation index	0.66
SVM decision value	0.41
SVM RNA-class probability	0.727252
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13249640 98 + 23771897
CAGACGACGGGCAAUUACCAUGUCGUUGGCUCCCCAUCUUGGCCAGGCUUUUAGCCUCU------GCCUGUGCCUGUGCCUGUGCCUGGUUUUGGCCACAUUGC
..(((((((((......)).)))))))((((..(((....((((((((...(((.(.(.------....).).))).))))).))))))....))))....... ( -32.30)
>DroSec_CAF1 12417 86 + 1
CAGACGACGGGCAAUUACCAUGUCGUUGGCUCCCCAUCUUGGCCAGGCUUUUAGCCUCU------GCCUG------------UGCCUGGUUUUGGCCACAUUGC
..(((((((((......)).)))))))((((..(((....((((((((...........------)))))------------.))))))....))))....... ( -30.30)
>DroSim_CAF1 12919 86 + 1
CAGACGACGGGCAAUUACCAUGUCGUUGGCUCCCCAUCUUGGCCAGGCUUUUAGCCUCU------GCCUG------------UGCCUGGUUUUGGCCACAUUGC
..(((((((((......)).)))))))((((..(((....((((((((...........------)))))------------.))))))....))))....... ( -30.30)
>DroEre_CAF1 11693 92 + 1
CAGACGACGGGCAAUUACCAUGUCGUUGGCUCCCCAUCUUGGCCAGGCUUUUAGCCUUAGCCUUUGCCUG------------UGCCUGGUUUUGGCCACAUUAC
..(((((((((......)).)))))))((((..(((....((((((((.....((....))....)))))------------.))))))....))))....... ( -31.50)
>DroYak_CAF1 12614 92 + 1
CAGACGACGGGCAAUUACCAUGUCGUUGGCUCCCCAUCUUGGCCAGGCUUUUAGCCUGUGCAUGGGCCUG------------UGCCUGGUUUUGGCCACAUUAC
..(((((((((......)).)))))))((((..(((....((((((((((...((....))..)))))))------------.))))))....))))....... ( -33.80)
>DroAna_CAF1 4461 83 + 1
CGGACGACUGGCAAUUACCAUGUCGUUCGCCAAUCUCCUUGGCCAGACCCUGGGCCU---------CCUG------------CUCCUAGUCCUGGCCACGGUGC
(((((((((((......))).)))))))).....(.((.(((((((..(..((((..---------...)------------).))..)..))))))).)).). ( -34.60)
>consensus
CAGACGACGGGCAAUUACCAUGUCGUUGGCUCCCCAUCUUGGCCAGGCUUUUAGCCUCU______GCCUG____________UGCCUGGUUUUGGCCACAUUGC
..(((((((((......)).)))))))((((.........((((((((...................................))))))))..))))....... (-21.24 = -21.80 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	13,249,640 – 13,249,738
Length	98
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	82.19
Mean single sequence MFE	-34.75
Consensus MFE	-23.04
Energy contribution	-23.04
Covariance contribution	0.00
Combinations/Pair	1.22
Mean z-score	-2.66
Structure conservation index	0.66
SVM decision value	0.77
SVM RNA-class probability	0.847161
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13249640 98 - 23771897
GCAAUGUGGCCAAAACCAGGCACAGGCACAGGCACAGGC------AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUG
((..((((.((.......)))))).)).(((((...(((------..((((.....)))).)))..((((((.(((((......))))...).))))))))))) ( -38.80)
>DroSec_CAF1 12417 86 - 1
GCAAUGUGGCCAAAACCAGGCA------------CAGGC------AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUG
((......))......(((((.------------..(((------..((((.....)))).)))..((((((.(((((......))))...).))))))))))) ( -31.30)
>DroSim_CAF1 12919 86 - 1
GCAAUGUGGCCAAAACCAGGCA------------CAGGC------AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUG
((......))......(((((.------------..(((------..((((.....)))).)))..((((((.(((((......))))...).))))))))))) ( -31.30)
>DroEre_CAF1 11693 92 - 1
GUAAUGUGGCCAAAACCAGGCA------------CAGGCAAAGGCUAAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUG
........(((.......))).------------(((((...(((((.(((.....))))))))..((((((.(((((......))))...).))))))))))) ( -36.20)
>DroYak_CAF1 12614 92 - 1
GUAAUGUGGCCAAAACCAGGCA------------CAGGCCCAUGCACAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUG
........(((.......))).------------(((((....((.(((((.....)))))))...((((((.(((((......))))...).))))))))))) ( -33.20)
>DroAna_CAF1 4461 83 - 1
GCACCGUGGCCAGGACUAGGAG------------CAGG---------AGGCCCAGGGUCUGGCCAAGGAGAUUGGCGAACGACAUGGUAAUUGCCAGUCGUCCG
......(((((((..((.((.(------------(...---------..)))).))..))))))).((((((((((((((......))..))))))))).))). ( -37.70)
>consensus
GCAAUGUGGCCAAAACCAGGCA____________CAGGC______AGAGGCUAAAAGCCUGGCCAAGAUGGGGAGCCAACGACAUGGUAAUUGCCCGUCGUCUG
......(((((....((...................)).........(((((...)))))))))).((((((.(((((......))))...).))))))..... (-23.04 = -23.04 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	13,249,680 – 13,249,772
Length	92
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	80.06
Mean single sequence MFE	-35.22
Consensus MFE	-21.17
Energy contribution	-21.65
Covariance contribution	0.48
Combinations/Pair	1.14
Mean z-score	-1.69
Structure conservation index	0.60
SVM decision value	0.16
SVM RNA-class probability	0.612953
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13249680 92 + 23771897
GGCCAGGCUUUUAGCCUCU------GCCUGUGCCUGUGCCUGUGCCUGGUUUUGGCCACAUUGCCAGUG------GCCCUGGGAUUGGCCAACUGCCCGAAUGG
((((((((...........------))))).)))((.(((....((..(....((((((.......)))------))))..))...)))))............. ( -35.30)
>DroSec_CAF1 12457 80 + 1
GGCCAGGCUUUUAGCCUCU------GCCUG------------UGCCUGGUUUUGGCCACAUUGCCAGUG------GCCCUGGGAUUGGCCAACUGCCCGAAUGG
((((((((...........------)))))------------.))).(((.(((((((...(.((((..------...)))).).)))))))..)))....... ( -33.10)
>DroSim_CAF1 12959 80 + 1
GGCCAGGCUUUUAGCCUCU------GCCUG------------UGCCUGGUUUUGGCCACAUUGCCAGUG------GCCCUGGGUUUGGCCAACUGCCCGAAUGG
((((((((...........------)))))------------.))).(((.(((((((.((..((((..------...)))))).)))))))..)))....... ( -31.90)
>DroEre_CAF1 11733 86 + 1
GGCCAGGCUUUUAGCCUUAGCCUUUGCCUG------------UGCCUGGUUUUGGCCACAUUACCAGUG------GCCCUGGGAUUGGCCAACUGCCCGAAUGG
((((((((.....((....))....)))))------------.))).(((.(((((((.(((.((((..------...))))))))))))))..)))....... ( -33.90)
>DroYak_CAF1 12654 86 + 1
GGCCAGGCUUUUAGCCUGUGCAUGGGCCUG------------UGCCUGGUUUUGGCCACAUUACCAGUG------GCCCUGGGAUUGGCCAACUGCCCCAAUGG
.(((((((.....))))).))..((((...------------((.(..(((((((((((.......)))------)))..)))))..).))...))))...... ( -36.30)
>DroAna_CAF1 4501 83 + 1
GGCCAGACCCUGGGCCU---------CCUG------------CUCCUAGUCCUGGCCACGGUGCACGUGCCCGGUGCCCGGGGACUGGCCAACUGCCCCAAUGG
((((((.((((((((..---------.(((------------....)))..((((.((((.....)))).)))).)))))))).)))))).............. ( -40.80)
>consensus
GGCCAGGCUUUUAGCCUCU______GCCUG____________UGCCUGGUUUUGGCCACAUUGCCAGUG______GCCCUGGGAUUGGCCAACUGCCCGAAUGG
((((((((...................................))))))))(((((((.(((.((((...........))))))))))))))............ (-21.17 = -21.65 +   0.48)

alignment

secondary structure

dotplot

Window 2

Location	13,249,680 – 13,249,772
Length	92
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	80.06
Mean single sequence MFE	-35.29
Consensus MFE	-24.41
Energy contribution	-23.75
Covariance contribution	-0.66
Combinations/Pair	1.21
Mean z-score	-2.40
Structure conservation index	0.69
SVM decision value	1.25
SVM RNA-class probability	0.935790
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13249680 92 - 23771897
CCAUUCGGGCAGUUGGCCAAUCCCAGGGC------CACUGGCAAUGUGGCCAAAACCAGGCACAGGCACAGGCACAGGC------AGAGGCUAAAAGCCUGGCC
.(((...(.((((.((((........)))------))))).)...)))(((.......)))...(((.(((((...(((------....)))....)))))))) ( -36.00)
>DroSec_CAF1 12457 80 - 1
CCAUUCGGGCAGUUGGCCAAUCCCAGGGC------CACUGGCAAUGUGGCCAAAACCAGGCA------------CAGGC------AGAGGCUAAAAGCCUGGCC
......((....(((((((...((((...------..)))).....)))))))..)).(((.------------(((((------...........)))))))) ( -32.50)
>DroSim_CAF1 12959 80 - 1
CCAUUCGGGCAGUUGGCCAAACCCAGGGC------CACUGGCAAUGUGGCCAAAACCAGGCA------------CAGGC------AGAGGCUAAAAGCCUGGCC
......((....(((((((...((((...------..)))).....)))))))..)).(((.------------(((((------...........)))))))) ( -32.50)
>DroEre_CAF1 11733 86 - 1
CCAUUCGGGCAGUUGGCCAAUCCCAGGGC------CACUGGUAAUGUGGCCAAAACCAGGCA------------CAGGCAAAGGCUAAGGCUAAAAGCCUGGCC
......((....(((((((...((((...------..)))).....)))))))..)).(((.------------(((((...(((....)))....)))))))) ( -35.90)
>DroYak_CAF1 12654 86 - 1
CCAUUGGGGCAGUUGGCCAAUCCCAGGGC------CACUGGUAAUGUGGCCAAAACCAGGCA------------CAGGCCCAUGCACAGGCUAAAAGCCUGGCC
......((((...(((((........(((------(((.......)))))).......))).------------)).))))..((.(((((.....))))))). ( -36.46)
>DroAna_CAF1 4501 83 - 1
CCAUUGGGGCAGUUGGCCAGUCCCCGGGCACCGGGCACGUGCACCGUGGCCAGGACUAGGAG------------CAGG---------AGGCCCAGGGUCUGGCC
((....))......((((((.(((.((((.((((.((((.....)))).)).)).((.....------------.)).---------..)))).))).)))))) ( -38.40)
>consensus
CCAUUCGGGCAGUUGGCCAAUCCCAGGGC______CACUGGCAAUGUGGCCAAAACCAGGCA____________CAGGC______AGAGGCUAAAAGCCUGGCC
.......(((..(((((((...((((...........)))).....)))))))..................................(((((...))))).))) (-24.41 = -23.75 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:11 2006