Locus 5738

Sequence ID	3L_DroMel_CAF1
Location	15,610,697 – 15,610,841
Length	144
Max. P	0.999883

overview

Window 3

Location	15,610,697 – 15,610,808
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.19
Mean single sequence MFE	-33.67
Consensus MFE	-31.33
Energy contribution	-31.53
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-2.51
Structure conservation index	0.93
SVM decision value	4.37
SVM RNA-class probability	0.999883
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15610697 111 + 23771897
GGCCACAGUUCGAAACGAAAGUAGAAGAAUUUAUUGCACUGACAUACUAAGAUGCU---------UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGUG
((((.((.((((((((((((...((((.((((.................)))).))---------))...))))))).))))).))))))..((((((....))))))............ ( -32.63)
>DroSec_CAF1 33797 111 + 1
GGCCACAGUUCGAAACGAAAGUGGAGGAAUUUAUUGCACUGACAUACUAAGAUGCU---------UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGGG
((((.((.((((((((((((....(((((......(((((.........)).))))---------)))).))))))).))))).))))))..((((((....))))))............ ( -35.80)
>DroSim_CAF1 33813 111 + 1
GGCCACAGUUCGAAACGAAAGUGGAGGAAUUUAUUGCACUGACAUACUAAGAUGCU---------UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGUG
((((.((.((((((((((((....(((((......(((((.........)).))))---------)))).))))))).))))).))))))..((((((....))))))............ ( -35.80)
>DroEre_CAF1 33882 109 + 1
GGCC--AGUUCGAAACGAAAGUGGAAGAAUUUAUUGCACUGACAUACUAAGAUGCU---------UCCUAUUUUGUUAUCGAAAUGGGGCAAGUGCGCUCGAGCGUAUAAAUUGAAUGUG
.(((--..((((((((((((..(((((.((((.................)))).))---------)))..))))))).)))))....)))..((((((....))))))............ ( -29.23)
>DroYak_CAF1 36096 120 + 1
GGCCACAGUUCGAAACGAAAGUGGAAGAAUUUAUUGCACUGACAUACUAAGAUGCUAUUCUGCUAUCCUAUUUUGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAAUGUG
((((.((.((((((((((((..((((((((.....(((((.........)).))).)))))....)))..))))))).))))).))))))..((((((....))))))............ ( -34.90)
>consensus
GGCCACAGUUCGAAACGAAAGUGGAAGAAUUUAUUGCACUGACAUACUAAGAUGCU_________UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGUG
((((.((.((((((((((((..(((..........(((((.........)).)))..........)))..))))))).))))).))))))..((((((....))))))............ (-31.33 = -31.53 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	15,610,697 – 15,610,808
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.19
Mean single sequence MFE	-26.14
Consensus MFE	-22.77
Energy contribution	-23.41
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.87
SVM decision value	1.51
SVM RNA-class probability	0.959814
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15610697 111 - 23771897
CACAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA---------AGCAUCUUAGUAUGUCAGUGCAAUAAAUUCUUCUACUUUCGUUUCGAACUGUGGCC
...............(((....))).....((((((.(((((.(((((((..(((---------((.......((((....))))........)))))..)))))))))))).)).)))) ( -28.66)
>DroSec_CAF1 33797 111 - 1
CCCAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA---------AGCAUCUUAGUAUGUCAGUGCAAUAAAUUCCUCCACUUUCGUUUCGAACUGUGGCC
...............(((....))).....((((((.(((((.(((((((.((((---------(........((((....))))......)))))....)))))))))))).)).)))) ( -28.24)
>DroSim_CAF1 33813 111 - 1
CACAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA---------AGCAUCUUAGUAUGUCAGUGCAAUAAAUUCCUCCACUUUCGUUUCGAACUGUGGCC
...............(((....))).....((((((.(((((.(((((((.((((---------(........((((....))))......)))))....)))))))))))).)).)))) ( -28.24)
>DroEre_CAF1 33882 109 - 1
CACAUUCAAUUUAUACGCUCGAGCGCACUUGCCCCAUUUCGAUAACAAAAUAGGA---------AGCAUCUUAGUAUGUCAGUGCAAUAAAUUCUUCCACUUUCGUUUCGAACU--GGCC
...............(((....)))........(((.(((((.(((.(((..(((---------((.......((((....))))........)))))..))).)))))))).)--)).. ( -19.26)
>DroYak_CAF1 36096 120 - 1
CACAUUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACAAAAUAGGAUAGCAGAAUAGCAUCUUAGUAUGUCAGUGCAAUAAAUUCUUCCACUUUCGUUUCGAACUGUGGCC
...............(((....))).....((((((.(((((.(((....((((((.((......))))))))((((....))))...................)))))))).)).)))) ( -26.30)
>consensus
CACAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA_________AGCAUCUUAGUAUGUCAGUGCAAUAAAUUCUUCCACUUUCGUUUCGAACUGUGGCC
...............(((....))).....((((((.(((((.(((((((..(((..........((((............))))..........)))..)))))))))))).)).)))) (-22.77 = -23.41 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	15,610,737 – 15,610,841
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.58
Mean single sequence MFE	-31.10
Consensus MFE	-28.78
Energy contribution	-28.46
Covariance contribution	-0.32
Combinations/Pair	1.10
Mean z-score	-2.26
Structure conservation index	0.93
SVM decision value	3.49
SVM RNA-class probability	0.999298
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15610737 104 + 23771897
GACAUACUAAGAUGCU---------UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGUGCCCCACCA-------UGAGGUAGGUACAGAGAAAUAUGUU
((((((..........---------.(((((((((....)))))))))....((((((....)))))).......(((((((..(((.-------...))).))))))).....)))))) ( -31.50)
>DroSec_CAF1 33837 104 + 1
GACAUACUAAGAUGCU---------UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGGGCCCCACCA-------UGAGGUAGGUACAAAGAAAUAUGUU
((((((..........---------.(((((((((....)))))))))....((((((....)))))).......(((..((..(((.-------...))).))..))).....)))))) ( -28.00)
>DroSim_CAF1 33853 104 + 1
GACAUACUAAGAUGCU---------UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGUGCCCCACCA-------UGAGGUAGGUACAAAGAAAUAUGUU
((((((..........---------.(((((((((....)))))))))....((((((....)))))).......(((((((..(((.-------...))).))))))).....)))))) ( -31.80)
>DroEre_CAF1 33920 104 + 1
GACAUACUAAGAUGCU---------UCCUAUUUUGUUAUCGAAAUGGGGCAAGUGCGCUCGAGCGUAUAAAUUGAAUGUGCCCCACCA-------AGAGGUAGGUACAAAGAAAUAUGUU
((((((......(((.---------.(((((((((....)))))))))))).((((((....))))))........((((((..(((.-------...))).))))))......)))))) ( -31.90)
>DroYak_CAF1 36136 120 + 1
GACAUACUAAGAUGCUAUUCUGCUAUCCUAUUUUGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAAUGUGCCCCACCAUGCGCCAUGUGGUAGGUGCAAAGAAAUAUGUU
((((((.........(((((......(((((((((....)))))))))....((((((....)))))).....)))))(((((.(((((.......))))).)).)))......)))))) ( -32.30)
>consensus
GACAUACUAAGAUGCU_________UCCUAUUUCGUUAUCGAAAUGGGCCAAAUGCGCUCGAGCGUAUAAAUUGAUUGUGCCCCACCA_______UGAGGUAGGUACAAAGAAAUAUGUU
((((((....................(((((((((....)))))))))....((((((....))))))........((((((..(((...........))).))))))......)))))) (-28.78 = -28.46 +  -0.32)

alignment

secondary structure

dotplot

Window 6

Location	15,610,737 – 15,610,841
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.58
Mean single sequence MFE	-25.55
Consensus MFE	-23.14
Energy contribution	-23.38
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.38
Structure conservation index	0.91
SVM decision value	0.69
SVM RNA-class probability	0.825042
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15610737 104 - 23771897
AACAUAUUUCUCUGUACCUACCUCA-------UGGUGGGGCACAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA---------AGCAUCUUAGUAUGUC
.(((((((........((((((...-------.))))))((..............(((....))).......((.((((((....)))))).)).---------.)).....))))))). ( -25.80)
>DroSec_CAF1 33837 104 - 1
AACAUAUUUCUUUGUACCUACCUCA-------UGGUGGGGCCCAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA---------AGCAUCUUAGUAUGUC
.(((((((....(((.((((((...-------.))))))(((.(((.........(((....))).))).)))((((((((....)))))).)).---------.)))....))))))). ( -26.80)
>DroSim_CAF1 33853 104 - 1
AACAUAUUUCUUUGUACCUACCUCA-------UGGUGGGGCACAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA---------AGCAUCUUAGUAUGUC
.(((((((....(((.((((((...-------.))))))................(((....))).......((.((((((....)))))).)).---------.)))....))))))). ( -26.00)
>DroEre_CAF1 33920 104 - 1
AACAUAUUUCUUUGUACCUACCUCU-------UGGUGGGGCACAUUCAAUUUAUACGCUCGAGCGCACUUGCCCCAUUUCGAUAACAAAAUAGGA---------AGCAUCUUAGUAUGUC
.(((((((....(((.((((((...-------.))(((((((.............(((....)))....)))))))..............)))).---------.)))....))))))). ( -23.83)
>DroYak_CAF1 36136 120 - 1
AACAUAUUUCUUUGCACCUACCACAUGGCGCAUGGUGGGGCACAUUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACAAAAUAGGAUAGCAGAAUAGCAUCUUAGUAUGUC
.((((((..((.(((.((........)).))).))..((((.((........((.(((....))).)).))))))...............((((((.((......)))))))))))))). ( -25.30)
>consensus
AACAUAUUUCUUUGUACCUACCUCA_______UGGUGGGGCACAAUCAAUUUAUACGCUCGAGCGCAUUUGGCCCAUUUCGAUAACGAAAUAGGA_________AGCAUCUUAGUAUGUC
.(((((((....(((.((((((...........))))))................(((....))).......((.((((((....)))))).))...........)))....))))))). (-23.14 = -23.38 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:19 2006