Locus 4212

Sequence ID	3R_DroMel_CAF1
Location	11,357,649 – 11,357,857
Length	208
Max. P	0.999985

overview

Window 0

Location	11,357,649 – 11,357,760
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.84
Mean single sequence MFE	-30.08
Consensus MFE	-28.46
Energy contribution	-28.22
Covariance contribution	-0.24
Combinations/Pair	1.10
Mean z-score	-3.04
Structure conservation index	0.95
SVM decision value	5.37
SVM RNA-class probability	0.999985
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11357649 111 - 27905053
U-------UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA--GAGGUCUUCAUUAAUUUUAACAUAAAUUGUUGUAUAGAAAUUUUAUGCCACACGAAGCGUUAAGUGU
.-------.(((((((((((...(((((.....((((.......))))...--)))))......................(((.(((((((...))))))).)))..))))))))))).. ( -29.60)
>DroSec_CAF1 105197 111 - 1
U-------UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA--GAGGUCUUCAUUAAUUUUAACAUAAAUUGUUGUAUAGAAAUUUUAUGCCACACGGAGCGUUAAGUGU
.-------.(((((((((((...(((((.....((((.......))))...--)))))......................(((.(((((((...))))))).)))..))))))))))).. ( -30.00)
>DroSim_CAF1 95979 111 - 1
U-------UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA--GAGGUCUUCAUUAAUUUUAACAUAAAUUGUUGUAUAGAAAUUUUAUGCCACACGGAGCGUUAAGUGU
.-------.(((((((((((...(((((.....((((.......))))...--)))))......................(((.(((((((...))))))).)))..))))))))))).. ( -30.00)
>DroEre_CAF1 92622 111 - 1
C-------CGCUUAAUGCUUAACACCUCAACACGCGGACCCACCCCGCCAA--GAGCUCUUCAUUAAUUUUAACAUAAAUUGUUGUAUAGAAAUUUUAUGCCACGCGGAGCGUUAAGUGU
.-------((((((((((((.............((((.......))))...--..((........(((((......)))))((.(((((((...))))))).)))).)))))))))))). ( -27.60)
>DroYak_CAF1 95285 120 - 1
UUGCUUAACGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCGAAACGAGCUCUUCAUUAAUUUCCACAUAAAUUGUUGUAUAGAAAUGUUAUGCCACGCGGAGCGUUAAGUGU
..(((((((((((...((.(((((.(((....(((((.......)))))....))).(((.((.((((((......)))))).))...)))..))))).))......))))))))))).. ( -33.20)
>consensus
U_______UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA__GAGGUCUUCAUUAAUUUUAACAUAAAUUGUUGUAUAGAAAUUUUAUGCCACACGGAGCGUUAAGUGU
........((((((((((((...(((((.....((((.......)))).....)))))......................(((.((((((.....)))))).)))..)))))))))))). (-28.46 = -28.22 +  -0.24)

alignment

secondary structure

dotplot

Window 1

Location	11,357,689 – 11,357,800
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.07
Mean single sequence MFE	-28.77
Consensus MFE	-23.76
Energy contribution	-23.76
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.28
Structure conservation index	0.83
SVM decision value	3.17
SVM RNA-class probability	0.998642
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11357689 111 - 27905053
CCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUCU-------UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA--GAGGUCUUCAUUAAUUUUAACAUAAAU
...((((...((((((((((((........)))))))....-------)))))...))))...(((((.....((((.......))))...--)))))...................... ( -26.70)
>DroSec_CAF1 105237 111 - 1
CCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUCU-------UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA--GAGGUCUUCAUUAAUUUUAACAUAAAU
...((((...((((((((((((........)))))))....-------)))))...))))...(((((.....((((.......))))...--)))))...................... ( -26.70)
>DroSim_CAF1 96019 111 - 1
CCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUCU-------UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA--GAGGUCUUCAUUAAUUUUAACAUAAAU
...((((...((((((((((((........)))))))....-------)))))...))))...(((((.....((((.......))))...--)))))...................... ( -26.70)
>DroEre_CAF1 92662 111 - 1
CCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUCC-------CGCUUAAUGCUUAACACCUCAACACGCGGACCCACCCCGCCAA--GAGCUCUUCAUUAAUUUUAACAUAAAU
..(((((((..(((....((((........))))(((...(-------(((......................)))).))).....)))..--))))))).................... ( -30.45)
>DroYak_CAF1 95325 120 - 1
CCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUCUUGCUUAACGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCGAAACGAGCUCUUCAUUAAUUUCCACAUAAAU
..(((((((.((((((((((((........)))))(((....)))........)))))))............(((((.......)))))....))))))).................... ( -33.30)
>consensus
CCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUCU_______UGCUUAAUGCUUAACACCUCAACACGCGGACACACCCCGCCAA__GAGGUCUUCAUUAAUUUUAACAUAAAU
..(((.(((.((((((((((((........)))))(((...........))).))))))).............((((.......)))).....))).))).................... (-23.76 = -23.76 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	11,357,760 – 11,357,857
Length	97
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	95.52
Mean single sequence MFE	-31.05
Consensus MFE	-28.26
Energy contribution	-28.07
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.91
SVM decision value	0.45
SVM RNA-class probability	0.740515
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11357760 97 - 27905053
AUCCAAAUGACAUUCAUUGCCAGCCAGCCGUCGGCCUGGGUCAACAGAAGCCC-------CUGUCCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUC
.....((((.....))))...((((.(((...(((((((....((((......-------)))))))).)))...)))...(((((........))))))))). ( -30.70)
>DroSec_CAF1 105308 97 - 1
AUCCAAAUGACAUUCAUUGCCAGCCAGCCGUCGGCCUGGGUCAACAGAAGCCC-------CUGUCCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUC
.....((((.....))))...((((.(((...(((((((....((((......-------)))))))).)))...)))...(((((........))))))))). ( -30.70)
>DroSim_CAF1 96090 97 - 1
AUCCAAAUGACAUUCAUUGCCAGCCAGUCGUCGGCCUGGGUCAACAGAAGCCC-------CUGUCCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUC
.....((((.....))))...((((........((((((((..((((......-------)))).....)).))))))...(((((........))))))))). ( -28.10)
>DroEre_CAF1 92733 104 - 1
AUCCGAAUGACAUUCAUUGCCAGCCAGCCGUCGGCCUGGGUCAACAGAAGCCCCUGGCCCCUGUCCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUC
.....((((.....))))...((((.(((...(((((((....((((..(((...)))..)))))))).)))...)))...(((((........))))))))). ( -34.70)
>consensus
AUCCAAAUGACAUUCAUUGCCAGCCAGCCGUCGGCCUGGGUCAACAGAAGCCC_______CUGUCCAGAGCUCCAGGCAUUCGGAAUUUACAUUUUCCGGGCUC
.....((((.....))))...((((.(((...(((((((....((((.............)))))))).)))...)))...(((((........))))))))). (-28.26 = -28.07 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:54 2006