Locus 3313

Sequence ID	2R_DroMel_CAF1
Location	11,296,091 – 11,296,217
Length	126
Max. P	0.999936

overview

Window 9

Location	11,296,091 – 11,296,186
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	93.58
Mean single sequence MFE	-31.20
Consensus MFE	-24.70
Energy contribution	-25.30
Covariance contribution	0.60
Combinations/Pair	1.08
Mean z-score	-3.32
Structure conservation index	0.79
SVM decision value	2.49
SVM RNA-class probability	0.994602
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11296091 95 + 20766785
AAAACACGAAUCGCAGGAGUAAAUGAAACCAAGAGCCCUUGAGUUCAGCUUGUAGCAUACUUUCAGGCAUGAACACAGCGCAGCCCGAAAGUAUG
............(((((......((((..((((....))))..)))).)))))..(((((((((.(((.((.........))))).))))))))) ( -25.20)
>DroSec_CAF1 83313 95 + 1
AAAACACGAAACGCAGGAGUGAAUGAAACCAAGAGCCCUUGAGCUCAGCGUGUAGCAUACUUUCAGGCAUGCACACAGCGCAGCCCGAAAGUAUG
...(((((...(((....)))...........((((......))))..)))))..(((((((((.(((.(((.......)))))).))))))))) ( -31.80)
>DroSim_CAF1 86970 95 + 1
AAAACACGAAACGCAGGAGUAAAUGAAACCAAGAGCCCUUGAGCUCAGCGUGUAGCAUACUUUCAGGCAUGCACACAGCGCAGCCCGAAAGUAUG
...(((((.......((...........))..((((......))))..)))))..(((((((((.(((.(((.......)))))).))))))))) ( -30.10)
>DroEre_CAF1 84443 95 + 1
AAAACUGGAAACGCAGGAGUAAAUGAAACCAAGAGCUCUUGUGCUCGGCUUGUAGCAUACUUUCAGGCGUGCACACAGCGCAGCCCGAAAGUAUG
....((((...(((((((((...((....))...))))))))).)))).......(((((((((.(((((((.....)))).))).))))))))) ( -34.10)
>DroYak_CAF1 85295 95 + 1
AAAACCCGAAACGCAGGAGUAAAUGAAACCAAGAGCUCUUGAGCUCAGCGCGUAGCAUACUUUCAGGCGUGCACACAGCACAGCCCGAAAGUAUG
..........((((.((...........))..(((((....)))))...))))..(((((((((.(((((((.....)))).))).))))))))) ( -34.80)
>consensus
AAAACACGAAACGCAGGAGUAAAUGAAACCAAGAGCCCUUGAGCUCAGCGUGUAGCAUACUUUCAGGCAUGCACACAGCGCAGCCCGAAAGUAUG
...(((((.......((...........))..((((......))))..)))))..(((((((((.(((.(((.......)))))).))))))))) (-24.70 = -25.30 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	11,296,091 – 11,296,186
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-34.34
Consensus MFE	-30.64
Energy contribution	-31.48
Covariance contribution	0.84
Combinations/Pair	1.10
Mean z-score	-3.37
Structure conservation index	0.89
SVM decision value	4.67
SVM RNA-class probability	0.999936
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11296091 95 - 20766785
CAUACUUUCGGGCUGCGCUGUGUUCAUGCCUGAAAGUAUGCUACAAGCUGAACUCAAGGGCUCUUGGUUUCAUUUACUCCUGCGAUUCGUGUUUU
(((((((((((((((.((...)).)).)))))))))))))....((((((((..((((....))))..)))).........(((...))))))). ( -26.00)
>DroSec_CAF1 83313 95 - 1
CAUACUUUCGGGCUGCGCUGUGUGCAUGCCUGAAAGUAUGCUACACGCUGAGCUCAAGGGCUCUUGGUUUCAUUCACUCCUGCGUUUCGUGUUUU
((((((((((((((((((...))))).)))))))))))))..(((((..(((((....))))).(((......)))...........)))))... ( -37.00)
>DroSim_CAF1 86970 95 - 1
CAUACUUUCGGGCUGCGCUGUGUGCAUGCCUGAAAGUAUGCUACACGCUGAGCUCAAGGGCUCUUGGUUUCAUUUACUCCUGCGUUUCGUGUUUU
((((((((((((((((((...))))).)))))))))))))..(((((..(((((....)))))..((...........)).......)))))... ( -36.90)
>DroEre_CAF1 84443 95 - 1
CAUACUUUCGGGCUGCGCUGUGUGCACGCCUGAAAGUAUGCUACAAGCCGAGCACAAGAGCUCUUGGUUUCAUUUACUCCUGCGUUUCCAGUUUU
((((((((((((((((((...))))).)))))))))))))....(((((((((......))))..))))).........(((......))).... ( -34.40)
>DroYak_CAF1 85295 95 - 1
CAUACUUUCGGGCUGUGCUGUGUGCACGCCUGAAAGUAUGCUACGCGCUGAGCUCAAGAGCUCUUGGUUUCAUUUACUCCUGCGUUUCGGGUUUU
(((((((((((((.((((.....)))))))))))))))))..((((...(((((....)))))..((...........)).)))).......... ( -37.40)
>consensus
CAUACUUUCGGGCUGCGCUGUGUGCAUGCCUGAAAGUAUGCUACACGCUGAGCUCAAGGGCUCUUGGUUUCAUUUACUCCUGCGUUUCGUGUUUU
((((((((((((((((((...))))).)))))))))))))....((((.(((((....)))))..((...........)).)))).......... (-30.64 = -31.48 +   0.84)

alignment

secondary structure

dotplot

Window 1

Location	11,296,124 – 11,296,217
Length	93
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	79.37
Mean single sequence MFE	-36.98
Consensus MFE	-18.79
Energy contribution	-20.67
Covariance contribution	1.88
Combinations/Pair	1.21
Mean z-score	-3.41
Structure conservation index	0.51
SVM decision value	1.91
SVM RNA-class probability	0.982262
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11296124 93 + 20766785
AGCCCUUGAGUUCAGCUUGUAGCAUACUUUCAGG--CAUGAACA----CAGCGC--AGCCCGAAAGUAUGCUCCACUAAGUGAGUGAGUGGCGGCAACAAG
.(((((((...(((.((((((((((((((((.((--(.((....----.....)--)))).)))))))))))..)).)))))).)))).)))(....)... ( -32.20)
>DroVir_CAF1 77545 86 + 1
ACACU--------UUUCCAUUGCAUACUUUCGGCUGCAAGCGCACAAAGCGCGCGGCGCGCAAAAGUAUGCUGUGAUAAAUGAGUGCG-----GC--CAAC
.((((--------(...(((.((((((((((((((((..((((.....))))))))).))..))))))))).)))......)))))..-----..--.... ( -32.30)
>DroSec_CAF1 83346 93 + 1
AGCCCUUGAGCUCAGCGUGUAGCAUACUUUCAGG--CAUGCACA----CAGCGC--AGCCCGAAAGUAUGCUCCACUAAGUGAGUGAGUGCCGGCAACAAG
.(((.....(((((..(((.(((((((((((.((--(.(((...----....))--)))).))))))))))).)))....))))).......)))...... ( -38.10)
>DroSim_CAF1 87003 93 + 1
AGCCCUUGAGCUCAGCGUGUAGCAUACUUUCAGG--CAUGCACA----CAGCGC--AGCCCGAAAGUAUGCUCCACUAAGUGAGUGAGUGGCGGCAACAAG
.((((((..(((((..(((.(((((((((((.((--(.(((...----....))--)))).))))))))))).)))....)))))))).)))(....)... ( -41.80)
>DroEre_CAF1 84476 93 + 1
AGCUCUUGUGCUCGGCUUGUAGCAUACUUUCAGG--CGUGCACA----CAGCGC--AGCCCGAAAGUAUGCUCCACUAAGUGAGUGAGUGGCGGCAACAAG
.((((((..(((((.((((((((((((((((.((--(((((...----..))))--.))).)))))))))))..)).))))))))))).)))(....)... ( -39.40)
>DroYak_CAF1 85328 93 + 1
AGCUCUUGAGCUCAGCGCGUAGCAUACUUUCAGG--CGUGCACA----CAGCAC--AGCCCGAAAGUAUGCUCCACUAAGUGAGUGAGUGGCGGCAACAAG
((((....))))..((.((((((((((((((.((--(((((...----..))))--.))).))))))))))).((((.....))))....)))))...... ( -38.10)
>consensus
AGCCCUUGAGCUCAGCGUGUAGCAUACUUUCAGG__CAUGCACA____CAGCGC__AGCCCGAAAGUAUGCUCCACUAAGUGAGUGAGUGGCGGCAACAAG
.(((((...(((((...((.(((((((((((.((....(((.........))).....)).))))))))))).)).....)))))....)).)))...... (-18.79 = -20.67 +   1.88)

alignment

secondary structure

dotplot

Window 2

Location	11,296,124 – 11,296,217
Length	93
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	79.37
Mean single sequence MFE	-41.13
Consensus MFE	-26.63
Energy contribution	-27.30
Covariance contribution	0.67
Combinations/Pair	1.32
Mean z-score	-4.49
Structure conservation index	0.65
SVM decision value	2.06
SVM RNA-class probability	0.986848
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11296124 93 - 20766785
CUUGUUGCCGCCACUCACUCACUUAGUGGAGCAUACUUUCGGGCU--GCGCUG----UGUUCAUG--CCUGAAAGUAUGCUACAAGCUGAACUCAAGGGCU
......(((.(((((.........)))))((((((((((((((((--(.((..----.)).)).)--))))))))))))))................))). ( -35.00)
>DroVir_CAF1 77545 86 - 1
GUUG--GC-----CGCACUCAUUUAUCACAGCAUACUUUUGCGCGCCGCGCGCUUUGUGCGCUUGCAGCCGAAAGUAUGCAAUGGAAA--------AGUGU
....--..-----.(((((..(((((....(((((((((((.((((.((((((...))))))..)).))))))))))))).)))))..--------))))) ( -33.10)
>DroSec_CAF1 83346 93 - 1
CUUGUUGCCGGCACUCACUCACUUAGUGGAGCAUACUUUCGGGCU--GCGCUG----UGUGCAUG--CCUGAAAGUAUGCUACACGCUGAGCUCAAGGGCU
((((..((((((..(((((.....)))))((((((((((((((((--((((..----.))))).)--))))))))))))))....)))).)).)))).... ( -46.40)
>DroSim_CAF1 87003 93 - 1
CUUGUUGCCGCCACUCACUCACUUAGUGGAGCAUACUUUCGGGCU--GCGCUG----UGUGCAUG--CCUGAAAGUAUGCUACACGCUGAGCUCAAGGGCU
.........(((.((......(((((((.((((((((((((((((--((((..----.))))).)--))))))))))))))...)))))))....))))). ( -45.50)
>DroEre_CAF1 84476 93 - 1
CUUGUUGCCGCCACUCACUCACUUAGUGGAGCAUACUUUCGGGCU--GCGCUG----UGUGCACG--CCUGAAAGUAUGCUACAAGCCGAGCACAAGAGCU
(((((.(((((((((.........)))))((((((((((((((((--((((..----.))))).)--))))))))))))))......)).))))))).... ( -44.00)
>DroYak_CAF1 85328 93 - 1
CUUGUUGCCGCCACUCACUCACUUAGUGGAGCAUACUUUCGGGCU--GUGCUG----UGUGCACG--CCUGAAAGUAUGCUACGCGCUGAGCUCAAGAGCU
.............(((.....(((((((((((((((((((((((.--((((..----...)))))--)))))))))))))).).))))))).....))).. ( -42.80)
>consensus
CUUGUUGCCGCCACUCACUCACUUAGUGGAGCAUACUUUCGGGCU__GCGCUG____UGUGCAUG__CCUGAAAGUAUGCUACACGCUGAGCUCAAGGGCU
.................((((....(((.((((((((((((((....((((.......)))).....)))))))))))))).)))..)))).......... (-26.63 = -27.30 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:28 2006