Locus 2874

Sequence ID	X_DroMel_CAF1
Location	7,689,954 – 7,690,053
Length	99
Max. P	0.957310

overview

Window 2

Location	7,689,954 – 7,690,053
Length	99
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	78.28
Mean single sequence MFE	-26.57
Consensus MFE	-15.48
Energy contribution	-16.96
Covariance contribution	1.47
Combinations/Pair	1.08
Mean z-score	-2.01
Structure conservation index	0.58
SVM decision value	0.85
SVM RNA-class probability	0.865421
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7689954 99 + 22224390
UGAGAGGCAUCAACCGCAUUUUACGUAAUGCGGUCAGAAAGACUAAUUAUGCUAAACGCG--AAAGCCGCAACAACCAGUUAGCCAUGGCCAAA--------AU-CCG-----UU
.....(((.((.((((((((......))))))))..))..((((.....(((.....((.--...)).)))......)))).)))((((.....--------..-)))-----). ( -23.50)
>DroVir_CAF1 9880 105 + 1
UAA--AGCUGAAACCGCAUUUCGCGAAACGCGGUCAAAUGGACUAAUUAUGCUAAACAGCGUAAAACCGCAACAACCACUUAGCCAUGGCCGAU--------AGAGCGAAUGGCC
...--..........((..(((((......((((((..(((.(((((((((((....)))))))...............)))))))))))))..--------...)))))..)). ( -27.06)
>DroPse_CAF1 29803 98 + 1
UAA--GGCCUGAACCGCAUUUUACGAAAUGCGGUCAGAAGGACUAAUUAUGCUAAACGUU--GUAACCGCAACAACCAGUUAGCCAUGGCCGAG--------UGCCCG-----CC
...--(((((((.((((((((....))))))))))))..(((((..(((((((((..(((--((.......)))))...)))).)))))...))--------).)).)-----)) ( -32.10)
>DroYak_CAF1 7988 104 + 1
UGA--GGCAUCAACCGCAUUUUACGAAAUGCGGUCA-AAGGACUAAUUAUGCUAAACGCG--AAAACCGCAACAACCAGUUAGCCAUGGUCAAAAUAAUAAAAU-GCG-----UC
.((--.((((..(((((((((....)))))))))..-...(((((.....(((....(((--.....)))(((.....))))))..)))))...........))-)).-----)) ( -25.90)
>DroAna_CAF1 53093 92 + 1
UAAG-GACCUCAACCGCAUUUUACGAAAUGCGGUCAGAAGGACUAAUUAUGCUAAAUGCC--AAAACCGCAACAACCAGUUAGCCAUGU--------------U-CCG-----UU
...(-((.....(((((((((....))))))))).....((.((((((........(((.--......)))......))))))))....--------------)-)).-----.. ( -20.64)
>DroPer_CAF1 30374 98 + 1
UAA--GGCCUGAACCGCAUUUUACGAAAUGCGGUCAGAAGGACUAAUUAUGCUAAACGUU--GUAACCGCAACAUCCAGUUAGCCAUGGCCGAG--------AGCCCG-----CC
...--(((((((.((((((((....))))))))))))..((.((((((..(.....)(((--((....)))))....))))))))..((.(...--------.).)))-----)) ( -30.20)
>consensus
UAA__GGCCUCAACCGCAUUUUACGAAAUGCGGUCAGAAGGACUAAUUAUGCUAAACGCC__AAAACCGCAACAACCAGUUAGCCAUGGCCGAA________AG_CCG_____CC
.....((((...(((((((((....))))))))).....((.((((((.(((................)))......))))))))..))))........................ (-15.48 = -16.96 +   1.47)

alignment

secondary structure

dotplot

Window 3

Location	7,689,954 – 7,690,053
Length	99
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	78.28
Mean single sequence MFE	-32.02
Consensus MFE	-21.24
Energy contribution	-21.57
Covariance contribution	0.34
Combinations/Pair	1.16
Mean z-score	-2.24
Structure conservation index	0.66
SVM decision value	1.48
SVM RNA-class probability	0.957310
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7689954 99 - 22224390
AA-----CGG-AU--------UUUGGCCAUGGCUAACUGGUUGUUGCGGCUUU--CGCGUUUAGCAUAAUUAGUCUUUCUGACCGCAUUACGUAAAAUGCGGUUGAUGCCUCUCA
..-----...-..--------...(((...((((((...((((.((((.....--))))..))))....)))))).....(((((((((......)))))))))...)))..... ( -27.70)
>DroVir_CAF1 9880 105 - 1
GGCCAUUCGCUCU--------AUCGGCCAUGGCUAAGUGGUUGUUGCGGUUUUACGCUGUUUAGCAUAAUUAGUCCAUUUGACCGCGUUUCGCGAAAUGCGGUUUCAGCU--UUA
((((.........--------...))))((((((((...((((..(((......)))....))))....)))).))))..((((((((((....))))))))))......--... ( -32.80)
>DroPse_CAF1 29803 98 - 1
GG-----CGGGCA--------CUCGGCCAUGGCUAACUGGUUGUUGCGGUUAC--AACGUUUAGCAUAAUUAGUCCUUCUGACCGCAUUUCGUAAAAUGCGGUUCAGGCC--UUA
((-----(((((.--------...(((....)))..((((.(((((......)--)))).))))........))))..((((((((((((....)))))))).)))))))--... ( -34.60)
>DroYak_CAF1 7988 104 - 1
GA-----CGC-AUUUUAUUAUUUUGACCAUGGCUAACUGGUUGUUGCGGUUUU--CGCGUUUAGCAUAAUUAGUCCUU-UGACCGCAUUUCGUAAAAUGCGGUUGAUGCC--UCA
((-----.((-(((................((((((...((((.((((.....--))))..))))....))))))...-.((((((((((....))))))))))))))).--)). ( -29.70)
>DroAna_CAF1 53093 92 - 1
AA-----CGG-A--------------ACAUGGCUAACUGGUUGUUGCGGUUUU--GGCAUUUAGCAUAAUUAGUCCUUCUGACCGCAUUUCGUAAAAUGCGGUUGAGGUC-CUUA
..-----.((-(--------------....((((((...((((.(((......--.)))..))))....))))))((((.((((((((((....))))))))))))))))-)... ( -28.30)
>DroPer_CAF1 30374 98 - 1
GG-----CGGGCU--------CUCGGCCAUGGCUAACUGGAUGUUGCGGUUAC--AACGUUUAGCAUAAUUAGUCCUUCUGACCGCAUUUCGUAAAAUGCGGUUCAGGCC--UUA
((-----((((((--------...(((....)))..((((((((((......)--))))))))).......)))))..((((((((((((....)))))))).)))))))--... ( -39.00)
>consensus
GA_____CGG_AU________CUCGGCCAUGGCUAACUGGUUGUUGCGGUUUU__AGCGUUUAGCAUAAUUAGUCCUUCUGACCGCAUUUCGUAAAAUGCGGUUGAGGCC__UUA
..............................((((.(((((((((.((................)))))))))))......((((((((((....))))))))))..))))..... (-21.24 = -21.57 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:35 2006