Locus 6066

Sequence ID	2L_DroMel_CAF1
Location	17,055,732 – 17,055,826
Length	94
Max. P	0.702381

overview

Window 9

Location	17,055,732 – 17,055,826
Length	94
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.46
Mean single sequence MFE	-33.35
Consensus MFE	-18.02
Energy contribution	-18.85
Covariance contribution	0.83
Combinations/Pair	1.00
Mean z-score	-1.96
Structure conservation index	0.54
SVM decision value	0.21
SVM RNA-class probability	0.636759
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17055732 94 + 22407834
AAAAU--------UGGCCAGACCCAUAAAUUUAAUUAGUUUGAGCCACGCUCACUGCGGUCUGGAGGUCAGAGG------------------CAGCAGGCUUUUGGCCAAGCAGAUGGCA
.....--------(((((((((...............))))).))))........((.(((((..(((((((((------------------(.....))))))))))...))))).)). ( -33.76)
>DroPse_CAF1 7963 117 + 1
AAAUCCAGAGACCCAGCCAGACCCAUAAAUUUAAUUAGUUUGAGCCACGCUCAGUGCGGUCUGAAGGUCAGUGGGAACACCAGCAGGAGCAGAAGCAGGCC---GUCCAAGCAGCUGCCA
...(((...((((....((((((((((((((.....)))))((((...)))).))).))))))..)))).(((....))).....)))((((..((.((..---..))..))..)))).. ( -35.70)
>DroSec_CAF1 19795 94 + 1
AAAAU--------UGGCCAGACCCAUAAAUUUAAUUAGUUUGAGCCACGCUCACUGCGGUCUGGAGGUCAGAGG------------------CAGCAGGCUUUUGGCCAAGCAGAUGGCA
.....--------(((((((((...............))))).))))........((.(((((..(((((((((------------------(.....))))))))))...))))).)). ( -33.76)
>DroEre_CAF1 19588 94 + 1
AAAAU--------UGGCCAGACCCAUAAAUUUAAUUAGUUUGAGCCACGCCCACUGCGGUCUGGAGGUCAGAGG------------------CAGCAGGCUUUUGGCCAAGCAGAUGCCA
.....--------((((((((((..((((((.....))))))......((.....))))))))..(((((((((------------------(.....))))))))))........)))) ( -31.20)
>DroYak_CAF1 17560 94 + 1
AAAAU--------UGGCCAGACCCAUAAAUUUAAUUAGUUUGAGCCACGCUCACUGCGGUCUGGAGGUCAGAGG------------------CAGCAGGCUUUAGGCCAAGCAGAUGGCA
.....--------(((((((((...............))))).))))........((.(((((..((((.((((------------------(.....))))).))))...))))).)). ( -29.96)
>DroPer_CAF1 4101 117 + 1
AAAUCCAGAGACCCAGCCAGACCCAUAAAUUUAAUUAGUUUGAGCCACGCUCAGUGCGGUCUGAAGGUCAGUGGGAACACCAGCAGGAGCAGAAGCAGGCC---GUCCAAGCAGCUGCCA
...(((...((((....((((((((((((((.....)))))((((...)))).))).))))))..)))).(((....))).....)))((((..((.((..---..))..))..)))).. ( -35.70)
>consensus
AAAAU________UGGCCAGACCCAUAAAUUUAAUUAGUUUGAGCCACGCUCACUGCGGUCUGGAGGUCAGAGG__________________CAGCAGGCUUUUGGCCAAGCAGAUGCCA
................(((((((((.(((((.....)))))((((...))))..)).)))))))..............................((.(((.....)))..))........ (-18.02 = -18.85 +   0.83)

alignment

secondary structure

dotplot

Window 0

Location	17,055,732 – 17,055,826
Length	94
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.46
Mean single sequence MFE	-33.00
Consensus MFE	-19.48
Energy contribution	-19.45
Covariance contribution	-0.03
Combinations/Pair	1.09
Mean z-score	-1.81
Structure conservation index	0.59
SVM decision value	0.36
SVM RNA-class probability	0.702381
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17055732 94 - 22407834
UGCCAUCUGCUUGGCCAAAAGCCUGCUG------------------CCUCUGACCUCCAGACCGCAGUGAGCGUGGCUCAAACUAAUUAAAUUUAUGGGUCUGGCCA--------AUUUU
..........(((((((...((..((((------------------(.((((.....))))..)))))..))..((((((...(((......)))))))))))))))--------).... ( -29.90)
>DroPse_CAF1 7963 117 - 1
UGGCAGCUGCUUGGAC---GGCCUGCUUCUGCUCCUGCUGGUGUUCCCACUGACCUUCAGACCGCACUGAGCGUGGCUCAAACUAAUUAAAUUUAUGGGUCUGGCUGGGUCUCUGGAUUU
.(((((..((..((..---..)).))..)))))((....)).....(((..((((((((((((.((.(((((...)))))...(((......))))))))))))..)))))..))).... ( -36.60)
>DroSec_CAF1 19795 94 - 1
UGCCAUCUGCUUGGCCAAAAGCCUGCUG------------------CCUCUGACCUCCAGACCGCAGUGAGCGUGGCUCAAACUAAUUAAAUUUAUGGGUCUGGCCA--------AUUUU
..........(((((((...((..((((------------------(.((((.....))))..)))))..))..((((((...(((......)))))))))))))))--------).... ( -29.90)
>DroEre_CAF1 19588 94 - 1
UGGCAUCUGCUUGGCCAAAAGCCUGCUG------------------CCUCUGACCUCCAGACCGCAGUGGGCGUGGCUCAAACUAAUUAAAUUUAUGGGUCUGGCCA--------AUUUU
.(((....)))((((((...(((..(((------------------(.((((.....))))..))))..)))..((((((...(((......)))))))))))))))--------..... ( -36.40)
>DroYak_CAF1 17560 94 - 1
UGCCAUCUGCUUGGCCUAAAGCCUGCUG------------------CCUCUGACCUCCAGACCGCAGUGAGCGUGGCUCAAACUAAUUAAAUUUAUGGGUCUGGCCA--------AUUUU
..........((((((....((..((((------------------(.((((.....))))..)))))..))..((((((...(((......))))))))).)))))--------).... ( -28.60)
>DroPer_CAF1 4101 117 - 1
UGGCAGCUGCUUGGAC---GGCCUGCUUCUGCUCCUGCUGGUGUUCCCACUGACCUUCAGACCGCACUGAGCGUGGCUCAAACUAAUUAAAUUUAUGGGUCUGGCUGGGUCUCUGGAUUU
.(((((..((..((..---..)).))..)))))((....)).....(((..((((((((((((.((.(((((...)))))...(((......))))))))))))..)))))..))).... ( -36.60)
>consensus
UGCCAUCUGCUUGGCCAAAAGCCUGCUG__________________CCUCUGACCUCCAGACCGCAGUGAGCGUGGCUCAAACUAAUUAAAUUUAUGGGUCUGGCCA________AUUUU
........((..(((.....))).))..............................(((((((.((.(((((...)))))...(((......))))))))))))................ (-19.48 = -19.45 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:28 2006