Locus 6677

Sequence ID	X_DroMel_CAF1
Location	16,676,245 – 16,676,352
Length	107
Max. P	0.941060

overview

Window 2

Location	16,676,245 – 16,676,352
Length	107
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	78.82
Mean single sequence MFE	-26.25
Consensus MFE	-16.44
Energy contribution	-17.30
Covariance contribution	0.86
Combinations/Pair	1.04
Mean z-score	-1.71
Structure conservation index	0.63
SVM decision value	0.55
SVM RNA-class probability	0.776668
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16676245 107 + 22224390
UAUGAUUUCUGUU--AACGG---UCUCACCUGCAUGAAUAUAAACUCCCACUUUCUGGAGAACAUCUUCUGCAGCUUGGCCAGAUUCUCGGCCUCGUAGUCGGCCAACUCCA
..........(((--...((---((....(((((.(((.((...((((........))))...)).))))))))...))))........((((........))))))).... ( -26.30)
>DroVir_CAF1 7377 109 + 1
AACAU---UGAAUUAGCCAUUUAACUCACCUGCAUGAAUAUGAACUCCCAUUUGCGUGAGAACAUCUUCUGCAGCUUGGCCAGGUUCUCGGCUUCGUAGUCCGCCAACUCCA
.....---.(((((.((((..........(((((.(((.(((..(((.(......).)))..))).))))))))..))))..)))))..(((..........)))....... ( -21.60)
>DroPse_CAF1 21575 104 + 1
CAGUUCC--UAUU-CGAU-----ACUUACCUGCAUGAAGAUGAACUCCCAUUUCCGAGAGAACAUCUUCUGCAACUUGGCCAGGUUCUCGGCUUCGUAGUCGGCCAAUUCCA
.......--....-....-----.......((((.(((((((..(((.(......).)))..)))))))))))..((((((..(....)((((....))))))))))..... ( -27.60)
>DroEre_CAF1 1256 103 + 1
UACAUUUUAUGUU--G-------GCCUACCUGCAUGAAUAUAAACUCCCACUUCCUGGAGAACAUCUUCUGCAGCUUGGCCAGAUUCUCGGCCUCAUAGUCGGCCAACUCGA
..........(((--(-------(((.(((((((.(((.((...((((........))))...)).))))))))...((((........)))).....)).))))))).... ( -32.70)
>DroMoj_CAF1 10443 109 + 1
AAUAUA-UCAAAU--GAUAUCCCACACACCUGCAUGAAUAUGAACUCCCAUUUGCGCGAGAACAUCUUCUGCAGCUUGGCCAGAUUCUCGGCCUCGUAGUCCGCCAGCUCCA
...(((-((....--))))).........(((((.(((.(((..(((.(......).)))..))).)))))))).(((((..((((..((....)).)))).)))))..... ( -21.60)
>DroPer_CAF1 19801 104 + 1
CAGUUCC--UAUU-CGAU-----ACUUACCUGCAUGAAGAUGAACUCCCAUUUCCGAGAGAACAUCUUCUGCAACUUGGCCAGGUUCUCGGCUUAGUAGUCGGCCAAUUCCA
.......--...(-((((-----.......((((.(((((((..(((.(......).)))..)))))))))))(((.((((........)))).))).)))))......... ( -27.70)
>consensus
AACAUC___UAUU__GAU_____ACUCACCUGCAUGAAUAUGAACUCCCAUUUCCGAGAGAACAUCUUCUGCAGCUUGGCCAGAUUCUCGGCCUCGUAGUCGGCCAACUCCA
.............................(((((.(((.(((..(((..........)))..))).)))))))).((((((.(.....)(((......)))))))))..... (-16.44 = -17.30 +   0.86)

alignment

secondary structure

dotplot

Window 3

Location	16,676,245 – 16,676,352
Length	107
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.82
Mean single sequence MFE	-34.52
Consensus MFE	-22.41
Energy contribution	-23.05
Covariance contribution	0.64
Combinations/Pair	1.14
Mean z-score	-2.23
Structure conservation index	0.65
SVM decision value	1.31
SVM RNA-class probability	0.941060
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16676245 107 - 22224390
UGGAGUUGGCCGACUACGAGGCCGAGAAUCUGGCCAAGCUGCAGAAGAUGUUCUCCAGAAAGUGGGAGUUUAUAUUCAUGCAGGUGAGA---CCGUU--AACAGAAAUCAUA
.((..((((((........))))))...(((.(((....(((((((.(((..((((........))))..))).))).))))))).)))---))...--............. ( -31.90)
>DroVir_CAF1 7377 109 - 1
UGGAGUUGGCGGACUACGAAGCCGAGAACCUGGCCAAGCUGCAGAAGAUGUUCUCACGCAAAUGGGAGUUCAUAUUCAUGCAGGUGAGUUAAAUGGCUAAUUCA---AUGUU
..((((((((.((((((...((((......))))....((((((((.(((..(((.((....)).)))..))).))).))))))).)))).....)))))))).---..... ( -31.30)
>DroPse_CAF1 21575 104 - 1
UGGAAUUGGCCGACUACGAAGCCGAGAACCUGGCCAAGUUGCAGAAGAUGUUCUCUCGGAAAUGGGAGUUCAUCUUCAUGCAGGUAAGU-----AUCG-AAUA--GGAACUG
.....(((((((.((.((....))))....))))))).((((((((((((..((((((....))))))..))))))).)))))...(((-----.((.-....--)).))). ( -34.50)
>DroEre_CAF1 1256 103 - 1
UCGAGUUGGCCGACUAUGAGGCCGAGAAUCUGGCCAAGCUGCAGAAGAUGUUCUCCAGGAAGUGGGAGUUUAUAUUCAUGCAGGUAGGC-------C--AACAUAAAAUGUA
....(((((((.((.....(((((......)))))...((((((((.(((..((((........))))..))).))).))))))).)))-------)--))).......... ( -40.00)
>DroMoj_CAF1 10443 109 - 1
UGGAGCUGGCGGACUACGAGGCCGAGAAUCUGGCCAAGCUGCAGAAGAUGUUCUCGCGCAAAUGGGAGUUCAUAUUCAUGCAGGUGUGUGGGAUAUC--AUUUGA-UAUAUU
((.((((..((.....)).(((((......))))).)))).))...(((((((.((((((..((.((((....))))...))..)))))))))))))--......-...... ( -35.60)
>DroPer_CAF1 19801 104 - 1
UGGAAUUGGCCGACUACUAAGCCGAGAACCUGGCCAAGUUGCAGAAGAUGUUCUCUCGGAAAUGGGAGUUCAUCUUCAUGCAGGUAAGU-----AUCG-AAUA--GGAACUG
.....(((((((....((......))....))))))).((((((((((((..((((((....))))))..))))))).)))))...(((-----.((.-....--)).))). ( -33.80)
>consensus
UGGAGUUGGCCGACUACGAAGCCGAGAACCUGGCCAAGCUGCAGAAGAUGUUCUCCCGGAAAUGGGAGUUCAUAUUCAUGCAGGUAAGU_____AUC__AAUA___AAUAUA
.....(((((((.((.((....))))....))))))).((((((((.(((..((((((....))))))..))).))).)))))............................. (-22.41 = -23.05 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:48 2006