Locus 7265

Sequence ID	3R_DroMel_CAF1
Location	19,192,895 – 19,193,000
Length	105
Max. P	0.838059

overview

Window 8

Location	19,192,895 – 19,193,000
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.83
Mean single sequence MFE	-31.16
Consensus MFE	-18.02
Energy contribution	-18.72
Covariance contribution	0.70
Combinations/Pair	1.28
Mean z-score	-1.92
Structure conservation index	0.58
SVM decision value	0.74
SVM RNA-class probability	0.838059
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19192895 105 + 27905053
GUUCCCAGACAUUUUGCAUGGCAAAACAAUUUGCAUGGAUCUCUGAUCCAAUUG--------------CAAUUAGACUGGCGUGCUGCCCUCGGGACAGUUGUGGCAACAUCA-ACCAUU
(((((.((.......(((((.((.......(((((((((((...))))))..))--------------)))......)).)))))....)).))))).((((((....)).))-)).... ( -32.42)
>DroSec_CAF1 4885 106 + 1
GUUCCCAGCCAUUUUGCAGCGCAAAACAAUUUGCAUGGAUCUCUGAUCCAAUUG--------------CAAUUAGACUGGCGUGCUGCCCUCGGGACAGUUGUGGCAACAUCAAACCAUU
(((.(((((((..((((((.(((((....))))).((((((...)))))).)))--------------)))......))))..((((((....)).))))..))).)))........... ( -32.40)
>DroSim_CAF1 5261 106 + 1
GUUCCCAGCCAUUUUGCAGCGCAAAACAAUUUGCAUGGAUCUCUGAUCCAAUUG--------------CAAUUAGACUGGCGUGCUGCCCUCGGGACAGUUGUGGCAACAUCAAACCAUU
(((.(((((((..((((((.(((((....))))).((((((...)))))).)))--------------)))......))))..((((((....)).))))..))).)))........... ( -32.40)
>DroEre_CAF1 6171 119 + 1
UUUCCCAGCCAUUUUGCAUGGCAAAACAAUUUGCAUGGAUCUCCGAUCCAAUUGGCGAAAAAUUGGAAAAAUUAGACUGGCGUGCUGCCCUCGGGACAGCAGUGGCAACAUCG-CCCAUU
(((((..(((((.....))))).......(((((.((((((...))))))....))))).....))))).........(((((((((((....)).)))))(((....)))))-)).... ( -39.70)
>DroYak_CAF1 8871 93 + 1
GUUCCCAGCUAUGUUGCAUGGCAAAACAAUUUGCAUGGAUCUCUGAUCCAAUUG--------------CAAUUAGACUGGCGUGCUGCCCUCGGGAC------------AUUG-GCCAUU
(((((.((....((.(((((.((.......(((((((((((...))))))..))--------------)))......)).))))).)).)).)))))------------....-...... ( -27.92)
>DroAna_CAF1 10991 88 + 1
----GUAGCAAUUUUACAUACCAAAGCAAUUUGCAUGGCUCUCCGAUCCACUUG--------------CAAUUAGGCUGGCGUGUUGCCCUCAGGAUGGCUGCAGC--------------
----(((((.(((((.........(((...((((((((.((...)).)))..))--------------)))....)))(((.....)))...))))).)))))...-------------- ( -22.10)
>consensus
GUUCCCAGCCAUUUUGCAUGGCAAAACAAUUUGCAUGGAUCUCUGAUCCAAUUG______________CAAUUAGACUGGCGUGCUGCCCUCGGGACAGUUGUGGCAACAUCA_ACCAUU
.......((((.((((....(((((....))))).((((((...))))))......................)))).))))..((((((....)).)))).................... (-18.02 = -18.72 +   0.70)

alignment

secondary structure

dotplot

Window 9

Location	19,192,895 – 19,193,000
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.83
Mean single sequence MFE	-31.98
Consensus MFE	-17.99
Energy contribution	-18.93
Covariance contribution	0.95
Combinations/Pair	1.09
Mean z-score	-1.62
Structure conservation index	0.56
SVM decision value	0.05
SVM RNA-class probability	0.560350
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19192895 105 - 27905053
AAUGGU-UGAUGUUGCCACAACUGUCCCGAGGGCAGCACGCCAGUCUAAUUG--------------CAAUUGGAUCAGAGAUCCAUGCAAAUUGUUUUGCCAUGCAAAAUGUCUGGGAAC
..((((-.......))))...((((((...))))))....((((.(...(((--------------((..((((((...)))))).(((((....)))))..)))))...).)))).... ( -31.50)
>DroSec_CAF1 4885 106 - 1
AAUGGUUUGAUGUUGCCACAACUGUCCCGAGGGCAGCACGCCAGUCUAAUUG--------------CAAUUGGAUCAGAGAUCCAUGCAAAUUGUUUUGCGCUGCAAAAUGGCUGGGAAC
..((((........))))...((((((...))))))....((((((...(((--------------((..((((((...)))))).(((((....)))))..)))))...)))))).... ( -35.80)
>DroSim_CAF1 5261 106 - 1
AAUGGUUUGAUGUUGCCACAACUGUCCCGAGGGCAGCACGCCAGUCUAAUUG--------------CAAUUGGAUCAGAGAUCCAUGCAAAUUGUUUUGCGCUGCAAAAUGGCUGGGAAC
..((((........))))...((((((...))))))....((((((...(((--------------((..((((((...)))))).(((((....)))))..)))))...)))))).... ( -35.80)
>DroEre_CAF1 6171 119 - 1
AAUGGG-CGAUGUUGCCACUGCUGUCCCGAGGGCAGCACGCCAGUCUAAUUUUUCCAAUUUUUCGCCAAUUGGAUCGGAGAUCCAUGCAAAUUGUUUUGCCAUGCAAAAUGGCUGGGAAA
....((-((.(((((((.((.(......))))))))))))))........(((((((.......((....((((((...)))))).))..........(((((.....)))))))))))) ( -39.50)
>DroYak_CAF1 8871 93 - 1
AAUGGC-CAAU------------GUCCCGAGGGCAGCACGCCAGUCUAAUUG--------------CAAUUGGAUCAGAGAUCCAUGCAAAUUGUUUUGCCAUGCAACAUAGCUGGGAAC
....((-...(------------((((...)))))))...((((.(((.(((--------------((..((((((...)))))).(((((....)))))..)))))..))))))).... ( -27.50)
>DroAna_CAF1 10991 88 - 1
--------------GCUGCAGCCAUCCUGAGGGCAACACGCCAGCCUAAUUG--------------CAAGUGGAUCGGAGAGCCAUGCAAAUUGCUUUGGUAUGUAAAAUUGCUAC----
--------------...((((((........))).(((..((((..((((((--------------((..(((.((...)).)))))).)))))..))))..))).....)))...---- ( -21.80)
>consensus
AAUGGU_UGAUGUUGCCACAACUGUCCCGAGGGCAGCACGCCAGUCUAAUUG______________CAAUUGGAUCAGAGAUCCAUGCAAAUUGUUUUGCCAUGCAAAAUGGCUGGGAAC
........................((((...(((.....)))((((........................((((((...)))))).(((((....)))))..........)))))))).. (-17.99 = -18.93 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:40 2006