Locus 2252

Sequence ID	3R_DroMel_CAF1
Location	6,393,132 – 6,393,234
Length	102
Max. P	0.979601

overview

Window 1

Location	6,393,132 – 6,393,234
Length	102
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	76.45
Mean single sequence MFE	-25.30
Consensus MFE	-11.81
Energy contribution	-14.32
Covariance contribution	2.50
Combinations/Pair	1.25
Mean z-score	-2.72
Structure conservation index	0.47
SVM decision value	1.84
SVM RNA-class probability	0.979601
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6393132 102 + 27905053
AAAAAAAUGGGAAAAAAUGUCGGAGAGAUGGGGUCUCCAGAACUUUGGACUCUAGUUUUCCUUAUUUUUUCCUCUUUUAAUUUGCACCUGAGUGCAUUUCUC
...((((.(((((((((((..((((((.((((((((..........)))))))).)))))).))))))))))).))))....(((((....)))))...... ( -32.30)
>DroPse_CAF1 155961 94 + 1
--AGAGA-GGGAGGGAG---GGGUACGGUAGGGAAGCAAGAACUUUGGACUGCAUUUU--GUAGUUUCCUCUUUUUUUAAUUUGCACUUGAGUGCAUUUCUC
--.((((-(((((((((---(((.........((((......))))(((((((.....--))))))))))))))))))....(((((....))))).))))) ( -26.40)
>DroSec_CAF1 157014 100 + 1
--AAAAAUGGGAAAAAAUGUCGGAGAGAUGGGGCCUCCAGAACUUUGGACUCUAGUUUUCCUUAUUUUUUCCUCUUUUAAUUUGCACUUGAGUGCAUUUCUC
--.((((.(((((((((((..((((((.(((((..(((((....)))))))))).)))))).))))))))))).))))....(((((....)))))...... ( -32.60)
>DroSim_CAF1 180453 102 + 1
AAAAAAAUGGGAAAAAAUGUCGGAGAGAUGGGGCCUCCAGAACUUUGGACUCUAGUUUUCCUUAUUUUUUCCUCUUUUAAUUUGCACUUGAGUGCAUUUCUC
...((((.(((((((((((..((((((.(((((..(((((....)))))))))).)))))).))))))))))).))))....(((((....)))))...... ( -32.60)
>DroEre_CAF1 168141 79 + 1
-----------------------AAAGAUGGGGCCUCCAGAACUUUGGACUCUAGUUCUCUUGAUUUUUUCCUCUUUUAAUUUGCACUCGAGUGCAUUUCUC
-----------------------(((((.((((..((.((((((.........))))))...))....))))))))).....(((((....)))))...... ( -14.40)
>DroYak_CAF1 160461 88 + 1
-----AACAGCAAA---------AAAAAACAGGCCUCCAGAACUUUGGACUCUAGUUUUCCUUAUUUUUUCCUCUUUUAAUUUGCACUUGAGUGCAUUUCUC
-----.........---------..(((((.((..(((((....)))))..)).))))).......................(((((....)))))...... ( -13.50)
>consensus
__AAAAAUGGGAAAAAA___CGGAAAGAUGGGGCCUCCAGAACUUUGGACUCUAGUUUUCCUUAUUUUUUCCUCUUUUAAUUUGCACUUGAGUGCAUUUCUC
........(((((((((...........(((((..(((((....))))))))))..........))))))))).........(((((....)))))...... (-11.81 = -14.32 +   2.50)

alignment

secondary structure

dotplot

Window 2

Location	6,393,132 – 6,393,234
Length	102
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	76.45
Mean single sequence MFE	-20.02
Consensus MFE	-10.14
Energy contribution	-10.45
Covariance contribution	0.31
Combinations/Pair	1.20
Mean z-score	-1.93
Structure conservation index	0.51
SVM decision value	0.46
SVM RNA-class probability	0.745037
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6393132 102 - 27905053
GAGAAAUGCACUCAGGUGCAAAUUAAAAGAGGAAAAAAUAAGGAAAACUAGAGUCCAAAGUUCUGGAGACCCCAUCUCUCCGACAUUUUUUCCCAUUUUUUU
(((((((((((....)))).........(.(((((((((..(((.........)))...(((..(((((.......))))))))))))))))))))))))). ( -23.90)
>DroPse_CAF1 155961 94 - 1
GAGAAAUGCACUCAAGUGCAAAUUAAAAAAAGAGGAAACUAC--AAAAUGCAGUCCAAAGUUCUUGCUUCCCUACCGUACCC---CUCCCUCCC-UCUCU--
((((..(((((....)))))...........((((..(((.(--.....).)))...((((....))))............)---)))......-)))).-- ( -15.90)
>DroSec_CAF1 157014 100 - 1
GAGAAAUGCACUCAAGUGCAAAUUAAAAGAGGAAAAAAUAAGGAAAACUAGAGUCCAAAGUUCUGGAGGCCCCAUCUCUCCGACAUUUUUUCCCAUUUUU--
......(((((....)))))....((((..(((((((((..(((...((((((.......)))))).(....).....)))...)))))))))..)))).-- ( -22.70)
>DroSim_CAF1 180453 102 - 1
GAGAAAUGCACUCAAGUGCAAAUUAAAAGAGGAAAAAAUAAGGAAAACUAGAGUCCAAAGUUCUGGAGGCCCCAUCUCUCCGACAUUUUUUCCCAUUUUUUU
(((((((((((....)))).........(.(((((((((..(((...((((((.......)))))).(....).....)))...))))))))))))))))). ( -22.90)
>DroEre_CAF1 168141 79 - 1
GAGAAAUGCACUCGAGUGCAAAUUAAAAGAGGAAAAAAUCAAGAGAACUAGAGUCCAAAGUUCUGGAGGCCCCAUCUUU-----------------------
......(((((....))))).....(((((((......((...((((((.........)))))).))....)).)))))----------------------- ( -15.00)
>DroYak_CAF1 160461 88 - 1
GAGAAAUGCACUCAAGUGCAAAUUAAAAGAGGAAAAAAUAAGGAAAACUAGAGUCCAAAGUUCUGGAGGCCUGUUUUUU---------UUUGCUGUU-----
......(((((....))))).......(((((((((((((.((....((((((.......))))))...))))))))))---------))).))...----- ( -19.70)
>consensus
GAGAAAUGCACUCAAGUGCAAAUUAAAAGAGGAAAAAAUAAGGAAAACUAGAGUCCAAAGUUCUGGAGGCCCCAUCUCUCCG___UUUUUUCCCAUUUUU__
((((..(((((....)))))...........................((((((.......))))))........))))........................ (-10.14 = -10.45 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:55 2006