Locus 3181

Sequence ID	3R_DroMel_CAF1
Location	8,450,491 – 8,450,585
Length	94
Max. P	0.935765

overview

Window 2

Location	8,450,491 – 8,450,585
Length	94
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.09
Mean single sequence MFE	-34.33
Consensus MFE	-31.40
Energy contribution	-31.10
Covariance contribution	-0.30
Combinations/Pair	1.15
Mean z-score	-2.02
Structure conservation index	0.91
SVM decision value	1.25
SVM RNA-class probability	0.935765
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8450491 94 + 27905053
--------------------------AUGGCGCGAGUCCCUAGGGUAGAAUUCGGCCAGGAUGGAGGCCGGGAUACGCUUGAGCAUCUCCUUGGGGAAGAUACGCAGCAGCUGCCAGCCA
--------------------------.((((((((.(((((((((.(((.(((((((........)))))))....((....)).))))))))))))...).))).((....))..)))) ( -40.60)
>DroVir_CAF1 3248 118 + 1
CAAAACAA--UUUUAAACAGAAUCUAAUGGCGCGAGUCCCUAGGAUAGAAUUCAGCCAAAAUGGAGGCUGGAAUACGCUUAAGCAUCUCCUUGGGGAAGAUACGCAGCAGCUGCCAGCCA
........--.................((((((((.((((((((..(((.(((((((........)))))))....((....)).))).))))))))...).))).((....))..)))) ( -35.00)
>DroGri_CAF1 2289 120 + 1
CAAAACAAAUUUUUAAACAGAAUCUAAUGGCGCGAGUCCCUAGGAUAGAAUUCAGCCAAAAUGGAGGCUGGAAUACGCUUGAGCAUCUCCUUGGGGAAAAUACGCAGCAGCUGCCAGCCA
...........................((((((((.((((((((..(((.(((((((........)))))))....((....)).))).))))))))...).))).((....))..)))) ( -35.00)
>DroWil_CAF1 1 98 + 1
----------------------UCUAAUGGCGGGAGUCCCUAGGAUAGAAUUCAGCCAAAAUGGAGGCUGGAAUACGUUUCAACAUCUCCUUGGGGAAGAUACGCAGCAGCUGCCAGCCA
----------------------.....((((.((..((((((((..(((.(((((((........)))))))....((....)).))).))))))))......((....))..)).)))) ( -30.90)
>DroMoj_CAF1 2399 118 + 1
CAAAACAA--UUUUAAACAAAAUCUAAUGGCGCGAGUCCCUAGGAUAGAAUUCAGCCAAAAUAGAGGCCGGAAUACGUUUAAGCAUUUCCUUGGGGAAGAUACGCAACAGCUGCCAGCCA
........--.................((((.....(((((((((..(.((((.(((........)))..)))).)((....))...))).))))))......(((.....)))..)))) ( -25.40)
>DroPer_CAF1 1 98 + 1
----------------------UCUAAUGGCGCGAGUCCCUAGGGUAGAAUUCAGCCAAGAUGGAGGCUGGGAUACGCUUGAGCAUCUCCUUGGGGAAGAUACGCAGCAACUGCCAGCCA
----------------------.....((((((((.(((((((((.(((.(((((((........)))))))....((....)).))))))))))))...).))).((....))..)))) ( -39.10)
>consensus
______________________UCUAAUGGCGCGAGUCCCUAGGAUAGAAUUCAGCCAAAAUGGAGGCUGGAAUACGCUUGAGCAUCUCCUUGGGGAAGAUACGCAGCAGCUGCCAGCCA
...........................((((((((.((((((((......(((((((........)))))))....((....)).....))))))))...).))).((....))..)))) (-31.40 = -31.10 +  -0.30)

alignment

secondary structure

dotplot

Window 3

Location	8,450,491 – 8,450,585
Length	94
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.09
Mean single sequence MFE	-33.27
Consensus MFE	-30.90
Energy contribution	-30.60
Covariance contribution	-0.30
Combinations/Pair	1.17
Mean z-score	-1.70
Structure conservation index	0.93
SVM decision value	0.89
SVM RNA-class probability	0.875882
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8450491 94 - 27905053
UGGCUGGCAGCUGCUGCGUAUCUUCCCCAAGGAGAUGCUCAAGCGUAUCCCGGCCUCCAUCCUGGCCGAAUUCUACCCUAGGGACUCGCGCCAU--------------------------
((((..((((...))))((((((((.....))))))))....(((..((((((((........))))(....).......))))..))))))).-------------------------- ( -37.30)
>DroVir_CAF1 3248 118 - 1
UGGCUGGCAGCUGCUGCGUAUCUUCCCCAAGGAGAUGCUUAAGCGUAUUCCAGCCUCCAUUUUGGCUGAAUUCUAUCCUAGGGACUCGCGCCAUUAGAUUCUGUUUAAAA--UUGUUUUG
.((((((....((((..((((((((.....))))))))...))))....)))))).......(((((((.((((......)))).))).)))).................--........ ( -34.20)
>DroGri_CAF1 2289 120 - 1
UGGCUGGCAGCUGCUGCGUAUUUUCCCCAAGGAGAUGCUCAAGCGUAUUCCAGCCUCCAUUUUGGCUGAAUUCUAUCCUAGGGACUCGCGCCAUUAGAUUCUGUUUAAAAAUUUGUUUUG
((((.(((....)))(((.....((((..((((.((((....))))....(((((........))))).......)))).))))..)))))))........................... ( -33.20)
>DroWil_CAF1 1 98 - 1
UGGCUGGCAGCUGCUGCGUAUCUUCCCCAAGGAGAUGUUGAAACGUAUUCCAGCCUCCAUUUUGGCUGAAUUCUAUCCUAGGGACUCCCGCCAUUAGA----------------------
((((.((..((....))........(((.((((.((((....))))....(((((........))))).......)))).)))...)).)))).....---------------------- ( -29.10)
>DroMoj_CAF1 2399 118 - 1
UGGCUGGCAGCUGUUGCGUAUCUUCCCCAAGGAAAUGCUUAAACGUAUUCCGGCCUCUAUUUUGGCUGAAUUCUAUCCUAGGGACUCGCGCCAUUAGAUUUUGUUUAAAA--UUGUUUUG
.((((((....((((..((((.((((....))))))))...))))....))))))((((...(((((((.((((......)))).))).)))).))))............--........ ( -30.50)
>DroPer_CAF1 1 98 - 1
UGGCUGGCAGUUGCUGCGUAUCUUCCCCAAGGAGAUGCUCAAGCGUAUCCCAGCCUCCAUCUUGGCUGAAUUCUACCCUAGGGACUCGCGCCAUUAGA----------------------
.((((((....(((((.((((((((.....)))))))).).))))....))))))....((((((((((.((((......)))).))).))))..)))---------------------- ( -35.30)
>consensus
UGGCUGGCAGCUGCUGCGUAUCUUCCCCAAGGAGAUGCUCAAGCGUAUUCCAGCCUCCAUUUUGGCUGAAUUCUAUCCUAGGGACUCGCGCCAUUAGA______________________
.((((((....((((..((((((((.....))))))))...))))....)))))).......(((((((.((((......)))).))).))))........................... (-30.90 = -30.60 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:02 2006