Locus 4488

Sequence ID	2L_DroMel_CAF1
Location	12,857,223 – 12,857,320
Length	97
Max. P	0.973677

overview

Window 9

Location	12,857,223 – 12,857,320
Length	97
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	79.49
Mean single sequence MFE	-26.90
Consensus MFE	-14.62
Energy contribution	-14.95
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.76
Structure conservation index	0.54
SVM decision value	1.35
SVM RNA-class probability	0.944672
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12857223 97 + 22407834
--------GGCCUCUGCGUUGGCCAUAUUUUC-GCAGUCAACUUUUGUGGCAAAUUAAUUUGCAACAAAAGUUGCACGGCGCAUUAC------ACAAAUUGAAAUAUGCAGA---
--------((((........))))........-((.((((((((((((.(((((....))))).)))))))))).)).))((((...------.(.....)....))))...--- ( -31.60)
>DroPse_CAF1 46990 103 + 1
GAU---UCUGCCACUGCGUCAGCCAUAUUUUCCAGAGUCAACUUUGGUGGCAAAUUAAUUUGCAACAAAAGUUGCACAGCGCAUUAC------ACAAAUUGAAAUAUGCAGA---
...---(((((...(((((..((((......((((((....)))))))))).........((((((....))))))..)))))...(------(.....))......)))))--- ( -28.40)
>DroWil_CAF1 54367 100 + 1
--------GGGAUAUGCCGCUGCCAUAUUUUG-CCAGUCAACUUUCAUGGCAAAUUAAUUUGCAACAAAAGUUGCAUGGCGCAUUAC------AUAAAUUGAAAUACGCAAAAAU
--------......(((.((.(((((..((((-(((...........))))))).......(((((....))))))))))))....(------(.....))......)))..... ( -25.30)
>DroYak_CAF1 39248 95 + 1
GCGCUG----------CCUUGGCCAUAUUUUC-GCAGUCAACUUUUGUGGCAAAUUAAUUUGCAACAAAAGUUGCACGGCGCAUUAC------ACAAAUUGAAAUAUGCAGA---
((((((----------(....)).........-...((((((((((((.(((((....))))).)))))))))).))))))).....------...................--- ( -28.30)
>DroAna_CAF1 61843 100 + 1
-----------AUUUGGCUUGGUCAUAUUUUU-GCAGUCAACUUUCGUGGCAAAUUAAUUUGCAACAAAAGUUGCGCAUCGCAUUAUACUCGUACAAAUUGAAAUAUGCAGA---
-----------...((((...))))......(-((.(.(((((((.((.(((((....))))).)).)))))))))))..((((.....(((.......)))...))))...--- ( -19.40)
>DroPer_CAF1 63768 103 + 1
GAU---UCUGCCACUGCGUCAGCCAUAUUUUCCAGAGUCAACUUUGGUGGCAAAUUAAUUUGCAACAAAAGUUGCACAGCGCAUUAC------ACAAAUUGAAAUAUGCAGA---
...---(((((...(((((..((((......((((((....)))))))))).........((((((....))))))..)))))...(------(.....))......)))))--- ( -28.40)
>consensus
_________GCCUCUGCCUCGGCCAUAUUUUC_GCAGUCAACUUUCGUGGCAAAUUAAUUUGCAACAAAAGUUGCACAGCGCAUUAC______ACAAAUUGAAAUAUGCAGA___
.....................(.((((((((........((((((.((.(((((....))))).)).))))))((.....))..................)))))))))...... (-14.62 = -14.95 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	12,857,223 – 12,857,320
Length	97
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	79.49
Mean single sequence MFE	-28.98
Consensus MFE	-18.91
Energy contribution	-18.80
Covariance contribution	-0.11
Combinations/Pair	1.20
Mean z-score	-2.99
Structure conservation index	0.65
SVM decision value	1.72
SVM RNA-class probability	0.973677
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12857223 97 - 22407834
---UCUGCAUAUUUCAAUUUGU------GUAAUGCGCCGUGCAACUUUUGUUGCAAAUUAAUUUGCCACAAAAGUUGACUGC-GAAAAUAUGGCCAACGCAGAGGCC--------
---..((((((........)))------)))...(((.((.((((((((((.(((((....))))).)))))))))))).))-).......((((........))))-------- ( -32.50)
>DroPse_CAF1 46990 103 - 1
---UCUGCAUAUUUCAAUUUGU------GUAAUGCGCUGUGCAACUUUUGUUGCAAAUUAAUUUGCCACCAAAGUUGACUCUGGAAAAUAUGGCUGACGCAGUGGCAGA---AUC
---(((((((((........))------))....(((((((((((....)))))..........(((((((.((....)).)))......))))....)))))))))))---... ( -28.80)
>DroWil_CAF1 54367 100 - 1
AUUUUUGCGUAUUUCAAUUUAU------GUAAUGCGCCAUGCAACUUUUGUUGCAAAUUAAUUUGCCAUGAAAGUUGACUGG-CAAAAUAUGGCAGCGGCAUAUCCC--------
....(((((((((.((.....)------).)))))((((..(((((((..(.(((((....))))).)..)))))))..)))-)........))))...........-------- ( -28.50)
>DroYak_CAF1 39248 95 - 1
---UCUGCAUAUUUCAAUUUGU------GUAAUGCGCCGUGCAACUUUUGUUGCAAAUUAAUUUGCCACAAAAGUUGACUGC-GAAAAUAUGGCCAAGG----------CAGCGC
---..((((((........)))------)))..(((((((.((((((((((.(((((....))))).))))))))))...))-)........((....)----------).)))) ( -31.10)
>DroAna_CAF1 61843 100 - 1
---UCUGCAUAUUUCAAUUUGUACGAGUAUAAUGCGAUGCGCAACUUUUGUUGCAAAUUAAUUUGCCACGAAAGUUGACUGC-AAAAAUAUGACCAAGCCAAAU-----------
---....(((((((....(((((....))))).....(((.((((((((((.(((((....))))).))))))))))...))-).)))))))............----------- ( -24.20)
>DroPer_CAF1 63768 103 - 1
---UCUGCAUAUUUCAAUUUGU------GUAAUGCGCUGUGCAACUUUUGUUGCAAAUUAAUUUGCCACCAAAGUUGACUCUGGAAAAUAUGGCUGACGCAGUGGCAGA---AUC
---(((((((((........))------))....(((((((((((....)))))..........(((((((.((....)).)))......))))....)))))))))))---... ( -28.80)
>consensus
___UCUGCAUAUUUCAAUUUGU______GUAAUGCGCCGUGCAACUUUUGUUGCAAAUUAAUUUGCCACAAAAGUUGACUGC_GAAAAUAUGGCCAACGCAGAGGC_________
......((((.....................))))((((((((((((((((.(((((....))))).))))))))))...........))))))..................... (-18.91 = -18.80 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:01 2006