Locus 1056

Sequence ID	2L_DroMel_CAF1
Location	2,937,848 – 2,937,951
Length	103
Max. P	0.753442

overview

Window 3

Location	2,937,848 – 2,937,951
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.01
Mean single sequence MFE	-33.72
Consensus MFE	-25.16
Energy contribution	-25.12
Covariance contribution	-0.04
Combinations/Pair	1.13
Mean z-score	-1.76
Structure conservation index	0.75
SVM decision value	0.48
SVM RNA-class probability	0.753442
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2937848 103 + 22407834
-------------GGAUUCCGAUUCGGAUUCGCGCACAUGUGUUGCCAAACGCAGGGCUGCCAAGCAAAGCUAUCUGCUUGGGCAUAUACUAUAUAUG----UAUGUGUCGGAUACACAC
-------------.((.((((...)))).))((((...((((((....))))))..)).))((((((........))))))(((((((((.......)----)))))))).......... ( -33.90)
>DroSec_CAF1 52907 108 + 1
--------GAUUGGGAUUGGGAUUCGGAUUCGCGCACAUGUGUUGCCAAACGCAGGGCUGCCAAGCAAAGCUAUCUGCUUGGGCAUAUACUAUACAUA----UAUGUGGCGGAUACACAC
--------.....((((....))))(.((((((.(((((((((.(((........)))(((((((((........))))).))))..........)))----)))))))))))).).... ( -32.60)
>DroSim_CAF1 54909 107 + 1
-------------GGAUUGGGAUUCGGAUUCGCGCACAUGUGUUGCCAAACGCAGGACUGCCAAGCAAAGCUAUCUGCUUGGGCAUAUACUAUAUAUGUAUGUAUGUGGCGGAUACACAC
-------------((((....))))(.((((((.(((((((.((((.....)))).))..(((((((........)))))))(((((((.......)))))))))))))))))).).... ( -33.20)
>DroEre_CAF1 55195 104 + 1
AGGAUGAAGAUGAGGGUUCGGAUUCGGAUUCGCGCACAUGUGUUGCCAAAUGCAGCGCUGCCAAGCAAAGCUAUCUGCUUGGGCAUAU---------------AUGU-GCGGAUACACAC
.............(((((((....))))))).(((((((((((.(((....(((....)))((((((........)))))))))))))---------------))))-)))......... ( -36.80)
>DroYak_CAF1 55056 97 + 1
--------GAUGAGAAUUCGGAUUUGGAUUCGCGCACAUGUGUUGCCAAACGCAGAGCUGCCAAGCAAAGCUAUCUGCUUGGGCAUAU---------------AUGUAGCGGAUACACAC
--------.....(((((((....))))))).(((((((((((.(((....(((....)))((((((........)))))))))))))---------------)))).)))......... ( -32.10)
>consensus
________GAU__GGAUUCGGAUUCGGAUUCGCGCACAUGUGUUGCCAAACGCAGGGCUGCCAAGCAAAGCUAUCUGCUUGGGCAUAUACUAUA_AU_____UAUGUGGCGGAUACACAC
.............((((....))))(.((((((.(((((((.((((.....)))).))(((((((((........))))).))))..................))))))))))).).... (-25.16 = -25.12 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	2,937,848 – 2,937,951
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.01
Mean single sequence MFE	-28.94
Consensus MFE	-22.54
Energy contribution	-22.38
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.44
Structure conservation index	0.78
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2937848 103 - 22407834
GUGUGUAUCCGACACAUA----CAUAUAUAGUAUAUGCCCAAGCAGAUAGCUUUGCUUGGCAGCCCUGCGUUUGGCAACACAUGUGCGCGAAUCCGAAUCGGAAUCC-------------
((((((.....)))))).----........(((((((.(((((((((....)))))))))..(((........)))....)))))))..((.((((...)))).)).------------- ( -31.70)
>DroSec_CAF1 52907 108 - 1
GUGUGUAUCCGCCACAUA----UAUGUAUAGUAUAUGCCCAAGCAGAUAGCUUUGCUUGGCAGCCCUGCGUUUGGCAACACAUGUGCGCGAAUCCGAAUCCCAAUCCCAAUC--------
.........((((((((.----..(((........((((.(((((((....)))))))))))(((........))).))).))))).)))......................-------- ( -26.90)
>DroSim_CAF1 54909 107 - 1
GUGUGUAUCCGCCACAUACAUACAUAUAUAGUAUAUGCCCAAGCAGAUAGCUUUGCUUGGCAGUCCUGCGUUUGGCAACACAUGUGCGCGAAUCCGAAUCCCAAUCC-------------
.........((((((((..((((.......)))).((((((((((((....))))))))(((....)))....))))....))))).))).................------------- ( -28.00)
>DroEre_CAF1 55195 104 - 1
GUGUGUAUCCGC-ACAU---------------AUAUGCCCAAGCAGAUAGCUUUGCUUGGCAGCGCUGCAUUUGGCAACACAUGUGCGCGAAUCCGAAUCCGAACCCUCAUCUUCAUCCU
(((((....)))-))..---------------...((((.(((((((....)))))))))))((((.((((.((....)).))))))))............................... ( -32.20)
>DroYak_CAF1 55056 97 - 1
GUGUGUAUCCGCUACAU---------------AUAUGCCCAAGCAGAUAGCUUUGCUUGGCAGCUCUGCGUUUGGCAACACAUGUGCGCGAAUCCAAAUCCGAAUUCUCAUC--------
(((((((.....)))))---------------)).((((.(((((((....)))))))))))((.(.((((.((....)).))))).))((((.(......).)))).....-------- ( -25.90)
>consensus
GUGUGUAUCCGCCACAUA_____AU_UAUAGUAUAUGCCCAAGCAGAUAGCUUUGCUUGGCAGCCCUGCGUUUGGCAACACAUGUGCGCGAAUCCGAAUCCGAAUCC__AUC________
.(((((.............................((((.(((((((....))))))))))).....((((.((....)).))))))))).............................. (-22.54 = -22.38 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:17 2006