Locus 4707

Sequence ID	3R_DroMel_CAF1
Location	12,364,911 – 12,365,021
Length	110
Max. P	0.841463

overview

Window 2

Location	12,364,911 – 12,365,007
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.83
Mean single sequence MFE	-28.55
Consensus MFE	-19.09
Energy contribution	-20.32
Covariance contribution	1.22
Combinations/Pair	1.08
Mean z-score	-1.44
Structure conservation index	0.67
SVM decision value	0.41
SVM RNA-class probability	0.723322
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12364911 96 + 27905053
-----------------------GCUGGCAAAUCAUGCUGUCUAA-AUUUGUAUUUAUUAGACAAUGCGCCACGGGGCGUAUGUGUAAUAUGCCAUGCUAUGCCAUUAGAUGCAUUCCAA
-----------------------(((((((.((.(((((((((((-...........)))))))(((((((....))))))))))).)).))))).)).((((........))))..... ( -28.40)
>DroPse_CAF1 31970 119 + 1
UCUGGCUACGAGGCGGACGUUGCUCUGGCAAAUCAUGCUGUCUAA-AUUUGUAUUUAUUAGACAAUGCGCCACGGGGCGUAUGUGUAAUAUGCCAUGCCAUGCCAUUAGAUGCAUUCCAG
(((((((....)))((.(((.((..(((((.((.(((((((((((-...........)))))))(((((((....))))))))))).)).))))).)).)))))..)))).......... ( -35.00)
>DroGri_CAF1 14481 100 + 1
A--GGGC--------AAAGUUCCGCUGGCAAUUCAUGCUGUCCAAAAUUUGUAUUUAUUAGACAGAACGCCACGGGGCGUAUGUGUAUUAUG----------CCAAUAUAAGCAUUCCAA
.--((((--------......(((.((((........(((((..((((....))))....)))))...)))))))((((((.......))))----------)).......))...)).. ( -23.90)
>DroYak_CAF1 29854 96 + 1
-----------------------GCUGGCAAAUCAUGCUGUCUAA-AUUUGUAUUUAUUAGAAAAUGCGCCACGGGGCGUAUGUGUAAUAUGCAAUGCUAUGCCAUUAGAUGCAUUCCAA
-----------------------((.((((.....))))((((((-.........(((((.(..(((((((....))))))).).))))).(((......)))..))))))))....... ( -21.70)
>DroAna_CAF1 15718 94 + 1
-------------------------CGGCAAAUCAUGCUGUCUAA-AUUUGUAUUUAUUAGACAAUGCGCCACAGGGCGUAUGUGUAAUAUGCCAUGCUAUGCCAUUAGAUGCAUUCCAA
-------------------------.((((.((.(((((((((((-...........)))))))(((((((....))))))))))).)).)))).((..((((........))))..)). ( -27.30)
>DroPer_CAF1 29071 119 + 1
UCUGGCUACGAGGCGGACGUUGCUCUGGCAAAUCAUGCUGUCUAA-AUUUGUAUUUAUUAGACAAUGCGCCACGGGGCGUAUGUGUAAUAUGCCAUGCCAUGCCAUUAGAUGCAUUCCAG
(((((((....)))((.(((.((..(((((.((.(((((((((((-...........)))))))(((((((....))))))))))).)).))))).)).)))))..)))).......... ( -35.00)
>consensus
_______________________GCUGGCAAAUCAUGCUGUCUAA_AUUUGUAUUUAUUAGACAAUGCGCCACGGGGCGUAUGUGUAAUAUGCCAUGCUAUGCCAUUAGAUGCAUUCCAA
..........................((((...((((((((((((.(........).)))))))(((((((....))))))).........)).)))...))))................ (-19.09 = -20.32 +   1.22)

alignment

secondary structure

dotplot

Window 3

Location	12,364,911 – 12,365,007
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.83
Mean single sequence MFE	-26.78
Consensus MFE	-18.45
Energy contribution	-19.37
Covariance contribution	0.92
Combinations/Pair	1.14
Mean z-score	-1.62
Structure conservation index	0.69
SVM decision value	0.75
SVM RNA-class probability	0.841463
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12364911 96 - 27905053
UUGGAAUGCAUCUAAUGGCAUAGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAU-UUAGACAGCAUGAUUUGCCAGC-----------------------
(((((.....)))))(((((...((((..............((((....))))..((((((((...........-))))))))))))...)))))..----------------------- ( -25.60)
>DroPse_CAF1 31970 119 - 1
CUGGAAUGCAUCUAAUGGCAUGGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAU-UUAGACAGCAUGAUUUGCCAGAGCAACGUCCGCCUCGUAGCCAGA
((((..(((......(((((...((((..............((((....))))..((((((((...........-))))))))))))...)))))((((.......).)))))).)))). ( -33.00)
>DroGri_CAF1 14481 100 - 1
UUGGAAUGCUUAUAUUGG----------CAUAAUACACAUACGCCCCGUGGCGUUCUGUCUAAUAAAUACAAAUUUUGGACAGCAUGAAUUGCCAGCGGAACUUU--------GCCC--U
..((.(((((......))----------)))..............((((((((..((((((((............)))))))).......))))).)))......--------..))--. ( -23.90)
>DroYak_CAF1 29854 96 - 1
UUGGAAUGCAUCUAAUGGCAUAGCAUUGCAUAUUACACAUACGCCCCGUGGCGCAUUUUCUAAUAAAUACAAAU-UUAGACAGCAUGAUUUGCCAGC-----------------------
(((((.....)))))(((((...(((.((............((((....)))).....(((((...........-)))))..)))))...)))))..----------------------- ( -20.60)
>DroAna_CAF1 15718 94 - 1
UUGGAAUGCAUCUAAUGGCAUAGCAUGGCAUAUUACACAUACGCCCUGUGGCGCAUUGUCUAAUAAAUACAAAU-UUAGACAGCAUGAUUUGCCG-------------------------
(((((.....))))).((((...((((..............((((....))))..((((((((...........-))))))))))))...)))).------------------------- ( -24.60)
>DroPer_CAF1 29071 119 - 1
CUGGAAUGCAUCUAAUGGCAUGGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAU-UUAGACAGCAUGAUUUGCCAGAGCAACGUCCGCCUCGUAGCCAGA
((((..(((......(((((...((((..............((((....))))..((((((((...........-))))))))))))...)))))((((.......).)))))).)))). ( -33.00)
>consensus
UUGGAAUGCAUCUAAUGGCAUAGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAU_UUAGACAGCAUGAUUUGCCAGC_______________________
...............(((((...((((..............((((....))))..((((((((............))))))))))))...)))))......................... (-18.45 = -19.37 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	12,364,928 – 12,365,021
Length	93
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	96.70
Mean single sequence MFE	-22.53
Consensus MFE	-20.30
Energy contribution	-21.13
Covariance contribution	0.83
Combinations/Pair	1.04
Mean z-score	-1.11
Structure conservation index	0.90
SVM decision value	0.09
SVM RNA-class probability	0.577387
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12364928 93 - 27905053
GCUGUCAUGUUGGAUUGGAAUGCAUCUAAUGGCAUAGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAUUUAGA
..((((((((((.((((((.....))))))....))))))))))(((((.(((..((((....))))...))).))))).............. ( -24.10)
>DroPse_CAF1 32010 93 - 1
GCUGUCAUGUUGGACUGGAAUGCAUCUAAUGGCAUGGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAUUUAGA
((((((((((((...((((.....)))).)))))))))..))).(((((.(((..((((....))))...))).))))).............. ( -22.90)
>DroSec_CAF1 33363 93 - 1
GCUGUCAUGUUGGAUUGGACUGCAUCUAAUGGCAUAGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAUUUAGA
..((((((((((.((((((.....))))))....))))))))))(((((.(((..((((....))))...))).))))).............. ( -23.90)
>DroYak_CAF1 29871 93 - 1
GCUGUCAUGUUGGAUUGGAAUGCAUCUAAUGGCAUAGCAUUGCAUAUUACACAUACGCCCCGUGGCGCAUUUUCUAAUAAAUACAAAUUUAGA
..(((..(((((((...((((((...((((((((......))).))))).......(((....))))))))))))))))...)))........ ( -19.60)
>DroAna_CAF1 15733 93 - 1
GCUGUCAUGUCGGUUUGGAAUGCAUCUAAUGGCAUAGCAUGGCAUAUUACACAUACGCCCUGUGGCGCAUUGUCUAAUAAAUACAAAUUUAGA
..((((((((..(((((((.....)))))..))...))))))))(((((.(((..((((....))))...))).))))).............. ( -21.80)
>DroPer_CAF1 29111 93 - 1
GCUGUCAUGUUGGACUGGAAUGCAUCUAAUGGCAUGGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAUUUAGA
((((((((((((...((((.....)))).)))))))))..))).(((((.(((..((((....))))...))).))))).............. ( -22.90)
>consensus
GCUGUCAUGUUGGAUUGGAAUGCAUCUAAUGGCAUAGCAUGGCAUAUUACACAUACGCCCCGUGGCGCAUUGUCUAAUAAAUACAAAUUUAGA
..((((((((((.((((((.....))))))....))))))))))(((((.(((..((((....))))...))).))))).............. (-20.30 = -21.13 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:02 2006