Locus 9376

Sequence ID	3R_DroMel_CAF1
Location	24,899,935 – 24,900,083
Length	148
Max. P	0.996848

overview

Window 4

Location	24,899,935 – 24,900,043
Length	108
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	95.66
Mean single sequence MFE	-34.33
Consensus MFE	-33.94
Energy contribution	-34.25
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-2.49
Structure conservation index	0.99
SVM decision value	2.13
SVM RNA-class probability	0.988724
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24899935 108 + 27905053
----GUGUAUCUGUCAUUGUGUUUGCUUAGGUAACGCGGGAGAGAGUGAGAUGGUCAGAUGGGGCUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUA
----...(((((((((.....(((((........(((........)))...(((((((......)))).))))))))....)))))))))(((((((......)).))))). ( -31.10)
>DroSec_CAF1 12951 110 + 1
--GUGGGUAUCUGUCAGUGUGUUUGCAUAGGUAACGCGGGAGAGAGCGAGAUGGUCAGAUGGGGCUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUA
--(..(((((((((((((.(.(((((........(((........)))...(((((((......)))).))))))))).))))))))))..)))..)............... ( -37.00)
>DroSim_CAF1 12282 112 + 1
GUGUGUGUAUCUGUCAGUGUGUUUGCAUAGGUAACGCGGGAGAGAGCGAGAUGGUCAGAUGGGGCUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUA
.......(((((((((((.(.(((((........(((........)))...(((((((......)))).))))))))).)))))))))))(((((((......)).))))). ( -35.90)
>DroYak_CAF1 13125 111 + 1
-UGUGUGUAUCUGUCAUUGUGUUUGCAUAGGUAACGCGGGAGAGAGCGAGAUGGUCAGAUGGGGCUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCAAUGAGGUGAGGUUA
-......(((((((((.....(((((........(((........)))...(((((((......)))).))))))))....)))))))))(((((((......)).))))). ( -33.30)
>consensus
__GUGUGUAUCUGUCAGUGUGUUUGCAUAGGUAACGCGGGAGAGAGCGAGAUGGUCAGAUGGGGCUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUA
.......(((((((((((.(.(((((........(((........)))...(((((((......)))).))))))))).)))))))))))(((((((......)).))))). (-33.94 = -34.25 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	24,899,935 – 24,900,043
Length	108
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	95.66
Mean single sequence MFE	-23.90
Consensus MFE	-23.02
Energy contribution	-23.27
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-3.65
Structure conservation index	0.96
SVM decision value	2.31
SVM RNA-class probability	0.992084
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24899935 108 - 27905053
UAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAGCCCCAUCUGACCAUCUCACUCUCUCCCGCGUUACCUAAGCAAACACAAUGACAGAUACAC----
.((((((........).)))))(((((((((.......(.(((.((((......))))))).)............((.........))........)))))))))...---- ( -21.80)
>DroSec_CAF1 12951 110 - 1
UAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAGCCCCAUCUGACCAUCUCGCUCUCUCCCGCGUUACCUAUGCAAACACACUGACAGAUACCCAC--
.((((((........).)))))(((((((((.......(((((.((((......)))))))....))........((((.....))))........))))))))).....-- ( -24.20)
>DroSim_CAF1 12282 112 - 1
UAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAGCCCCAUCUGACCAUCUCGCUCUCUCCCGCGUUACCUAUGCAAACACACUGACAGAUACACACAC
.((((((........).)))))(((((((((.......(((((.((((......)))))))....))........((((.....))))........)))))))))....... ( -24.20)
>DroYak_CAF1 13125 111 - 1
UAACCUCACCUCAUUGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAGCCCCAUCUGACCAUCUCGCUCUCUCCCGCGUUACCUAUGCAAACACAAUGACAGAUACACACA-
.(((((((......)).)))))(((((((((.......(((((.((((......)))))))....))........((((.....))))........)))))))))......- ( -25.40)
>consensus
UAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAGCCCCAUCUGACCAUCUCGCUCUCUCCCGCGUUACCUAUGCAAACACAAUGACAGAUACACAC__
.((((((........).)))))(((((((((.......(.(((.((((......))))))).)............((((.....))))........)))))))))....... (-23.02 = -23.27 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	24,899,964 – 24,900,083
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.99
Mean single sequence MFE	-37.48
Consensus MFE	-34.48
Energy contribution	-34.76
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-1.30
Structure conservation index	0.92
SVM decision value	0.26
SVM RNA-class probability	0.658075
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24899964 119 + 27905053
ACGCGGGAGAGAGUGAGAUGGUCAGAUGGGG-CUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUAUGUUUACUGGACCACCUUCGCAGGUUCGCUCAAACAAAUA
..........((((((....(((((....((-(...)))..(....).)))))......((((((((..(((((.(((.......)))....)))))))))))))))))))......... ( -36.20)
>DroSec_CAF1 12982 119 + 1
ACGCGGGAGAGAGCGAGAUGGUCAGAUGGGG-CUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUAUGUUUACUGGACCACCUUCGCAGGUUCGCUCAAACAAAUA
..........((((((....(((((....((-(...)))..(....).)))))......((((((((..(((((.(((.......)))....)))))))))))))))))))......... ( -38.10)
>DroSim_CAF1 12315 119 + 1
ACGCGGGAGAGAGCGAGAUGGUCAGAUGGGG-CUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUAUGUUUACUGGACCACCUUCGCAGGUUCGCUCAAACAAAUA
..........((((((....(((((....((-(...)))..(....).)))))......((((((((..(((((.(((.......)))....)))))))))))))))))))......... ( -38.10)
>DroEre_CAF1 13074 120 + 1
GCGCGGGAGAGAGCGAGAUGGUCAGAUGGGGCCUGAGCCAACGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUAUGUUUACUGGACCACCUUCGCAGGUUCGCUCAAACAAAUA
..........((((((....(((((....(((....)))..(....).)))))......((((((((..(((((.(((.......)))....)))))))))))))))))))......... ( -39.50)
>DroYak_CAF1 13157 119 + 1
ACGCGGGAGAGAGCGAGAUGGUCAGAUGGGG-CUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCAAUGAGGUGAGGUUAUGUUUACUGGACCACCUUCGCAGGUUCCCUCAAACAAAUA
..(.(((((...(((((.((((((((((..(-((..(((..(....)((((.(((......)))))))..)))..)))..)))))....)))))..)))))...))))).)......... ( -35.50)
>consensus
ACGCGGGAGAGAGCGAGAUGGUCAGAUGGGG_CUGAGCCAGCGAGAGAUUGACAGAUAAACCUGCGAUGAGGUGAGGUUAUGUUUACUGGACCACCUUCGCAGGUUCGCUCAAACAAAUA
..........((((((....(((((.(((........))).(....).)))))......((((((((..(((((.(((.......)))....)))))))))))))))))))......... (-34.48 = -34.76 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	24,899,964 – 24,900,083
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.99
Mean single sequence MFE	-33.18
Consensus MFE	-30.37
Energy contribution	-30.61
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.24
Structure conservation index	0.92
SVM decision value	2.76
SVM RNA-class probability	0.996848
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24899964 119 - 27905053
UAUUUGUUUGAGCGAACCUGCGAAGGUGGUCCAGUAAACAUAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAG-CCCCAUCUGACCAUCUCACUCUCUCCCGCGU
...(((...((..((((((((((((((((................))))))..)))))))))).))...))).....((((((.((((-......)))))))..............))). ( -30.02)
>DroSec_CAF1 12982 119 - 1
UAUUUGUUUGAGCGAACCUGCGAAGGUGGUCCAGUAAACAUAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAG-CCCCAUCUGACCAUCUCGCUCUCUCCCGCGU
.........((((((((((((((((((((................))))))..)))))))).................(.(((.((((-......))))))).))))))).......... ( -34.09)
>DroSim_CAF1 12315 119 - 1
UAUUUGUUUGAGCGAACCUGCGAAGGUGGUCCAGUAAACAUAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAG-CCCCAUCUGACCAUCUCGCUCUCUCCCGCGU
.........((((((((((((((((((((................))))))..)))))))).................(.(((.((((-......))))))).))))))).......... ( -34.09)
>DroEre_CAF1 13074 120 - 1
UAUUUGUUUGAGCGAACCUGCGAAGGUGGUCCAGUAAACAUAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGUUGGCUCAGGCCCCAUCUGACCAUCUCGCUCUCUCCCGCGC
.....((((((((((((((((((((((((................))))))..))))))))))......((((.....))))))))))))...............(((........))). ( -35.19)
>DroYak_CAF1 13157 119 - 1
UAUUUGUUUGAGGGAACCUGCGAAGGUGGUCCAGUAAACAUAACCUCACCUCAUUGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAG-CCCCAUCUGACCAUCUCGCUCUCUCCCGCGU
...........((((....((((.((((((((((.......(((((((......)).)))))...)))..........((((...)))-).......)))))))))))....)))).... ( -32.50)
>consensus
UAUUUGUUUGAGCGAACCUGCGAAGGUGGUCCAGUAAACAUAACCUCACCUCAUCGCAGGUUUAUCUGUCAAUCUCUCGCUGGCUCAG_CCCCAUCUGACCAUCUCGCUCUCUCCCGCGU
.........((((((((((((((((((((................))))))..)))))))).................(.(((.((((.......))))))).))))))).......... (-30.37 = -30.61 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:33:03 2006