Locus 6249

Sequence ID	2L_DroMel_CAF1
Location	17,355,593 – 17,355,749
Length	156
Max. P	0.988365

overview

Window 4

Location	17,355,593 – 17,355,713
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.28
Mean single sequence MFE	-21.40
Consensus MFE	-20.74
Energy contribution	-20.88
Covariance contribution	0.14
Combinations/Pair	1.08
Mean z-score	-0.99
Structure conservation index	0.97
SVM decision value	0.81
SVM RNA-class probability	0.856852
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17355593 120 + 22407834
UUCCCCUCAAAACCUUCCUCAGUUUGUCUGUUUGGUGAAGCAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGACUAACAGCUUCAAACUCUCGACUCC
.....................(((.(((((...(((...((((...((((......(((((....)))))....))))..)))).)))...))))).))).................... ( -22.40)
>DroSec_CAF1 57437 120 + 1
UUUCCCUCAAAACCUUCCUCAGUUUGUCUGUUUGGUGAAGCAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCC
.....................(((.(((((...(((...((((...((((......(((((....)))))....))))..)))).)))...))))).))).................... ( -21.80)
>DroSim_CAF1 58034 120 + 1
UUCCCCUCAAAACCUUCCUCAGUUUGUCUGUUUGGUGAAGCAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCC
.....................(((.(((((...(((...((((...((((......(((((....)))))....))))..)))).)))...))))).))).................... ( -21.80)
>DroEre_CAF1 55194 120 + 1
UUCCCCUCAAAACCUUCCUCAGUUUGUCUGUUUGGUGAAGCGAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCCCGACUCC
.....................(((.(((((...(((...((((...((((......(((((....)))))....))))..)))).)))...))))).))).................... ( -21.50)
>DroYak_CAF1 51585 120 + 1
UUCCCCUUAAAACCUUCCACAGUUUGUCUGUUUGGUGAAGCGAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCC
.....................(((.(((((...(((...((((...((((......(((((....)))))....))))..)))).)))...))))).))).................... ( -21.50)
>DroAna_CAF1 58030 114 + 1
CUCCCCUC------UCUCUCUCCCUGUCUGUUUGGUGAAGCAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCAACUCC
........------..........((...((((((..(((.((((....)))))))..)(((((.(((((...........)))))((.....))....))))).)))))...))..... ( -19.40)
>consensus
UUCCCCUCAAAACCUUCCUCAGUUUGUCUGUUUGGUGAAGCAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCC
.....................(((.(((((...(((...((((...((((......(((((....)))))....))))..)))).)))...))))).))).................... (-20.74 = -20.88 +   0.14)

alignment

secondary structure

dotplot

Window 5

Location	17,355,633 – 17,355,749
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.26
Mean single sequence MFE	-21.63
Consensus MFE	-20.32
Energy contribution	-20.98
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.94
SVM decision value	2.12
SVM RNA-class probability	0.988365
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17355633 116 + 22407834
CAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGACUAACAGCUUCAAACUCUCGACUCCUUUGGCCCAGGAAUUUUCAGCUACACAACACAACA--C--
................((.(((((((((((...........)))))((((...(.((((..(..((........))..)..))))).)))).....)))))).))..........--.-- ( -17.40)
>DroSec_CAF1 57477 116 + 1
CAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCCUUUGGCCCAGGAAUUUUCAGCUACACAACACAACA--C--
................((.(((((((((((...........)))))((((...((((((..(..((........))..)..)))))))))).....)))))).))..........--.-- ( -24.00)
>DroSim_CAF1 58074 116 + 1
CAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCCUUUGGCCCAGGAAUUUUCAGCUACACAACACAACA--C--
................((.(((((((((((...........)))))((((...((((((..(..((........))..)..)))))))))).....)))))).))..........--.-- ( -24.00)
>DroEre_CAF1 55234 116 + 1
CGAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCCCGACUCCUUUGGCCCAGGAAUUUUCAGCUACACAACGCAACA--C--
.((((.....)))).(((((((((((((((...........)))))((((...((((((..(..((........))..)..)))))))))).....)))))).......))))..--.-- ( -24.61)
>DroYak_CAF1 51625 111 + 1
CGAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCCUUUGGCCCAAGAAUUUUCAGCUACACA-----ACA--C--
.((((.....))))..((.(((((((((((...........))))).......((((((..(..((........))..)..)))))).........)))))).))..-----...--.-- ( -19.40)
>DroAna_CAF1 58064 120 + 1
CAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCAACUCCUUUGGCCCAGGAAUUUUCAGCAACACACCGAGCCAUUCCC
....................((((((((((...........)))))((((...((((((......................)))))))))).....)))))................... ( -20.35)
>consensus
CAAAACCUAUUUUCUUUGCAGCUGAUUGCAUUUUAUAGCAUUGCAACCUGUCAGGCUAACAGCUUCAAACUCUCGACUCCUUUGGCCCAGGAAUUUUCAGCUACACAACACAACA__C__
................((.(((((((((((...........)))))((((...((((((..(..((........))..)..)))))))))).....)))))).))............... (-20.32 = -20.98 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	17,355,633 – 17,355,749
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.26
Mean single sequence MFE	-30.80
Consensus MFE	-26.91
Energy contribution	-26.93
Covariance contribution	0.03
Combinations/Pair	1.04
Mean z-score	-1.29
Structure conservation index	0.87
SVM decision value	-0.01
SVM RNA-class probability	0.526575
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17355633 116 - 22407834
--G--UGUUGUGUUGUGUAGCUGAAAAUUCCUGGGCCAAAGGAGUCGAGAGUUUGAAGCUGUUAGUCUGACAGGUUGCAAUGCUAUAAAAUGCAAUCAGCUGCAAAGAAAAUAGGUUUUG
--.--((((......(((((((((..((((((.......)))))).......(((((.(((((.....))))).)).)))(((........))).))))))))).....))))....... ( -28.90)
>DroSec_CAF1 57477 116 - 1
--G--UGUUGUGUUGUGUAGCUGAAAAUUCCUGGGCCAAAGGAGUCGAGAGUUUGAAGCUGUUAGCCUGACAGGUUGCAAUGCUAUAAAAUGCAAUCAGCUGCAAAGAAAAUAGGUUUUG
--.--((((......(((((((((.....(((((((.((.((..((((....))))..)).)).)))...))))(((((.(.......).)))))))))))))).....))))....... ( -29.50)
>DroSim_CAF1 58074 116 - 1
--G--UGUUGUGUUGUGUAGCUGAAAAUUCCUGGGCCAAAGGAGUCGAGAGUUUGAAGCUGUUAGCCUGACAGGUUGCAAUGCUAUAAAAUGCAAUCAGCUGCAAAGAAAAUAGGUUUUG
--.--((((......(((((((((.....(((((((.((.((..((((....))))..)).)).)))...))))(((((.(.......).)))))))))))))).....))))....... ( -29.50)
>DroEre_CAF1 55234 116 - 1
--G--UGUUGCGUUGUGUAGCUGAAAAUUCCUGGGCCAAAGGAGUCGGGAGUUUGAAGCUGUUAGCCUGACAGGUUGCAAUGCUAUAAAAUGCAAUCAGCUGCAAAGAAAAUAGGUUUCG
--.--(((.(((((((.(((((..((((((((((.((...))..))))))))))..)))))..((((.....))))))))))).)))...((((......))))..((((.....)))). ( -35.00)
>DroYak_CAF1 51625 111 - 1
--G--UGU-----UGUGUAGCUGAAAAUUCUUGGGCCAAAGGAGUCGAGAGUUUGAAGCUGUUAGCCUGACAGGUUGCAAUGCUAUAAAAUGCAAUCAGCUGCAAAGAAAAUAGGUUUCG
--.--...-----..(((((((((((((((((((.((...))..)))))))))).((.(((((.....))))).))....(((........))).)))))))))..((((.....)))). ( -31.20)
>DroAna_CAF1 58064 120 - 1
GGGAAUGGCUCGGUGUGUUGCUGAAAAUUCCUGGGCCAAAGGAGUUGAGAGUUUGAAGCUGUUAGCCUGACAGGUUGCAAUGCUAUAAAAUGCAAUCAGCUGCAAAGAAAAUAGGUUUUG
.....((((((((.(.(((......))).)))))))))..(.((((((..((((..((((((.((((.....)))))))..)))...))))....)))))).)................. ( -30.70)
>consensus
__G__UGUUGUGUUGUGUAGCUGAAAAUUCCUGGGCCAAAGGAGUCGAGAGUUUGAAGCUGUUAGCCUGACAGGUUGCAAUGCUAUAAAAUGCAAUCAGCUGCAAAGAAAAUAGGUUUUG
...............(((((((((..((((((.......)))))).......(((((.(((((.....))))).)).)))(((........))).)))))))))................ (-26.91 = -26.93 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:21 2006