Locus 3939

Sequence ID	2L_DroMel_CAF1
Location	11,485,404 – 11,485,617
Length	213
Max. P	0.994667

overview

Window 9

Location	11,485,404 – 11,485,503
Length	99
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.58
Mean single sequence MFE	-26.60
Consensus MFE	-21.51
Energy contribution	-21.20
Covariance contribution	-0.31
Combinations/Pair	1.25
Mean z-score	-1.70
Structure conservation index	0.81
SVM decision value	0.54
SVM RNA-class probability	0.773397
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11485404 99 + 22407834
GUCCACCUCCACCA---CCGCCCCAUUAUCCACCACCAGGGGGAUAUCUGUAUGGUGGCCACCAUUGGCAGGGAUAUCCUCCUCCGCCACCUCCGCCU------------------CCUU
...........(((---(((..(...(((((.((....)).)))))...)..)))))).......((((.((((.....))))..)))).........------------------.... ( -26.50)
>DroSec_CAF1 49226 99 + 1
GUCCACCUCCACCA---CCGCCCCAUUAUCCACCACCGGGGGGAUAUCCGUAUGGUGGCCACUAUUGGCAGGGAUAUCCUCCUCCGCCACCUCCGCCU------------------CCUU
...........(((---(((..(...(((((.((....)).)))))...)..)))))).......((((.((((.....))))..)))).........------------------.... ( -26.40)
>DroSim_CAF1 53008 99 + 1
GUCCACCUCCACCA---CCGCCCCACUAUCCACCACCAGGGGGAUAUCCGUAUGGUGGCCACUAUUGGCAGGGAUAUCCCCCUCCGCCACCACCUCCU------------------CCUU
...........(((---(((..(...(((((.((....)).)))))...)..)))))).......((((((((......))))..)))).........------------------.... ( -27.30)
>DroYak_CAF1 54880 120 + 1
GUCCACCUCCACCACCACCACCCCAUUGUCUACCACCGGGGGGAUAUCCGCAUGCUGGUCACUAUUGGCAUGGUCAUCCUCCUCCGCCAACUCCGCCAACUCCGCCGCCUCCGGUACCAU
..................................(((((((((....))((..(.((((.....(((((..((.......))...)))))....)))).)...))...)))))))..... ( -26.20)
>consensus
GUCCACCUCCACCA___CCGCCCCAUUAUCCACCACCAGGGGGAUAUCCGUAUGGUGGCCACUAUUGGCAGGGAUAUCCUCCUCCGCCACCUCCGCCU__________________CCUU
.....................................((((((((((((........((((....))))..))))))))))))..................................... (-21.51 = -21.20 +  -0.31)

alignment

secondary structure

dotplot

Window 0

Location	11,485,481 – 11,485,583
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.23
Mean single sequence MFE	-37.45
Consensus MFE	-27.76
Energy contribution	-28.58
Covariance contribution	0.81
Combinations/Pair	1.05
Mean z-score	-3.26
Structure conservation index	0.74
SVM decision value	2.50
SVM RNA-class probability	0.994667
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11485481 102 + 22407834
CCUCCGCCACCUCCGCCU------------------CCUUCUUCACACCACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGUCCGCAUUGCGGUUGCCCAGGAGGCGGUCCACCUCAA
............((((((------------------(((..................((..((((....))))..)).(((((.((((...)))).)))))))))))))).......... ( -38.40)
>DroSec_CAF1 49303 102 + 1
CCUCCGCCACCUCCGCCU------------------CCUUCAUCACACCACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGUCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAA
............((((((------------------(((..................((..((((....))))..)).(((((.((((...)))).)))))))))))))).......... ( -36.50)
>DroSim_CAF1 53085 102 + 1
CCUCCGCCACCACCUCCU------------------CCUUCAUCACACUACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGCCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAA
........(((.((((((------------------.....................((..((((....))))..)).((((..((((...))))..)))))))))).)))......... ( -33.50)
>DroYak_CAF1 54960 120 + 1
CCUCCGCCAACUCCGCCAACUCCGCCGCCUCCGGUACCAUCACCACAUCACCCGCAACCAUCAGGAUCUCCACCACGAGGGUGUCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAG
.......................((((((((((((......))).........((((((((..((((..((.......))..)))).....))))))))...)))))))))......... ( -41.40)
>consensus
CCUCCGCCACCUCCGCCU__________________CCUUCAUCACACCACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGUCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAA
...(((((.((..............................................((..((((....))))..)).((((..((((...))))..)))).)).))))).......... (-27.76 = -28.58 +   0.81)

alignment

secondary structure

dotplot

Window 1

Location	11,485,481 – 11,485,583
Length	102
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.23
Mean single sequence MFE	-46.45
Consensus MFE	-35.99
Energy contribution	-37.17
Covariance contribution	1.19
Combinations/Pair	1.07
Mean z-score	-2.23
Structure conservation index	0.77
SVM decision value	1.32
SVM RNA-class probability	0.941728
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11485481 102 - 22407834
UUGAGGUGGACCGCCUCCUGGGCAACCGCAAUGCGGACACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUGGUGUGAAGAAGG------------------AGGCGGAGGUGGCGGAGG
.....((.(.(((((((((...((.((((...)))).((((((((..((((....)))).....))))))))...))....)))------------------))))))...).))..... ( -48.10)
>DroSec_CAF1 49303 102 - 1
UUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGACACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUGGUGUGAUGAAGG------------------AGGCGGAGGUGGCGGAGG
.....((.(.(((((((((((....)).((.((((..((((((((..((((....)))).....)))))))).)))).)).)))------------------))))))...).))..... ( -48.70)
>DroSim_CAF1 53085 102 - 1
UUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGGCACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUAGUGUGAUGAAGG------------------AGGAGGUGGUGGCGGAGG
.....((.(.(((((((((((....)).((...((.(((((((((..((((....)))).....))))))).)).)).))....------------------)))))))))).))..... ( -45.80)
>DroYak_CAF1 54960 120 - 1
CUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGACACCCUCGUGGUGGAGAUCCUGAUGGUUGCGGGUGAUGUGGUGAUGGUACCGGAGGCGGCGGAGUUGGCGGAGUUGGCGGAGG
........(.((((((((.((...((((((..(((..(((((((((.(.((....))).))))....))))).)))..)).)))).)))))))))))...((..((...))..))..... ( -43.20)
>consensus
UUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGACACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUGGUGUGAUGAAGG__________________AGGCGGAGGUGGCGGAGG
........(.(((((((((((....)))((.((((..((((((((..((((....)))).....)))))))).)))).))..........................)))))))))..... (-35.99 = -37.17 +   1.19)

alignment

secondary structure

dotplot

Window 2

Location	11,485,503 – 11,485,617
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.03
Mean single sequence MFE	-39.27
Consensus MFE	-32.22
Energy contribution	-32.48
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-1.72
Structure conservation index	0.82
SVM decision value	0.52
SVM RNA-class probability	0.766086
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11485503 114 + 22407834
CUUCACACCACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGUCCGCAUUGCGGUUGCCCAGGAGGCGGUCCACCUCAAAGUGGAUUUCCUGGUACCGAAAGAC------CUCACAACG
......(((.....((.((..((((....))))..)).(((((.((((...)))).))))).))(((..((((((......))))))..))))))..(....)..------......... ( -39.10)
>DroSec_CAF1 49325 114 + 1
CAUCACACCACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGUCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAAAGUGGAUCUCCCGGUACCGAAAGAC------CUCACAACG
......(((.....((.((..((((....))))..)).(((((.((((...)))).))))).)).((.(((((((......))))))).)).)))..(....)..------......... ( -37.40)
>DroSim_CAF1 53107 114 + 1
CAUCACACUACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGCCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAAAAUGGAUCUCCCGGUACCGAAAGAC------CUCACAACG
........((((..((.((..((((....))))..)).((((..((((...))))..)))).)).((.((((((........)))))).)).)))).(....)..------......... ( -35.10)
>DroYak_CAF1 55000 120 + 1
CACCACAUCACCCGCAACCAUCAGGAUCUCCACCACGAGGGUGUCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAGAGUGGAUCGCCUGGUACCGAAAGACACCCAACUCCCAACG
.............((((((((..((((..((.......))..)))).....))))))))...(((((((((((((......)))))))))))(((..(....)..)))......)).... ( -45.50)
>consensus
CAUCACACCACCCCCCACCAUCUGGAUCUCCAGCAGGAGGGUGUCCGCAUUGUGGUUGCCCAGGAGGCGGUCCACCUCAAAGUGGAUCUCCCGGUACCGAAAGAC______CUCACAACG
......(((..((....((..((((....))))..)).((((..((((...))))..)))).)).((.(((((((......))))))).)).)))..(....)................. (-32.22 = -32.48 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	11,485,503 – 11,485,617
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.03
Mean single sequence MFE	-48.53
Consensus MFE	-39.45
Energy contribution	-40.07
Covariance contribution	0.62
Combinations/Pair	1.12
Mean z-score	-1.37
Structure conservation index	0.81
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11485503 114 - 22407834
CGUUGUGAG------GUCUUUCGGUACCAGGAAAUCCACUUUGAGGUGGACCGCCUCCUGGGCAACCGCAAUGCGGACACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUGGUGUGAAG
(((((((((------....)))(((.((((((..((((((....)))))).....))))))...)))))))))....((((((((..((((....)))).....))))))))........ ( -45.80)
>DroSec_CAF1 49325 114 - 1
CGUUGUGAG------GUCUUUCGGUACCGGGAGAUCCACUUUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGACACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUGGUGUGAUG
(((((((.(------((((..((....))..)))((((((....))))))))(((.....)))...)))))))....((((((((..((((....)))).....))))))))........ ( -51.00)
>DroSim_CAF1 53107 114 - 1
CGUUGUGAG------GUCUUUCGGUACCGGGAGAUCCAUUUUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGGCACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUAGUGUGAUG
(((((((.(------((((..((....))..)))((((((....))))))))(((.....)))...)))))))((.(((((((((..((((....)))).....))))))).)).))... ( -48.60)
>DroYak_CAF1 55000 120 - 1
CGUUGGGAGUUGGGUGUCUUUCGGUACCAGGCGAUCCACUCUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGACACCCUCGUGGUGGAGAUCCUGAUGGUUGCGGGUGAUGUGGUG
(((..(((((..(((..(....)..)))..))..((((((.(((((((..((((....(((....)))....)))).)).))))).))))))..)))..)))(..(((.....)))..). ( -48.70)
>consensus
CGUUGUGAG______GUCUUUCGGUACCAGGAGAUCCACUUUGAGGUGGACCGCCUCCUGGGCAACCACAAUGCGGACACCCUCCUGCUGGAGAUCCAGAUGGUGGGGGGUGGUGUGAUG
(((((((((..........)))(((.(((((((.((((((....))))))....)))))))...)))))))))((.(((((((((..((((....)))).....))))))).)).))... (-39.45 = -40.07 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:18 2006