Locus 2935

Sequence ID	X_DroMel_CAF1
Location	7,850,856 – 7,851,084
Length	228
Max. P	0.998178

overview

Window 9

Location	7,850,856 – 7,850,974
Length	118
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	77.36
Mean single sequence MFE	-32.43
Consensus MFE	-23.13
Energy contribution	-23.80
Covariance contribution	0.67
Combinations/Pair	1.11
Mean z-score	-1.92
Structure conservation index	0.71
SVM decision value	1.48
SVM RNA-class probability	0.957806
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7850856 118 + 22224390
UAUAUGGUGUAUGCUAUAUAUGCUAUAUAUGCA-AUACAUAUAGGAUAUGGUACGUGGAUGGCACAGGUCAGGGGGUCAGGAGAGGCCAAUGAUGGCCAUUCUGCGACGUUUGCCAAUU
....((((((((.((((((.(((.......)))-....)))))).)))).((.((..((((((....((((...((((......))))..)))).)))).))..))))....))))... ( -36.70)
>DroEre_CAF1 35616 104 + 1
--CUU--------AUAUAUA-----CAUACAUAUAUAUGGUCUACAUAUAGGAUAUGGAUGGCACAGGUUAGGGGGUCAGGAGGGGCCAAUGAUGGCCAUUCUGCGACGUUUGCCAAUU
--...--------.......-----(((((...((((((.....)))))).).))))..(((((.(.(((.....(.(((((..(((((....))))).))))))))).).)))))... ( -29.20)
>DroYak_CAF1 31145 111 + 1
UACUU--------AUAUAUAUACUACAAACUUAUAUAUAUAUAGAAUAUGGUACGUGGAUGGCACAGGUCAGGGGGUCAGGAGAGGCCAAUGAUGGCCAUUCUGCGACGUUUGCCAAUU
..(((--------(((((((((.........)))))))))).))....(((((((..((((((....((((...((((......))))..)))).)))).))..)).....)))))... ( -31.40)
>consensus
UACUU________AUAUAUAU_CUACAUACAUAUAUAUAUAUAGAAUAUGGUACGUGGAUGGCACAGGUCAGGGGGUCAGGAGAGGCCAAUGAUGGCCAUUCUGCGACGUUUGCCAAUU
..............((((((((.........))))))))....................(((((.(.(((.....(.(((((..(((((....))))).))))))))).).)))))... (-23.13 = -23.80 +   0.67)

alignment

secondary structure

dotplot

Window 0

Location	7,850,856 – 7,850,974
Length	118
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	77.36
Mean single sequence MFE	-26.05
Consensus MFE	-20.52
Energy contribution	-20.97
Covariance contribution	0.45
Combinations/Pair	1.14
Mean z-score	-2.47
Structure conservation index	0.79
SVM decision value	3.03
SVM RNA-class probability	0.998178
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7850856 118 - 22224390
AAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCUCUCCUGACCCCCUGACCUGUGCCAUCCACGUACCAUAUCCUAUAUGUAU-UGCAUAUAUAGCAUAUAUAGCAUACACCAUAUA
...(((((...(((((((...(((((....)))))....)))......))))...))))).....((...((((.((((((((..-...)))))))).))))...))............ ( -28.00)
>DroEre_CAF1 35616 104 - 1
AAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCCCUCCUGACCCCCUAACCUGUGCCAUCCAUAUCCUAUAUGUAGACCAUAUAUAUGUAUG-----UAUAUAU--------AAG--
...(((((...((((..((..(((((....)))))..)).))))...........))))).........((((((((...(((((....)))))-----)))))))--------)..-- ( -22.84)
>DroYak_CAF1 31145 111 - 1
AAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCUCUCCUGACCCCCUGACCUGUGCCAUCCACGUACCAUAUUCUAUAUAUAUAUAAGUUUGUAGUAUAUAUAU--------AAGUA
...(((((...(((((((...(((((....)))))....)))......))))...)))))................(((((((((((.........))))))))))--------).... ( -27.30)
>consensus
AAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCUCUCCUGACCCCCUGACCUGUGCCAUCCACGUACCAUAUCCUAUAUAUAUAUAAGUAUGUAG_AUAUAUAU________AAGUA
...(((((...(((((((...(((((....)))))....)))......))))...)))))..........((((....(((((((....)))))))....))))............... (-20.52 = -20.97 +   0.45)

alignment

secondary structure

dotplot

Window 1

Location	7,850,894 – 7,851,014
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.06
Mean single sequence MFE	-26.58
Consensus MFE	-25.47
Energy contribution	-25.80
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.96
SVM decision value	0.23
SVM RNA-class probability	0.644196
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7850894 120 - 22224390
AUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGAAAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCUCUCCUGACCCCCUGACCUGUGCCAUCCACGUACCAUAUCCUAUA
..((((((((((.(((...))).))))))..............(((((...(((((((...(((((....)))))....)))......))))...))))).......))))......... ( -27.60)
>DroEre_CAF1 35640 120 - 1
AUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGAAAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCCCUCCUGACCCCCUAACCUGUGCCAUCCAUAUCCUAUAUGUAGAC
.(((((((((((.(((...))).))))).)))))).(((....(((((...((((..((..(((((....)))))..)).))))...........)))))..(((((...)))))))).. ( -24.54)
>DroYak_CAF1 31176 120 - 1
AUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGAAAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCUCUCCUGACCCCCUGACCUGUGCCAUCCACGUACCAUAUUCUAUA
..((((((((((.(((...))).))))))..............(((((...(((((((...(((((....)))))....)))......))))...))))).......))))......... ( -27.60)
>consensus
AUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGAAAUUGGCAAACGUCGCAGAAUGGCCAUCAUUGGCCUCUCCUGACCCCCUGACCUGUGCCAUCCACGUACCAUAUCCUAUA
.(((((((((((.(((...))).))))).))))))........(((((...(((((((...(((((....)))))....)))......))))...))))).................... (-25.47 = -25.80 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	7,850,974 – 7,851,084
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.59
Mean single sequence MFE	-32.54
Consensus MFE	-20.95
Energy contribution	-21.89
Covariance contribution	0.94
Combinations/Pair	1.12
Mean z-score	-1.58
Structure conservation index	0.64
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7850974 110 - 22224390
GCACCACUGUGCACACACUGCACUCGGGGGAACGAGUUGUGCAAGUGUU----------UGUGCGAGCAGGACAUACAUCAUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGA
((((((((.((((((......(((((......)))))))))))))))..----------.))))...(((((......)).(((((((((((.(((...))).))))).)))))).))). ( -30.60)
>DroEre_CAF1 35720 106 - 1
GCCCCACUGUGCA--CACUGCACUCGGGGGACAGAGUUGUGCAAGUGU------------UUGCGAGCAGGACAUACAUCAUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGA
.((((...((((.--....))))...)))).(((.(((.(((..((..------------..))..))).)))........(((((((((((.(((...))).))))).)))))).))). ( -33.10)
>DroYak_CAF1 31256 120 - 1
GCACCACUGUGCACACACUGCACUCGGGGGACAGAGUUGUGCAAGUGUGUGUGUGUGUGUGUGCGAGCAGGACAUACAUCAUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGA
(((((((((..((((((((((((((.(....).))...)))).))))))))..)).))).))))...(((((......)).(((((((((((.(((...))).))))).)))))).))). ( -42.10)
>DroAna_CAF1 21361 104 - 1
GUUCCACUGUCCA--UACUGCACUCAUGGGACAGAGUUCCGCAAGUGUG--------------UGAGCGAGACAUACAUCAUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGA
((..(.((((((.--.............)))))).(((((((....)))--------------.)))))..))........(((((((((((.(((...))).))))).))))))..... ( -24.34)
>consensus
GCACCACUGUGCA__CACUGCACUCGGGGGACAGAGUUGUGCAAGUGUG___________GUGCGAGCAGGACAUACAUCAUUGGUUAUUUAUUGGUUUCCACUAAAUAAAUCGAACUGA
.((((...(((((.....)))))...)))).(((.(((.(((..((................))..))).)))........(((((((((((.(((...))).))))).)))))).))). (-20.95 = -21.89 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:04 2006