Locus 2704

Sequence ID	3R_DroMel_CAF1
Location	7,276,403 – 7,276,538
Length	135
Max. P	0.793285

overview

Window 1

Location	7,276,403 – 7,276,513
Length	110
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	85.38
Mean single sequence MFE	-28.73
Consensus MFE	-23.30
Energy contribution	-23.63
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.81
SVM decision value	0.48
SVM RNA-class probability	0.751354
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7276403 110 + 27905053
AAAGUGCUUAAAAAAAAAACAAAUAUAUCGGACGGGAUAUUUUGGGAACUGGCCAUUCAUAACGCCCCUCCAGAGAGAUUUAUUAGAUCGAUUGGCCAGUGACAAGAGCU----------
.....((((..........((((.(((((......)))))))))(..((((((((.((.........((....)).((((.....)))))).))))))))..)..)))).---------- ( -29.30)
>DroSim_CAF1 1492 102 + 1
AAAGUGCUUAAAAAAA--------AUAUCGGACGGGAUAUUUUGGGAACAGGCCAUUCAUAACGCCCCUCCAGAGAGAUUUAUUAGAUCGAUUGGCCAGUGACAAGAGCU----------
.....((((....(((--------(((((......)))))))).(..((.(((((.((.........((....)).((((.....)))))).))))).))..)..)))).---------- ( -24.40)
>DroYak_CAF1 2066 108 + 1
AAAGUGCCUCAAA-----------AUAUCGGACG-GAUAUUUUGGGAACUGGCCAUUCAUAACGCCCCUCCAGAGAGAUUUAUUAGAUCGAUUGGCCAGUGACAAGAGCUGAAGCAAAGC
....(((((((((-----------(((((.....-))))))))))).((((((((.((.........((....)).((((.....)))))).)))))))).............))).... ( -32.50)
>consensus
AAAGUGCUUAAAAAAA________AUAUCGGACGGGAUAUUUUGGGAACUGGCCAUUCAUAACGCCCCUCCAGAGAGAUUUAUUAGAUCGAUUGGCCAGUGACAAGAGCU__________
.....((..................((((......))))(((((...((((((((.((.........((....)).((((.....)))))).))))))))..)))))))........... (-23.30 = -23.63 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	7,276,403 – 7,276,513
Length	110
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	85.38
Mean single sequence MFE	-26.60
Consensus MFE	-22.62
Energy contribution	-22.73
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.85
SVM decision value	0.17
SVM RNA-class probability	0.618579
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7276403 110 - 27905053
----------AGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCAGUUCCCAAAAUAUCCCGUCCGAUAUAUUUGUUUUUUUUUUAAGCACUUU
----------.(((......((((((((.(((...((((...((((....))))...))))))).))))))))...(((((((((......))))).))))...........)))..... ( -25.80)
>DroSim_CAF1 1492 102 - 1
----------AGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCUGUUCCCAAAAUAUCCCGUCCGAUAU--------UUUUUUUAAGCACUUU
----------.(((......((.(((((.(((...((((...((((....))))...))))))).))))).))....((((((((......)))))--------))).....)))..... ( -21.90)
>DroYak_CAF1 2066 108 - 1
GCUUUGCUUCAGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCAGUUCCCAAAAUAUC-CGUCCGAUAU-----------UUUGAGGCACUUU
....((((((..........((((((((.(((...((((...((((....))))...))))))).))))))))....((((((((-.....)))))-----------))))))))).... ( -32.10)
>consensus
__________AGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCAGUUCCCAAAAUAUCCCGUCCGAUAU________UUUUUUUAAGCACUUU
...........(((.(((..((((((((.(((...((((...((((....))))...))))))).))))))))...))).(((((......)))))................)))..... (-22.62 = -22.73 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	7,276,443 – 7,276,538
Length	95
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.28
Mean single sequence MFE	-33.90
Consensus MFE	-28.98
Energy contribution	-29.09
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.68
Structure conservation index	0.85
SVM decision value	0.59
SVM RNA-class probability	0.793285
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7276443 95 - 27905053
UGUACAUUUGGGCGGCAAUAUGCGC-------------------------AGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCAGUUCCCAAA
......((((((.(((((...((..-------------------------.))..)))))((((((((.(((...((((...((((....))))...))))))).)))))))).)))))) ( -30.40)
>DroSim_CAF1 1524 95 - 1
UGUACAUUUGGGCGGCGAAAUGCGC-------------------------AGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCUGUUCCCAAA
.(((((...((((.(((.....)))-------------------------.)))).))).)).(((((.(((...((((...((((....))))...))))))).))))).......... ( -26.00)
>DroYak_CAF1 2094 120 - 1
UGUACAUUUGGGCGGCGAAAUGCGCAGAGCUUGCGAAAGCGCUUUGCUUCAGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCAGUUCCCAAA
......((((((.(((((...(((((((((..((....)))))))))....))..)))))((((((((.(((...((((...((((....))))...))))))).)))))))).)))))) ( -45.30)
>consensus
UGUACAUUUGGGCGGCGAAAUGCGC_________________________AGCUCUUGUCACUGGCCAAUCGAUCUAAUAAAUCUCUCUGGAGGGGCGUUAUGAAUGGCCAGUUCCCAAA
......((((((.(((((...((............................))..)))))((((((((.(((...((((...((((....))))...))))))).)))))))).)))))) (-28.98 = -29.09 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:44 2006