Locus 487

Sequence ID	2R_DroMel_CAF1
Location	2,701,550 – 2,701,669
Length	119
Max. P	0.989359

overview

Window 2

Location	2,701,550 – 2,701,640
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-30.18
Consensus MFE	-25.68
Energy contribution	-25.32
Covariance contribution	-0.36
Combinations/Pair	1.14
Mean z-score	-2.12
Structure conservation index	0.85
SVM decision value	2.16
SVM RNA-class probability	0.989359
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2701550 90 - 20766785
AAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGUCCGCCAGCCAAACUAGUUUGGGCGAAAGCCCGGCGAUCUAAUGAGCC
..(((((((((......))))))..............(((((((.(((....(((....)))((((....))))))))))))))..))). ( -33.80)
>DroSec_CAF1 16475 90 - 1
AAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCCAAACUAGUUUGGGCGAAAGCCAAGAGAUCUAAUGAGCC
..(((..((((((.(..((((...................)))).)))))))....(((.((.(((....)))....)).)))...))). ( -29.71)
>DroSim_CAF1 13875 90 - 1
AAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCCAAACUAGUUUGGGCGAAAGCCAAGAGAUCUAAUGAGCC
..(((..((((((.(..((((...................)))).)))))))....(((.((.(((....)))....)).)))...))). ( -29.71)
>DroEre_CAF1 13890 90 - 1
AAGUUGCGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCGAAACUAGUUUGGGCCAAAGCCAAGCGAUCUAAUGAGCC
...(((((((.(((((((((.((.........)).)))).)))))))).)))).....((((((.......))))))............. ( -28.20)
>DroYak_CAF1 13561 90 - 1
AAGUUACGGCUGGGCCAUGCCGUAAUAAUUACAAAGUUUAGGCCUGCCAGCCAAACUAGUUUGGGCGAAAGCCAAGCGAUCUAAUGAGCC
..((((((((........))))))))........(((((.(((......)))))))).((((((.(....)))))))............. ( -29.50)
>consensus
AAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCCAAACUAGUUUGGGCGAAAGCCAAGCGAUCUAAUGAGCC
..(((..(((.(((((((((.(((.....)))...)))).))))))))...............(((....))).............))). (-25.68 = -25.32 +  -0.36)

alignment

secondary structure

dotplot

Window 3

Location	2,701,574 – 2,701,669
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	92.84
Mean single sequence MFE	-29.66
Consensus MFE	-23.93
Energy contribution	-23.97
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	0.81
SVM decision value	0.47
SVM RNA-class probability	0.750792
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2701574 95 + 20766785
GCCCAAACUAGUUUGGCUGGCGGACCUAAACUGUGUAAUUAUUACGGCCUGGCCCAGCCGUAGCUUUCAGAGGCUCAAAUUAUAGUUUGGCAGUA
(((.((((((....((((((..(.((....(((((.......)))))...)))))))))(.(((((....))))))......))))))))).... ( -29.70)
>DroSec_CAF1 16499 95 + 1
GCCCAAACUAGUUUGGCUGGCGGGCCUAAACUGUGUAAUUAUUACGGCCUGGCCCAGCCGUAGCUUUCAGAGUCUCAAAUUAUAGUUCGGCGGUA
(((..(((((((((((..((((((((....(((((.......)))))...))))).)))...((((...)))).))))))..))))).))).... ( -30.20)
>DroSim_CAF1 13899 95 + 1
GCCCAAACUAGUUUGGCUGGCGGGCCUAAACUGUGUAAUUAUUACGGCCUGGCCCAGCCGUAGCUUUCAGAGUCUCAAAUUAUAGUUCGGCGGUA
(((..(((((((((((..((((((((....(((((.......)))))...))))).)))...((((...)))).))))))..))))).))).... ( -30.20)
>DroEre_CAF1 13914 95 + 1
GCCCAAACUAGUUUCGCUGGCGGGCCUAAACUGUGUAAUUAUUACGGCCUGGCCCAGCCGCAACUUUCAGAGGCUCAAACCAUAGUUCGGCCAUA
(((..(((((.....((.((((((((....(((((.......)))))...))))).)))))..........((......)).))))).))).... ( -30.40)
>DroYak_CAF1 13585 95 + 1
GCCCAAACUAGUUUGGCUGGCAGGCCUAAACUUUGUAAUUAUUACGGCAUGGCCCAGCCGUAACUUCCAGAGGCUAAAAUUAUAGUUCGGCCGUA
(((..(((((.((((((.((....))....(((((......(((((((........)))))))....)))))))))))....))))).))).... ( -27.80)
>consensus
GCCCAAACUAGUUUGGCUGGCGGGCCUAAACUGUGUAAUUAUUACGGCCUGGCCCAGCCGUAGCUUUCAGAGGCUCAAAUUAUAGUUCGGCCGUA
(((......(((((((((((((((((...................))))))..))))))).))))....(((.((........)))))))).... (-23.93 = -23.97 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	2,701,574 – 2,701,669
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	92.84
Mean single sequence MFE	-29.42
Consensus MFE	-26.40
Energy contribution	-25.72
Covariance contribution	-0.68
Combinations/Pair	1.16
Mean z-score	-1.60
Structure conservation index	0.90
SVM decision value	1.54
SVM RNA-class probability	0.962495
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2701574 95 - 20766785
UACUGCCAAACUAUAAUUUGAGCCUCUGAAAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGUCCGCCAGCCAAACUAGUUUGGGC
.....((((((((...((((.((.......(((....)))(((((((((.((.........)).)))).)))))....)))))).)))))))).. ( -28.00)
>DroSec_CAF1 16499 95 - 1
UACCGCCGAACUAUAAUUUGAGACUCUGAAAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCCAAACUAGUUUGGGC
.....((((((((...((((.(...(((..(((....)))(((((((((.((.........)).)))).)))))..)))))))).)))))))).. ( -28.40)
>DroSim_CAF1 13899 95 - 1
UACCGCCGAACUAUAAUUUGAGACUCUGAAAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCCAAACUAGUUUGGGC
.....((((((((...((((.(...(((..(((....)))(((((((((.((.........)).)))).)))))..)))))))).)))))))).. ( -28.40)
>DroEre_CAF1 13914 95 - 1
UAUGGCCGAACUAUGGUUUGAGCCUCUGAAAGUUGCGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCGAAACUAGUUUGGGC
...(.((((((((.(((....)))........(((((((.(((((((((.((.........)).)))).)))))))).))))...)))))))).) ( -33.60)
>DroYak_CAF1 13585 95 - 1
UACGGCCGAACUAUAAUUUUAGCCUCUGGAAGUUACGGCUGGGCCAUGCCGUAAUAAUUACAAAGUUUAGGCCUGCCAGCCAAACUAGUUUGGGC
...(.(((((((....((((((...))))))((((((((........))))))))........(((((.(((......))))))))))))))).) ( -28.70)
>consensus
UACCGCCGAACUAUAAUUUGAGCCUCUGAAAGCUACGGCUGGGCCAGGCCGUAAUAAUUACACAGUUUAGGCCCGCCAGCCAAACUAGUUUGGGC
.....((((((((...(((.((...)).)))(((..(((.(((((((((.(((.....)))...)))).))))))))))).....)))))))).. (-26.40 = -25.72 +  -0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:52 2006