Locus 1194

Sequence ID	3L_DroMel_CAF1
Location	3,380,787 – 3,381,043
Length	256
Max. P	0.999937

overview

Window 0

Location	3,380,787 – 3,380,896
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.57
Mean single sequence MFE	-36.04
Consensus MFE	-33.30
Energy contribution	-33.14
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-3.45
Structure conservation index	0.92
SVM decision value	4.68
SVM RNA-class probability	0.999937
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3380787 109 + 23771897
AACACCAC--AACAAGCGGCAA-------GCAGCAACUAC--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAA
...(((..--..(....)....-------(((((......--...((((((....))))))...((((((.((((((....))))))....)))))).............)))))))).. ( -34.90)
>DroSec_CAF1 48193 111 + 1
AACACCACUAAGCAAGCGGCAA-------GCAGCAACUAC--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAA
...(((.....((.....))..-------(((((......--...((((((....))))))...((((((.((((((....))))))....)))))).............)))))))).. ( -38.30)
>DroSim_CAF1 46370 109 + 1
AACGCCAC--AACAAGCGGUAA-------GCAGCAACUAC--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAA
..(((...--.....)))....-------(((((......--...((((((....))))))...((((((.((((((....))))))....)))))).............)))))..... ( -36.80)
>DroEre_CAF1 47140 89 + 1
-----------------------------GCAGCAACUAC--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAA
-----------------------------(((((......--...((((((....))))))...((((((.((((((....))))))....)))))).............)))))..... ( -33.60)
>DroYak_CAF1 47065 118 + 1
AACACCAC--AACAAGCGGCAAGCAGCAAGCAGCAACUAUAGAAGGGGUUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAA
...(((..--.....((.....)).....(((((...........((((((....))))))...((((((.((((((....))))))....)))))).............)))))))).. ( -36.60)
>consensus
AACACCAC__AACAAGCGGCAA_______GCAGCAACUAC__AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAA
.............................(((((...........((((((....))))))...((((((.((((((....))))))....)))))).............)))))..... (-33.30 = -33.14 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	3,380,787 – 3,380,896
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.57
Mean single sequence MFE	-31.04
Consensus MFE	-25.59
Energy contribution	-26.24
Covariance contribution	0.65
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.82
SVM decision value	0.45
SVM RNA-class probability	0.742834
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3380787 109 - 23771897
UUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--GUAGUUGCUGC-------UUGCCGCUUGUU--GUGGUGUU
.(((((((((.............(((((..((((.((((....)))))))))))))...((((.(((..((((..(..--...)..)))).-------.))).)))))))--)))))).. ( -34.60)
>DroSec_CAF1 48193 111 - 1
UUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--GUAGUUGCUGC-------UUGCCGCUUGCUUAGUGGUGUU
.....(((((((...........(((((..((((.((((....)))))))))))))...((((........))))...--...).))))))-------..((((((.....))))))... ( -33.20)
>DroSim_CAF1 46370 109 - 1
UUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--GUAGUUGCUGC-------UUACCGCUUGUU--GUGGCGUU
...((((((((((..........(((((..((((.((((....)))))))))))))..(((((.((((((((....))--).)).))).))-------))).)))..)))--)))).... ( -31.10)
>DroEre_CAF1 47140 89 - 1
UUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--GUAGUUGCUGC-----------------------------
.....(((((((...........(((((..((((.((((....)))))))))))))...((((........))))...--...).))))))----------------------------- ( -24.60)
>DroYak_CAF1 47065 118 - 1
UUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAACCCCUUCUAUAGUUGCUGCUUGCUGCUUGCCGCUUGUU--GUGGUGUU
.((((((((((((..........(((((..((((.((((....)))))))))))))...((((.(((..((((..........)))).....))).))))..)))..)))--)))))).. ( -31.70)
>consensus
UUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU__GUAGUUGCUGC_______UUGCCGCUUGUU__GUGGUGUU
.....(((((((...........(((((..((((.((((....)))))))))))))...((((........))))........).)))))).........(((((.......)))))... (-25.59 = -26.24 +   0.65)

alignment

secondary structure

dotplot

Window 2

Location	3,380,818 – 3,380,932
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.31
Mean single sequence MFE	-36.20
Consensus MFE	-29.54
Energy contribution	-29.58
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.43
Structure conservation index	0.82
SVM decision value	1.66
SVM RNA-class probability	0.970445
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3380818 114 + 23771897
--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAAUUAUGUGCUUCAAGCA---GCAACAACUACAC-GCCAGCA
--...((((((....))))))...((((((.((((((....))))))....)))))).............(((((((((.((...((((......)---)))..)).))).)-).)))). ( -37.00)
>DroSec_CAF1 48226 114 + 1
--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAAUUAUGUGCUUCAAGCA---GCAACAACUACAC-GCCAGCA
--...((((((....))))))...((((((.((((((....))))))....)))))).............(((((((((.((...((((......)---)))..)).))).)-).)))). ( -37.00)
>DroSim_CAF1 46401 114 + 1
--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAAUUAUGUGCUUCAAGCA---GCAACAACUACAC-GCCAGCA
--...((((((....))))))...((((((.((((((....))))))....)))))).............(((((((((.((...((((......)---)))..)).))).)-).)))). ( -37.00)
>DroEre_CAF1 47151 114 + 1
--AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAAUUAUGUGCUUCAAGCA---GCAACAACUACGC-GCGAGCA
--...((((((....))))))...((((((.((((((....))))))....)))))).............(((((((((......))))....)))---)).........((-....)). ( -37.40)
>DroYak_CAF1 47103 120 + 1
AGAAGGGGUUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAAUUAUGUGCUUCAAGCAGCAGCAACAACUACACUACAAGCA
......(.(((((((..(......((((((.((((((....))))))....))))))...........(((((((((((......))))....))))).)).....)..)))).))).). ( -32.60)
>consensus
__AAGGGGCUGAGUGCGGCCCAUAGACAAAGUUCAACUAAGGUUGAAACCAUUUGUCGGAUUAAAUACGCGCUGCGGUAAUUAUGUGCUUCAAGCA___GCAACAACUACAC_GCCAGCA
.....((((((....))))))...((((((.((((((....))))))....)))))).............(((((.(((.((...(((...........)))..)).)))...)).))). (-29.54 = -29.58 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	3,380,818 – 3,380,932
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.31
Mean single sequence MFE	-34.76
Consensus MFE	-26.74
Energy contribution	-26.78
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.97
Structure conservation index	0.77
SVM decision value	0.02
SVM RNA-class probability	0.542377
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3380818 114 - 23771897
UGCUGGC-GUGUAGUUGUUGC---UGCUUGAAGCACAUAAUUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--
.((((.(-(.(((((((((((---(......)))).)))))))))))))).............(((((..((((.((((....)))))))))))))...((((........))))...-- ( -36.20)
>DroSec_CAF1 48226 114 - 1
UGCUGGC-GUGUAGUUGUUGC---UGCUUGAAGCACAUAAUUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--
.((((.(-(.(((((((((((---(......)))).)))))))))))))).............(((((..((((.((((....)))))))))))))...((((........))))...-- ( -36.20)
>DroSim_CAF1 46401 114 - 1
UGCUGGC-GUGUAGUUGUUGC---UGCUUGAAGCACAUAAUUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--
.((((.(-(.(((((((((((---(......)))).)))))))))))))).............(((((..((((.((((....)))))))))))))...((((........))))...-- ( -36.20)
>DroEre_CAF1 47151 114 - 1
UGCUCGC-GCGUAGUUGUUGC---UGCUUGAAGCACAUAAUUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU--
.(((.((-(.(((((((((((---(......)))).)))))))))))))).............(((((..((((.((((....)))))))))))))...((((........))))...-- ( -36.20)
>DroYak_CAF1 47103 120 - 1
UGCUUGUAGUGUAGUUGUUGCUGCUGCUUGAAGCACAUAAUUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAACCCCUUCU
...(((.(((((((((((.(.((((......))))))))))))).((.((.((((........(((((..((((.((((....))))))))))))))))).)).))))))))........ ( -29.00)
>consensus
UGCUGGC_GUGUAGUUGUUGC___UGCUUGAAGCACAUAAUUACCGCAGCGCGUAUUUAAUCCGACAAAUGGUUUCAACCUUAGUUGAACUUUGUCUAUGGGCCGCACUCAGCCCCUU__
.(((.((.(.(((((((((((...........))).)))))))))))))).............(((((..((((.((((....)))))))))))))...((((........))))..... (-26.74 = -26.78 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	3,380,932 – 3,381,043
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.80
Mean single sequence MFE	-34.04
Consensus MFE	-28.90
Energy contribution	-28.46
Covariance contribution	-0.44
Combinations/Pair	1.14
Mean z-score	-1.41
Structure conservation index	0.85
SVM decision value	0.46
SVM RNA-class probability	0.744949
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3380932 111 - 23771897
GCUAUAUAGCUUUGGCUAUAAAGGCCCAGCUGAAUCUGAAGUUCGAAACUUGUUUCGGCUUUCGG---------GGCUUUCGAAGUCGCAUUCUCAGCAUGUUUGCCAUGUUGUCUAUGU
(((.((((((....))))))((((((((((((((....((((.....))))..)))))))....)---------))))))...))).((((...(((((((.....)))))))...)))) ( -34.10)
>DroSec_CAF1 48340 120 - 1
GCUAUAUAGCUUUGGCUAUAAAGGCCCAGCUGAAUCUGAAGUUGGAAACUUGUUUCGGCUUUCGGUGCUUUCGAGGCUUUCGAAGUCGCAUUCUCAGCGUGUUUGCCAUGUUGUCUAUGU
(((.((((((....))))))..)))((((((........))))))...........(((((.(((.(((.....)))..))))))))((((...(((((((.....)))))))...)))) ( -35.30)
>DroSim_CAF1 46515 111 - 1
GCUAUAUAGCUUUGGCUAUAAAGGCCCAGCUGAAUCUGAAGUUGGAAACUUGUUUCGGCUUUCGG---------GGCUUUCGAAGUCGCAUUCUCAGCGUGUUUGCCAUGUUGUCUAUGU
(((.((((((....))))))((((((((((((((....((((.....))))..)))))))....)---------))))))...))).((((...(((((((.....)))))))...)))) ( -33.70)
>DroEre_CAF1 47265 111 - 1
GCUAUAUAGCUCUGGCCAUAAAGGCCCAGCCGAAUCCGAAGUUGGAAACUUGUUUCGGCUUUUGG---------GGCUCUCGAAGUCGCAUUCUCAGCAUGUUUGCCAUGUUGUCUAUGU
(((....((((((((((.....)))).(((((((((((....)))).......)))))))...))---------)))).....))).((((...(((((((.....)))))))...)))) ( -34.31)
>DroYak_CAF1 47223 111 - 1
GCUAUAUAGCUUCGAGUAUAAAGCACCAGCUGAGUCUGAAGUUGGAAACUUGUUUCGGCUUUCGG---------GGCUUUCGAAGUCGCAUUCUCAGCGUGUUUGCCAUGUUGUCUAUGU
........(((((((.....((((.((....(((.((((((..(....)...)))))))))...)---------)))))))))))).((((...(((((((.....)))))))...)))) ( -32.80)
>consensus
GCUAUAUAGCUUUGGCUAUAAAGGCCCAGCUGAAUCUGAAGUUGGAAACUUGUUUCGGCUUUCGG_________GGCUUUCGAAGUCGCAUUCUCAGCGUGUUUGCCAUGUUGUCUAUGU
......(((((..((((.....)))).)))))...((((((((((((.....))))))).))))).........((((.....))))((((...(((((((.....)))))))...)))) (-28.90 = -28.46 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:47 2006