Locus 1951

Sequence ID	3R_DroMel_CAF1
Location	5,504,051 – 5,504,209
Length	158
Max. P	0.984794

overview

Window 5

Location	5,504,051 – 5,504,169
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.09
Mean single sequence MFE	-39.14
Consensus MFE	-29.46
Energy contribution	-29.90
Covariance contribution	0.44
Combinations/Pair	1.18
Mean z-score	-1.54
Structure conservation index	0.75
SVM decision value	0.02
SVM RNA-class probability	0.544025
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5504051 118 + 27905053
CGGAGGGUCCAGUGUUUGAGGUUAUGUU-UUCGGCUGGCGGUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUUGCCUGGGCUUAUGGUUUAUGCAAAUCUAGCUAGCUGGGAAGCUAUUUA
.((.....))................((-..((((((((((.(((((...))))).)).((((((((-(...((....))....))))))))).......))))))))..))........ ( -37.20)
>DroSec_CAF1 3743 116 + 1
CGGAGGGUCCAGUGUUUGAGGUUAUGUU-UUCGGCUGGCGGUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUCGCCUGGGCCUACGGUUUAUGCAAAU--GGCUAGCUGGGCAGCUAUUUG
((..((((((((.((..(((..((((((-....(((((((....))))).))......))))))..)-))..)))))))))).)).......(((((--((((.((...))))))))))) ( -42.20)
>DroSim_CAF1 4204 116 + 1
CGGAGGGUCCAGUGUUUGAGGUUAUGUU-UUCGGCUGGCGGUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUCGCCUGGGCCUACGGUUUAUGCAAAU--GGCUAGCUGGGCAGCUAUUUG
((..((((((((.((..(((..((((((-....(((((((....))))).))......))))))..)-))..)))))))))).)).......(((((--((((.((...))))))))))) ( -42.20)
>DroEre_CAF1 3717 114 + 1
CGGAUGGUCCAGUCUUUGAGGUUAUGUU-UUCGGCUGGCUCUAAUGCCGUGGAUUUUCGGCAUGAACCUUUGGCCUGGGCUUAUGGUUUAUGCAAAU--GGUCAGUUC---UGCUAUUUG
((((.(((((((((...((((......)-)))))))(((......)))..)))))))))(((((((((...(((....)))...)))))))))((((--((.((....---)))))))). ( -37.90)
>DroYak_CAF1 3876 114 + 1
CGGAGGGUCCAGUCUUUGAGGUUAUGUUCUUCGGCUGGCGCUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUCGCCUGGGCUUAUGGUUUAUGCAAAU--GGUCAGCUC---GUUUAUUUG
..((((((((.(((.((((((.......))))))..)))....((((((........))))))))))-))))....(((((.((.((((....))))--.)).)))))---......... ( -36.20)
>consensus
CGGAGGGUCCAGUGUUUGAGGUUAUGUU_UUCGGCUGGCGGUAAUGCCGUGCAUUUUCGGCAUGGAC_UUUCGCCUGGGCUUAUGGUUUAUGCAAAU__GGCUAGCUGGG_AGCUAUUUG
.((.....))........((((...(((.((((((((((....((((((........)))))).........((.((((((...)))))).)).......)))))))))).))).)))). (-29.46 = -29.90 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	5,504,090 – 5,504,209
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.80
Mean single sequence MFE	-44.28
Consensus MFE	-33.72
Energy contribution	-33.44
Covariance contribution	-0.28
Combinations/Pair	1.17
Mean z-score	-2.87
Structure conservation index	0.76
SVM decision value	1.99
SVM RNA-class probability	0.984794
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5504090 119 + 27905053
GUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUUGCCUGGGCUUAUGGUUUAUGCAAAUCUAGCUAGCUGGGAAGCUAUUUACAUAGUUCGUGCACCCGCUUCCAGAAAGUCCGACGCGAGU
...((((((........))))))((((-((((((...((((...(((((....))))).)))).))..((((((....(((.......))).....)))))).)))))))).((....)) ( -36.90)
>DroSec_CAF1 3782 117 + 1
GUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUCGCCUGGGCCUACGGUUUAUGCAAAU--GGCUAGCUGGGCAGCUAUUUGCAUAGUUCGUGCACCCGCUUCCAGAAUGUCCGACGCGAGU
...((((((........))))))((((-.(((...((((..((((..((((((((((--((((.((...))))))))))))))))..))))..))))......))).)))).((....)) ( -48.20)
>DroSim_CAF1 4243 117 + 1
GUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUCGCCUGGGCCUACGGUUUAUGCAAAU--GGCUAGCUGGGCAGCUAUUUGCAUAGUUCGUGCACCCGCUUCCAGAAAGUCCGACGCGAGU
...((((((........))))))((((-((((...((((..((((..((((((((((--((((.((...))))))))))))))))..))))..))))......)))))))).((....)) ( -52.30)
>DroEre_CAF1 3756 115 + 1
CUAAUGCCGUGGAUUUUCGGCAUGAACCUUUGGCCUGGGCUUAUGGUUUAUGCAAAU--GGUCAGUUC---UGCUAUUUGCAUAAUUCGUGCACCCGGUUCCAGAAAGUCCGUUGCGAGU
....(((..(((((((((((......))..(((.(((((..((((..((((((((((--((.((....---))))))))))))))..))))..)))))..))))))))))))..)))... ( -45.90)
>DroYak_CAF1 3916 114 + 1
CUAAUGCCGUGCAUUUUCGGCAUGGAC-UUUCGCCUGGGCUUAUGGUUUAUGCAAAU--GGUCAGCUC---GUUUAUUUGCAUAGUUCGUGCACCCGCUUCCAGAAUGUCCGACGCGAGU
...((((((........))))))((((-.(((...((((..((((..((((((((((--((.(.....---).))))))))))))..))))..))))......))).)))).((....)) ( -38.10)
>consensus
GUAAUGCCGUGCAUUUUCGGCAUGGAC_UUUCGCCUGGGCUUAUGGUUUAUGCAAAU__GGCUAGCUGGG_AGCUAUUUGCAUAGUUCGUGCACCCGCUUCCAGAAAGUCCGACGCGAGU
...((((((........))))))((((.(((....((((..((((..((((((((((..((((........))))))))))))))..))))..))))......))).))))......... (-33.72 = -33.44 +  -0.28)

alignment

secondary structure

dotplot

Window 7

Location	5,504,090 – 5,504,209
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.80
Mean single sequence MFE	-37.29
Consensus MFE	-27.57
Energy contribution	-27.81
Covariance contribution	0.24
Combinations/Pair	1.11
Mean z-score	-2.22
Structure conservation index	0.74
SVM decision value	0.87
SVM RNA-class probability	0.871790
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5504090 119 - 27905053
ACUCGCGUCGGACUUUCUGGAAGCGGGUGCACGAACUAUGUAAAUAGCUUCCCAGCUAGCUAGAUUUGCAUAAACCAUAAGCCCAGGCAAAA-GUCCAUGCCGAAAAUGCACGGCAUUAC
.........(((((((((((..((.(((........(((((((((((((........)))))..)))))))).)))....)))))))...))-))))((((((........))))))... ( -34.80)
>DroSec_CAF1 3782 117 - 1
ACUCGCGUCGGACAUUCUGGAAGCGGGUGCACGAACUAUGCAAAUAGCUGCCCAGCUAGCC--AUUUGCAUAAACCGUAGGCCCAGGCGAAA-GUCCAUGCCGAAAAUGCACGGCAUUAC
....((.((((.....))))..))((((..(((...(((((((((.(((((...)).))).--)))))))))...)))..)))).(((....-))).((((((........))))))... ( -40.90)
>DroSim_CAF1 4243 117 - 1
ACUCGCGUCGGACUUUCUGGAAGCGGGUGCACGAACUAUGCAAAUAGCUGCCCAGCUAGCC--AUUUGCAUAAACCGUAGGCCCAGGCGAAA-GUCCAUGCCGAAAAUGCACGGCAUUAC
.........((((((((.(....)((((..(((...(((((((((.(((((...)).))).--)))))))))...)))..))))....))))-))))((((((........))))))... ( -44.00)
>DroEre_CAF1 3756 115 - 1
ACUCGCAACGGACUUUCUGGAACCGGGUGCACGAAUUAUGCAAAUAGCA---GAACUGACC--AUUUGCAUAAACCAUAAGCCCAGGCCAAAGGUUCAUGCCGAAAAUCCACGGCAUUAG
.........(((((((.(((..((((((.......((((((((((.(((---....)).).--)))))))))).......)))).))))))))))))((((((........))))))... ( -35.84)
>DroYak_CAF1 3916 114 - 1
ACUCGCGUCGGACAUUCUGGAAGCGGGUGCACGAACUAUGCAAAUAAAC---GAGCUGACC--AUUUGCAUAAACCAUAAGCCCAGGCGAAA-GUCCAUGCCGAAAAUGCACGGCAUUAG
....((.((((.....))))..))((((........(((((((((....---.........--)))))))))........)))).(((....-))).((((((........))))))... ( -30.91)
>consensus
ACUCGCGUCGGACUUUCUGGAAGCGGGUGCACGAACUAUGCAAAUAGCU_CCCAGCUAGCC__AUUUGCAUAAACCAUAAGCCCAGGCGAAA_GUCCAUGCCGAAAAUGCACGGCAUUAC
.........((((.....(....)((((........(((((((((.(((........)))...)))))))))........)))).........))))((((((........))))))... (-27.57 = -27.81 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:42 2006