Locus 9129

Sequence ID	3R_DroMel_CAF1
Location	24,371,485 – 24,371,661
Length	176
Max. P	0.997009

overview

Window 3

Location	24,371,485 – 24,371,605
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-29.79
Consensus MFE	-28.14
Energy contribution	-28.03
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.33
Structure conservation index	0.94
SVM decision value	1.41
SVM RNA-class probability	0.951396
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24371485 120 + 27905053
UUAAUUCGGUUUUGAAGCGAGUUGCAUGUCAAAAUGAUUGCUCUUCUGCAAACAGCGCAUCUGUGUUUGAAUUAUGAUGGAGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACU
........(((((((.((.....))...)))))))....(((((((..((((((.((....))))))))......)).)))))(((((((((((.........)))))))))))...... ( -30.10)
>DroVir_CAF1 181068 120 + 1
UUAAUUCGGUUUUGAAGCGAGUUGCAUGUCAAAAUGAUUGCUCUUCUACAAACAGCGCAUCUGUGUUUGAAUUAUGAUGGAGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCUCAAAACU
.......((((((((...((((..(((......)))...))))...........((((.(((((............)))))))))(((((((((.........))))))))))))))))) ( -29.20)
>DroSec_CAF1 193899 120 + 1
UUAAUUCGGUUUUGAAGCGAGUUGCAUGUCAAAAUGAUUGCUCUUCUGCAAACAGUGCAUCUGUGUUUGAAUUAUGAUGGAGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACU
.......(((((((....((((..(((......)))...))))....(((((...((((((((((((((..((......)).....))))))...))))))))....))))).))))))) ( -30.30)
>DroSim_CAF1 201817 120 + 1
UUAAUUCGGUUUUGAAGCGAGUUGCAUGUCAAAAUGAUUGCUCUUCUGCAAACAGCGCAUCUGUGUUUGAAUUAUGAUGGAGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAUACU
........(((((((.((.....))...)))))))....(((((((..((((((.((....))))))))......)).)))))(((((((((((.........)))))))))))...... ( -30.10)
>DroWil_CAF1 168348 120 + 1
UUAAUUCGGUUUUGAAGCGAGUUGCAUGUCAAAAUGAUUGCUCUUCUGCAAACAUCGCAUCUGUGUUUGAAUUAUGAUGGAGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGUGCAAAACU
........(((((((.((.....))...)))))))....(((((((..(((((((.......)))))))......)).)))))(((((((((((.........)))))))))))...... ( -29.30)
>DroMoj_CAF1 157016 120 + 1
UUAAUUCGGUUUUGAAGCGAGUUGCAUGUCAAAAUGAUUGCUCUUCUACAAACAGCGCAUCUGUGUUUGAAUUAUGAUGGAGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACU
........(((((((.((.....))...)))))))....(((((((.......(((((....)))))........)).)))))(((((((((((.........)))))))))))...... ( -29.76)
>consensus
UUAAUUCGGUUUUGAAGCGAGUUGCAUGUCAAAAUGAUUGCUCUUCUGCAAACAGCGCAUCUGUGUUUGAAUUAUGAUGGAGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACU
........(((((((.((.....))...)))))))....(((((((..((((((.((....))))))))......)).)))))(((((((((((.........)))))))))))...... (-28.14 = -28.03 +  -0.11)

alignment

secondary structure

dotplot

Window 4

Location	24,371,485 – 24,371,605
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-28.70
Consensus MFE	-26.29
Energy contribution	-26.57
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-2.22
Structure conservation index	0.92
SVM decision value	2.78
SVM RNA-class probability	0.997009
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24371485 120 - 27905053
AGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCUCCAUCAUAAUUCAAACACAGAUGCGCUGUUUGCAGAAGAGCAAUCAUUUUGACAUGCAACUCGCUUCAAAACCGAAUUAA
......((((((((((((.......)))))))))))).........((((((.......(((((.(((....)))....)).))).((((((...((.....)).))))))..)))))). ( -30.40)
>DroVir_CAF1 181068 120 - 1
AGUUUUGAGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCUCCAUCAUAAUUCAAACACAGAUGCGCUGUUUGUAGAAGAGCAAUCAUUUUGACAUGCAACUCGCUUCAAAACCGAAUUAA
.(((((((((((((((((.......))))))))))((((..((((..............)))).))(((.(((((((((....)).)))).))).)))....)).)))))))........ ( -26.74)
>DroSec_CAF1 193899 120 - 1
AGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCUCCAUCAUAAUUCAAACACAGAUGCACUGUUUGCAGAAGAGCAAUCAUUUUGACAUGCAACUCGCUUCAAAACCGAAUUAA
......((((((((((((.......))))))))))))((((((((..............))))..(((....)))..))))..((.((((((...((.....)).))))))..))..... ( -28.84)
>DroSim_CAF1 201817 120 - 1
AGUAUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCUCCAUCAUAAUUCAAACACAGAUGCGCUGUUUGCAGAAGAGCAAUCAUUUUGACAUGCAACUCGCUUCAAAACCGAAUUAA
......((((((((((((.......)))))))))))).........((((((.......(((((.(((....)))....)).))).((((((...((.....)).))))))..)))))). ( -30.40)
>DroWil_CAF1 168348 120 - 1
AGUUUUGCACAAAUAUUUGCAUCUGGAAUAUUUGCGCGCUCCAUCAUAAUUCAAACACAGAUGCGAUGUUUGCAGAAGAGCAAUCAUUUUGACAUGCAACUCGCUUCAAAACCGAAUUAA
......((.(((((((((.......))))))))).)).........((((((.......((.(((((((.(((((((((....)).))))).)).)))..)))).))......)))))). ( -26.32)
>DroMoj_CAF1 157016 120 - 1
AGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCUCCAUCAUAAUUCAAACACAGAUGCGCUGUUUGUAGAAGAGCAAUCAUUUUGACAUGCAACUCGCUUCAAAACCGAAUUAA
......((((((((((((.......)))))))))))).........((((((.......(((..(((.(((...))).))).))).((((((...((.....)).))))))..)))))). ( -29.50)
>consensus
AGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCUCCAUCAUAAUUCAAACACAGAUGCGCUGUUUGCAGAAGAGCAAUCAUUUUGACAUGCAACUCGCUUCAAAACCGAAUUAA
......((((((((((((.......)))))))))))).........((((((.......((.(((.(((.(((((((((....)).))))).)).)))...))).))......)))))). (-26.29 = -26.57 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	24,371,565 – 24,371,661
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	86.81
Mean single sequence MFE	-22.46
Consensus MFE	-18.57
Energy contribution	-19.61
Covariance contribution	1.04
Combinations/Pair	1.05
Mean z-score	-1.72
Structure conservation index	0.83
SVM decision value	0.65
SVM RNA-class probability	0.812177
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24371565 96 + 27905053
AGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACUACACACACGCAUGCAUAGUGAGGGGCCAGCACACACACACACACGCACACAUGCGG
...(((((((((((.........))))))))))).............((((((....(((.(.................).))).....)))))). ( -23.63)
>DroSec_CAF1 193979 94 + 1
AGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACUACACACACGCAUGCAUAGUGAGGGGCCAGCACACAC--ACACACGCACACAUGCGG
...(((((((((((.........))))))))))).............((((((....(((.(.(.........)..--.).))).....)))))). ( -23.80)
>DroSim_CAF1 201897 94 + 1
AGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAUACUACACACACGCAUGCAUAGUGAGGGGCCGGCACACAC--ACACACGCACAUAUGCGG
.(((((((((((((.........)))))))))))..(((((..((......))..)))))........))......--.....((((....)))). ( -22.30)
>DroEre_CAF1 207906 90 + 1
AGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACUACACACACGCAUGCAUAGUGAGGGGCCAGCACA------CACACGCACACAUGCGG
...(((((((((((.........))))))))))).............((((((....(((.(..(....)...------).))).....)))))). ( -25.00)
>DroAna_CAF1 196684 87 + 1
AGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACUACACACACGCAGGCUCAUC------CCCCCUCCCCC--GAUCACUCACGCAGGCG-
...(((((((((((.........))))))))))).............(((..((.....------...........--..........))..)))- ( -17.57)
>consensus
AGCGCGCAAAUAUUCCAGAUGCAAAUAUUUGCGCAAAACUACACACACGCAUGCAUAGUGAGGGGCCAGCACACAC__ACACACGCACACAUGCGG
...(((((((((((.........))))))))))).............((((((....(((.(.................).))).....)))))). (-18.57 = -19.61 +   1.04)

alignment

secondary structure

dotplot

Window 6

Location	24,371,565 – 24,371,661
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	86.81
Mean single sequence MFE	-34.44
Consensus MFE	-27.29
Energy contribution	-28.57
Covariance contribution	1.28
Combinations/Pair	1.07
Mean z-score	-2.70
Structure conservation index	0.79
SVM decision value	2.20
SVM RNA-class probability	0.990119
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24371565 96 - 27905053
CCGCAUGUGUGCGUGUGUGUGUGUGUGCUGGCCCCUCACUAUGCAUGCGUGUGUGUAGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCU
.((((((((((((((.(((.(.(.((....)).)).))))))))))))))))).........((((((((((((.......))))))))))))... ( -36.60)
>DroSec_CAF1 193979 94 - 1
CCGCAUGUGUGCGUGUGU--GUGUGUGCUGGCCCCUCACUAUGCAUGCGUGUGUGUAGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCU
.((((((((((((((.((--(.(.(.(....).)).))))))))))))))))).........((((((((((((.......))))))))))))... ( -36.20)
>DroSim_CAF1 201897 94 - 1
CCGCAUAUGUGCGUGUGU--GUGUGUGCCGGCCCCUCACUAUGCAUGCGUGUGUGUAGUAUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCU
..(((((..(((((((((--(.(((.(.......).)))))))))))))..)))))......((((((((((((.......))))))))))))... ( -36.50)
>DroEre_CAF1 207906 90 - 1
CCGCAUGUGUGCGUGUG------UGUGCUGGCCCCUCACUAUGCAUGCGUGUGUGUAGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCU
.((((((((((((((.(------((....(....).))))))))))))))))).........((((((((((((.......))))))))))))... ( -35.50)
>DroAna_CAF1 196684 87 - 1
-CGCCUGCGUGAGUGAUC--GGGGGAGGGGG------GAUGAGCCUGCGUGUGUGUAGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCU
-(.(((.(.(((....))--).)...))).)------....((((((((....)))))....((((((((((((.......))))))))))))))) ( -27.40)
>consensus
CCGCAUGUGUGCGUGUGU__GUGUGUGCUGGCCCCUCACUAUGCAUGCGUGUGUGUAGUUUUGCGCAAAUAUUUGCAUCUGGAAUAUUUGCGCGCU
.((((((((((((((((...................))).))))))))))))).........((((((((((((.......))))))))))))... (-27.29 = -28.57 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:27:13 2006