Locus 2384

Sequence ID	3R_DroMel_CAF1
Location	6,740,065 – 6,740,343
Length	278
Max. P	0.816716

overview

Window 9

Location	6,740,065 – 6,740,183
Length	118
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-23.99
Consensus MFE	-22.25
Energy contribution	-22.03
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.93
SVM decision value	0.37
SVM RNA-class probability	0.710713
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6740065 118 + 27905053
AAAUGCUUGUUUGUUUGUAUGCGUAAAUAGGUAGUGUUUGCACGGGCACUCCUCACACCAAUGCAAAUAACACCA--ACACCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACC
...((((((((.((((((.(((((....(((.(((((((....)))))))))).......))))).)))).)).)--)))..))))....................((....))...... ( -22.70)
>DroSec_CAF1 4872 120 + 1
AAAUUCUUGUUUGUUUGUAUGCGUAAAUAGGUAGUGUUUGCACGGGCACUCCUCACACCAAUGCAAACAACACCAACACACCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACC
...........(((..((.(((((.....(((..((((((((..((...........))..))))))))..)))..(......)...)))))..))..))).....((....))...... ( -23.20)
>DroSim_CAF1 9203 119 + 1
AAAUGCUUGUUUGUUUGUAUGCGUAAAUAGGUAGUGUUUGCACGGGCACUCCUCACACCAAUGCAAACAACAC-AACACACCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACC
...(((((((((((((((((........(((.(((((((....)))))))))).......)))))))))).))-)).......((....))...............)))........... ( -26.06)
>consensus
AAAUGCUUGUUUGUUUGUAUGCGUAAAUAGGUAGUGUUUGCACGGGCACUCCUCACACCAAUGCAAACAACACCAACACACCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACC
.......((((.((((((((........(((.(((((((....)))))))))).......))))))))))))...........((....))...............((....))...... (-22.25 = -22.03 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	6,740,143 – 6,740,263
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	99.44
Mean single sequence MFE	-25.00
Consensus MFE	-24.37
Energy contribution	-24.37
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.97
SVM decision value	0.67
SVM RNA-class probability	0.816716
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6740143 120 + 27905053
CCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACCGACUGGCACUUGAAUAAACAUAAAUGCAAGACGUUUAUGUUAAAAGCACCCAACGGGGGCACUUAUCAAGCACCGAACGU
...((....))...............((....)).....((..(((..(((((...((((((((((.....))))))))))....((.(((....))))).....)))))..)))..)). ( -26.40)
>DroSec_CAF1 4952 120 + 1
CCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACCGACUGACACUUGAAUAAACAUAAAUGCAAGACGUUUAUGUUAAAAGCACCCAACGGGGGCACUUAUCAAGCACCGAACGU
...((....)).............(((((.(((......))).))...(((((...((((((((((.....))))))))))....((.(((....))))).....)))))...))).... ( -24.30)
>DroSim_CAF1 9282 120 + 1
CCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACCGACUGACACUUGAAUAAACAUAAAUGCAAGACGUUUAUGUUAAAAGCACCCAACGGGGGCACUUAUCAAGCACCGAACGU
...((....)).............(((((.(((......))).))...(((((...((((((((((.....))))))))))....((.(((....))))).....)))))...))).... ( -24.30)
>consensus
CCAGCACACGCACCACCUACACCAUCGCAAUCGCACCACCGACUGACACUUGAAUAAACAUAAAUGCAAGACGUUUAUGUUAAAAGCACCCAACGGGGGCACUUAUCAAGCACCGAACGU
...((....)).............(((((.(((......))).))...(((((...((((((((((.....))))))))))....((.(((....))))).....)))))...))).... (-24.37 = -24.37 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	6,740,223 – 6,740,343
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.57
Mean single sequence MFE	-40.00
Consensus MFE	-36.75
Energy contribution	-36.87
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.92
SVM decision value	0.06
SVM RNA-class probability	0.563613
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6740223 120 - 27905053
GGAGGGGGAGUGUCAGUGGCAGUGGGCGUGGCAGGAUAAGGGAGCGGGCUCUGAAGUUAGAAGUGAAUCCUUAGCUGACAACGUUCGGUGCUUGAUAAGUGCCCCCGUUGGGUGCUUUUA
...(((((..(((((..((((.(((((((..(((..((((((.((.((((....))))....))...)))))).)))...))))))).)))))))))....))))).............. ( -43.50)
>DroSec_CAF1 5032 110 - 1
GG----GG------AGUGGCAGUGGGCGUGGCAGGAUAAGGGAGCGGGCUCUGAAGUUAGAACUGAAUCCUUAGCUGACAACGUUCGGUGCUUGAUAAGUGCCCCCGUUGGGUGCUUUUA
..----..------...((((.(((((((..(((..((((((..(((..((((....)))).)))..)))))).)))...))))))).))))....(((..(((.....)))..)))... ( -40.30)
>DroSim_CAF1 9362 110 - 1
GG----GG------AGUGGCAGUGGGCGUGGCAGGAUAAGGGAACGGGCUCUGAAGUUAGAACUGAAUCUUUAGCUGACAACGUUCGGUGCUUGAUAAGUGCCCCCGUUGGGUGCUUUUA
..----..------...((((.(((((((..(((..((((((..(((..((((....)))).)))..)))))).)))...))))))).))))....(((..(((.....)))..)))... ( -36.20)
>consensus
GG____GG______AGUGGCAGUGGGCGUGGCAGGAUAAGGGAGCGGGCUCUGAAGUUAGAACUGAAUCCUUAGCUGACAACGUUCGGUGCUUGAUAAGUGCCCCCGUUGGGUGCUUUUA
.................((((.(((((((..(((..((((((..(((..((((....)))).)))..)))))).)))...))))))).))))....(((..(((.....)))..)))... (-36.75 = -36.87 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:04 2006