Locus 4406

Sequence ID	3R_DroMel_CAF1
Location	11,643,814 – 11,643,995
Length	181
Max. P	0.999669

overview

Window 3

Location	11,643,814 – 11,643,915
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-33.92
Consensus MFE	-29.62
Energy contribution	-30.42
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-3.09
Structure conservation index	0.87
SVM decision value	3.86
SVM RNA-class probability	0.999669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11643814 101 + 27905053
CUCAUUUGUGGGCCAUUAAUUUAUUUGGCCGCAAUGGGUUGGCCAUGGAUUGUGUGGAGUUCAUAGCUCCAUUAUGGUGAAAAAAGUUUGUGGCAAACUAU
..((((.((((.(((..........)))))))))))((((.((((..((((..(((((((.....)))))))............))))..)))).)))).. ( -33.24)
>DroSec_CAF1 24692 101 + 1
CUCAUUUGUGGGCCAUUAAUUUAUUUGGCCGCAAUGGGUUGGCCAUGGAUUGUGUGGAGUUCAUAGCUCCAUUAUGGUGGUAAAAGUUUGUGGCAAACUAU
..((((.((((.(((..........)))))))))))((((.((((..((((..(((((((.....)))))))............))))..)))).)))).. ( -33.24)
>DroSim_CAF1 26855 101 + 1
UUCAUUUGUGGGCCAUUAAUUUAUUUGCCCGCAAUAGGUUGGCCAUGGAUUGUGUGGAGUUCAUAGCUCCAUUAUGGUGGUAAAAGUUUGUGGCAAACUAU
.....((((((((.............))))))))..((((.((((..((((..(((((((.....)))))))............))))..)))).)))).. ( -33.76)
>DroEre_CAF1 22591 101 + 1
CUCAUUUGUGGGCCAUUAAUUUAUUUGCCCGCAAUGGGUUGGCCAUGGAUUGUCCGGAGUUCAUAGCUCCAUUACGGUGGAGAAAGUUUGUGGCAAACUAU
..((((.((((((.............))))))))))((((.((((..((((.((((((((.....)))))((....)))))...))))..)))).)))).. ( -35.02)
>DroYak_CAF1 25188 101 + 1
CUCAUUUGUGGGCCAUUAAUUUAUUUGCCCGCAAUGGGUUGGCCAUGGAUUGUGUGGAGUUCAUAGCUCCAUUACGGUAGAGAAAGUUUGUGGCAAACUAU
..((((.((((((.............))))))))))((((.((((..((((..(((((((.....)))))))............))))..)))).)))).. ( -34.36)
>consensus
CUCAUUUGUGGGCCAUUAAUUUAUUUGCCCGCAAUGGGUUGGCCAUGGAUUGUGUGGAGUUCAUAGCUCCAUUAUGGUGGAAAAAGUUUGUGGCAAACUAU
.....((((((((.............))))))))..((((.((((..((((..(((((((.....)))))))............))))..)))).)))).. (-29.62 = -30.42 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	11,643,814 – 11,643,915
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	95.25
Mean single sequence MFE	-21.74
Consensus MFE	-18.57
Energy contribution	-18.41
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.20
Structure conservation index	0.85
SVM decision value	2.29
SVM RNA-class probability	0.991769
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11643814 101 - 27905053
AUAGUUUGCCACAAACUUUUUUCACCAUAAUGGAGCUAUGAACUCCACACAAUCCAUGGCCAACCCAUUGCGGCCAAAUAAAUUAAUGGCCCACAAAUGAG
..((((((...))))))....(((...((((((.((((((..............))))))....)))))).(((((..........)))))......))). ( -19.74)
>DroSec_CAF1 24692 101 - 1
AUAGUUUGCCACAAACUUUUACCACCAUAAUGGAGCUAUGAACUCCACACAAUCCAUGGCCAACCCAUUGCGGCCAAAUAAAUUAAUGGCCCACAAAUGAG
...((..((((...................(((((.......))))).........(((((..........)))))..........))))..))....... ( -19.60)
>DroSim_CAF1 26855 101 - 1
AUAGUUUGCCACAAACUUUUACCACCAUAAUGGAGCUAUGAACUCCACACAAUCCAUGGCCAACCUAUUGCGGGCAAAUAAAUUAAUGGCCCACAAAUGAA
...(((.((((.......(((......)))(((((.......))))).........)))).)))...(((.((((.............)))).)))..... ( -18.72)
>DroEre_CAF1 22591 101 - 1
AUAGUUUGCCACAAACUUUCUCCACCGUAAUGGAGCUAUGAACUCCGGACAAUCCAUGGCCAACCCAUUGCGGGCAAAUAAAUUAAUGGCCCACAAAUGAG
...((..((((.............(((((((((.((((((..............))))))....))))))))).............))))..))....... ( -25.31)
>DroYak_CAF1 25188 101 - 1
AUAGUUUGCCACAAACUUUCUCUACCGUAAUGGAGCUAUGAACUCCACACAAUCCAUGGCCAACCCAUUGCGGGCAAAUAAAUUAAUGGCCCACAAAUGAG
...((..((((.............(((((((((.((((((..............))))))....))))))))).............))))..))....... ( -25.31)
>consensus
AUAGUUUGCCACAAACUUUUUCCACCAUAAUGGAGCUAUGAACUCCACACAAUCCAUGGCCAACCCAUUGCGGGCAAAUAAAUUAAUGGCCCACAAAUGAG
...((..((((.............((.((((((.((((((..............))))))....)))))).)).............))))..))....... (-18.57 = -18.41 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	11,643,887 – 11,643,995
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.60
Mean single sequence MFE	-23.07
Consensus MFE	-17.19
Energy contribution	-16.69
Covariance contribution	-0.50
Combinations/Pair	1.13
Mean z-score	-3.78
Structure conservation index	0.75
SVM decision value	0.82
SVM RNA-class probability	0.859190
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11643887 108 - 27905053
AAACGAACUAUGCAAACUGCAAACUCAAUCAAAAACUCUUCACAUGUUCGCAGAACUUUUCACAAUGAUGAAAUUAUUGCAUAGUUUGCCACAAACUUUUUU-CA-----------CCAU
...((((((((((((.((((.(((.....................))).))))....(((((......)))))...))))))))))))..............-..-----------.... ( -22.90)
>DroSec_CAF1 24765 108 - 1
AAACGAACUAUGCAAACUGCAAACUCAAUCAAAAACUCUUCACAUGUUCGCAGAACUUUUCGCAAUGAUGAAAUUAUUGCAUAGUUUGCCACAAACUUUUAC-CA-----------CCAU
...((((((((((((.((((.(((.....................))).))))....(((((......)))))...))))))))))))..............-..-----------.... ( -22.20)
>DroSim_CAF1 26928 108 - 1
AAACGAACUAUGCAAACUGCAAACUCAAUCAAAAACUCUUCACAUGUUCGCAGAACUUUUCGCAAUGAUGAAAUUAUUGCAUAGUUUGCCACAAACUUUUAC-CA-----------CCAU
...((((((((((((.((((.(((.....................))).))))....(((((......)))))...))))))))))))..............-..-----------.... ( -22.20)
>DroEre_CAF1 22664 108 - 1
AAACGAACUAUGCAAACUGAAAACUCAAUCAAAAACUCUUCACAUGCUCGCAGAACUUUUUGCAAUGAUGAAAUUAUUGCAUAGUUUGCCACAAACUUUCUC-CA-----------CCGU
...((((((((((((..(((....)))...........(((((((....(((((....))))).))).))))....))))))))))))..............-..-----------.... ( -22.10)
>DroYak_CAF1 25261 108 - 1
AAACGAACUAUGCAAACUGAAAACUCAAUCAAAAACUCUUCACAUGCUCGCAGAACUUUUUGCAAUGAUGAAAUUAUUGCAUAGUUUGCCACAAACUUUCUC-UA-----------CCGU
...((((((((((((..(((....)))...........(((((((....(((((....))))).))).))))....))))))))))))..............-..-----------.... ( -22.10)
>DroAna_CAF1 22562 120 - 1
AAACGAACUGUGCAAACUGAAAACUCAAUCAAAAACUCUUCACAUGUUCGCAGAACUUUUUGCAAUGAUGAAAUUAUUGCAUAGUUUGGUGGAAACUUUCUGCCAACGACCGCUCCCCCU
...((((((((((((..(((....)))...........(((((((....(((((....))))).))).))))....))))))))))(((..((.....))..))).))............ ( -26.90)
>consensus
AAACGAACUAUGCAAACUGAAAACUCAAUCAAAAACUCUUCACAUGUUCGCAGAACUUUUCGCAAUGAUGAAAUUAUUGCAUAGUUUGCCACAAACUUUCUC_CA___________CCAU
...((((((((((((..((......))...........(((((((((..............)).))).))))....))))))))))))................................ (-17.19 = -16.69 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:18 2006