Locus 1907

Sequence ID	2L_DroMel_CAF1
Location	5,216,041 – 5,216,201
Length	160
Max. P	0.940171

overview

Window 6

Location	5,216,041 – 5,216,161
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.47
Mean single sequence MFE	-38.65
Consensus MFE	-32.35
Energy contribution	-33.23
Covariance contribution	0.88
Combinations/Pair	1.05
Mean z-score	-2.56
Structure conservation index	0.84
SVM decision value	1.31
SVM RNA-class probability	0.940171
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5216041 120 + 22407834
AGCUACGUAUUUGGCAUUGUGCACCGCUUCCGUAUAGCAGGGUUCAUAGGCUAGUUUUGGAUAAUCCAAGGAUAUCAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGGUAUU
((((((((.....((.....)).((((((((.....((((((((((...(.((.((((((.....)))))).)).)....)).))))))))....)))..)))))))))))))....... ( -41.80)
>DroSec_CAF1 5282 120 + 1
AGCUACGUAUUUGGCAUUGUGAACCGCUUCCAUAUAGCACGGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAUUAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGAUAUU
((((((((...((((.((((((((((((.......)))..)))))))))))))((((..((((.....(((((((......)).))))).))))..)))).....))))))))....... ( -38.70)
>DroSim_CAF1 5302 120 + 1
AGCUACGUAUUUGGCAUUGUGCACCGCUUCCGUAUAGCAGGGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAUCAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGAUAUU
((((((((.....((.....)).((((((((.....((((((((((...(.((.((((((.....)))))).)).)....)).))))))))....)))..)))))))))))))....... ( -41.80)
>DroYak_CAF1 11511 120 + 1
ACCUACAUAUUUGGCAUUGUGAACCGCUUCCGUAUAGCACGGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAACACAUUAUAAUCCUGUUUCAAGAACAGCGGGCGUAGCUGAAUAUU
......(((((..((.((((((((((((.......)))..)))))))))(((..(((((((.......(((((...........)))))..)))))))..))).......))..))))). ( -32.30)
>consensus
AGCUACGUAUUUGGCAUUGUGAACCGCUUCCGUAUAGCACGGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAUCAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGAUAUU
((((((((...((((.((((((((((((.......)))..)))))))))))))(((((.((((.....(((((...........))))).)))).))))).....))))))))....... (-32.35 = -33.23 +   0.88)

alignment

secondary structure

dotplot

Window 7

Location	5,216,041 – 5,216,161
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-29.50
Consensus MFE	-25.81
Energy contribution	-25.93
Covariance contribution	0.13
Combinations/Pair	1.07
Mean z-score	-1.74
Structure conservation index	0.87
SVM decision value	0.59
SVM RNA-class probability	0.790560
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5216041 120 - 22407834
AAUACCCAGCUACGUCCGCUGUUCCUGACACAGGAUUACAAUUUGAUAUCCUUGGAUUAUCCAAAACUAGCCUAUGAACCCUGCUAUACGGAAGCGGUGCACAAUGCCAAAUACGUAGCU
.......(((((((((((((..(((((...))))).............(((((((.....))))...((((...........))))...)))))))).((.....)).....)))))))) ( -31.00)
>DroSec_CAF1 5282 120 - 1
AAUAUCCAGCUACGUCCGCUGUUCCUGACACAGGAUUACAAUUUAAUAUCCUUGGACUAUCCAAAACUAGCCUAUGAACCGUGCUAUAUGGAAGCGGUUCACAAUGCCAAAUACGUAGCU
.......((((((((..((((.(((((...)))))................((((.....))))...))))...((((((((.((....))..))))))))...........)))))))) ( -32.20)
>DroSim_CAF1 5302 120 - 1
AAUAUCCAGCUACGUCCGCUGUUCCUGACACAGGAUUACAAUUUGAUAUCCUUGGACUAUCCAAAACUAGCCUAUGAACCCUGCUAUACGGAAGCGGUGCACAAUGCCAAAUACGUAGCU
.......(((((((((((((..(((((...))))).............(((((((.....))))...((((...........))))...)))))))).((.....)).....)))))))) ( -31.00)
>DroYak_CAF1 11511 120 - 1
AAUAUUCAGCUACGCCCGCUGUUCUUGAAACAGGAUUAUAAUGUGUUAUCCUUGGACUAUCCAAAACUAGCCUAUGAACCGUGCUAUACGGAAGCGGUUCACAAUGCCAAAUAUGUAGGU
.........(((((...((((((.........((((.((.....)).))))((((.....))))))).)))...((((((((.((....))..))))))))............))))).. ( -23.80)
>consensus
AAUAUCCAGCUACGUCCGCUGUUCCUGACACAGGAUUACAAUUUGAUAUCCUUGGACUAUCCAAAACUAGCCUAUGAACCCUGCUAUACGGAAGCGGUGCACAAUGCCAAAUACGUAGCU
.......(((((((((((((..(((((...))))).............(((((((.....))))...((((...........))))...))))))))...............)))))))) (-25.81 = -25.93 +   0.13)

alignment

secondary structure

dotplot

Window 8

Location	5,216,081 – 5,216,201
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-37.45
Consensus MFE	-31.74
Energy contribution	-32.05
Covariance contribution	0.31
Combinations/Pair	1.08
Mean z-score	-1.84
Structure conservation index	0.85
SVM decision value	0.54
SVM RNA-class probability	0.775800
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5216081 120 + 22407834
GGUUCAUAGGCUAGUUUUGGAUAAUCCAAGGAUAUCAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGGUAUUGGGACUGAAAUCGCGGUGCCCGUUGAAUCCAUGGAUCAGA
(((((((..(((.((((..((((.....(((((..(.....)..))))).))))..)))))))(((..((((.((((((((.((......)).))))))))))))..))))))))))... ( -42.30)
>DroSec_CAF1 5322 120 + 1
GGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAUUAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGAUAUUGGGACUGAAAUCGCGGUGCCCGUUGAAUCCAUGGAUCAGA
(((((((..(((.((((..((((.....(((((((......)).))))).))))..)))))))(((..((((.((.(((((.((......)).))))))).))))..))))))))))... ( -35.30)
>DroSim_CAF1 5342 120 + 1
GGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAUCAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGAUAUUGGGACUGAAAUCGCGGUGCCCGUUGAAUCCAUGGAUCAGA
(((((((.(((((........)))))...((((.((((.......(((((...))))).((((.......))))......(((((((......)))).))).)))))))))))))))... ( -36.10)
>DroYak_CAF1 11551 120 + 1
GGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAACACAUUAUAAUCCUGUUUCAAGAACAGCGGGCGUAGCUGAAUAUUGGGGCUGAAAUCUCGGUGCCCAUUAAAGCCAUGGAUCAGA
(((((((.((((...((..(...((((.(((((...........)))))((((...))))...))))....)..))((.(((((((((....))))).)))).)).)))))))))))... ( -36.10)
>consensus
GGUUCAUAGGCUAGUUUUGGAUAGUCCAAGGAUAUCAAAUUGUAAUCCUGUGUCAGGAACAGCGGACGUAGCUGGAUAUUGGGACUGAAAUCGCGGUGCCCGUUGAAUCCAUGGAUCAGA
(((((((.((.....(((((.....)))))((((((.........(((((...))))).((((.......))))))))))(((((((......)))).))).......)))))))))... (-31.74 = -32.05 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:13 2006