Locus 5151

Sequence ID	3R_DroMel_CAF1
Location	13,539,447 – 13,539,660
Length	213
Max. P	0.993903

overview

Window 9

Location	13,539,447 – 13,539,555
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.56
Mean single sequence MFE	-19.97
Consensus MFE	-12.06
Energy contribution	-13.06
Covariance contribution	1.00
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.60
SVM decision value	0.87
SVM RNA-class probability	0.871985
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13539447 108 + 27905053
CUGC------------GGCGGGUUAGCCCCCUAACUACCACACUACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGAAAAAAUCAUAUCACGUGCUUCUCCAUU
..((------------((.(((....))))).............................((((((.(((...))).))))))....((((((..........))))))))......... ( -18.30)
>DroSec_CAF1 14256 102 + 1
CUGC---------------GGGUAAGCCCCCUAACUACCACACUACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUU
....---------------((..((((.................................((((((.(((...))).))))))....((((((---.......))))))))))..))... ( -17.90)
>DroSim_CAF1 11209 102 + 1
CUGC---------------GGGUAAGCCCCCUAACUACCACACUUCCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUU
....---------------((..((((.................................((((((.(((...))).))))))....((((((---.......))))))))))..))... ( -17.90)
>DroYak_CAF1 18137 102 + 1
CUGC---------------GGGUAAGCCCCCGAACUAUAACUCUACCCCACUAAUGAAACAAUUAACCGGUUUAUAUUUAAUUCAAAACGUGA---AAUCACAUCACGUGCUUCUCCUUU
....---------------((..((((....(((.((.......(((....((((......))))...))).......)).)))...((((((---.......))))))))))..))... ( -16.94)
>DroAna_CAF1 12189 114 + 1
CUGCUAAUAUAUGUAUGGUAUGUGGGCUCUCCACCUCGCUCACUGCCUCGCCAAUAAAACAAUUAACCGGUUUCCGUUUAAAUGGAAACGUGA---AGUCGCAUCACGUGCACC---GAG
............((..((((.((((((..........))))))))))..))................((((((((((....))))))((((((---.......))))))..)))---).. ( -28.80)
>consensus
CUGC_______________GGGUAAGCCCCCUAACUACCACACUACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA___AAUCAUAUCACGUGCUUCUCCAUU
...................(((.((((.................................((((((.((.....)).))))))....((((((..........)))))))))).)))... (-12.06 = -13.06 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	13,539,475 – 13,539,586
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.14
Mean single sequence MFE	-19.46
Consensus MFE	-14.10
Energy contribution	-14.58
Covariance contribution	0.48
Combinations/Pair	1.11
Mean z-score	-2.74
Structure conservation index	0.72
SVM decision value	2.43
SVM RNA-class probability	0.993903
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13539475 111 + 27905053
CACUACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGAAAAAAUCAUAUCACGUGCUUCUCCAUUGGGGCC---AACAAACCAAGCA------AACCAAACCAAA
.....(((((..........((((((.(((...))).))))))....((((((..........))))))..........)))))..---.............------............ ( -18.00)
>DroSec_CAF1 14281 108 + 1
CACUACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUUGGGGCC---AAUAAACCAAGCA------AACCAAACCAAA
.....(((((..........((((((.(((...))).))))))....((((((---.......))))))..........)))))..---.............------............ ( -18.60)
>DroSim_CAF1 11234 108 + 1
CACUUCCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUUGGGGCC---AAUAAACCAAGCA------AACCAAACCAAA
.....(((((..........((((((.(((...))).))))))....((((((---.......))))))..........)))))..---.............------............ ( -18.20)
>DroYak_CAF1 18162 114 + 1
CUCUACCCCACUAAUGAAACAAUUAACCGGUUUAUAUUUAAUUCAAAACGUGA---AAUCACAUCACGUGCUUCUCCUUUGGGGCC---AAUAAACCAGGCAAAAAAAAACCAAACCAAA
.......((..((((......))))...(((((((............((((((---.......))))))(((((......))))).---.))))))).)).................... ( -19.70)
>DroAna_CAF1 12229 95 + 1
CACUGCCUCGCCAAUAAAACAAUUAACCGGUUUCCGUUUAAAUGGAAACGUGA---AGUCGCAUCACGUGCACC---GAGCGGGCCGGCCAUCAACCAAAC-------------------
..(.(((.(((.(((......)))...((((((((((....))))))((((((---.......))))))..)))---).)))))).)..............------------------- ( -22.80)
>consensus
CACUACCCCACUAAUAAAACAAUUAACCGGUUUCCGUUUAAUUCAAAACGUGA___AAUCAUAUCACGUGCUUCUCCAUUGGGGCC___AAUAAACCAAGCA______AACCAAACCAAA
.....(((((..........((((((.((.....)).))))))....((((((..........))))))..........))))).................................... (-14.10 = -14.58 +   0.48)

alignment

secondary structure

dotplot

Window 1

Location	13,539,515 – 13,539,624
Length	109
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	91.10
Mean single sequence MFE	-18.55
Consensus MFE	-16.23
Energy contribution	-16.97
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.50
Structure conservation index	0.87
SVM decision value	1.90
SVM RNA-class probability	0.982076
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13539515 109 + 27905053
AUUCAAAACGUGAAAAAAUCAUAUCACGUGCUUCUCCAUUGGGGCCAACAAACCAAGCA------AACCAAACCAAACACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAU
..(((..((((((..........))))))(((((......)))))..............------....................(((((((......)))))))......))). ( -19.30)
>DroSec_CAF1 14321 106 + 1
AUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCA------AACCAAACCAAAAACCAACUUCAAGCGCUUUAUCGCUUGACACAACUGAU
..(((..((((((---.......))))))((((....((((....)))).....)))).------....................(((((((......)))))))......))). ( -20.20)
>DroSim_CAF1 11274 106 + 1
AUUCAAAACGUGA---AAUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCA------AACCAAACCAAAAACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAU
..(((..((((((---.......))))))((((....((((....)))).....)))).------....................(((((((......)))))))......))). ( -20.20)
>DroYak_CAF1 18202 108 + 1
AUUCAAAACGUGA---AAUCACAUCACGUGCUUCUCCUUUGGGGCCAAUAAACCAGGCAAAAAAAAACCAAACCAAAAACCAACUUCAA----CUUAUCGCUUGACACAACUGAU
..(((..((((((---.......))))))(((((......)))))........(((((...............................----......))))).......))). ( -14.49)
>consensus
AUUCAAAACGUGA___AAUCAUAUCACGUGCUUCUCCAUUGGGGCCAAUAAACCAAGCA______AACCAAACCAAAAACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAU
..(((..((((((..........))))))(((((......)))))........................................(((((((......)))))))......))). (-16.23 = -16.97 +   0.75)

alignment

secondary structure

dotplot

Window 2

Location	13,539,555 – 13,539,660
Length	105
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	88.19
Mean single sequence MFE	-21.07
Consensus MFE	-13.10
Energy contribution	-15.35
Covariance contribution	2.25
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.62
SVM decision value	0.06
SVM RNA-class probability	0.566007
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13539555 105 + 27905053
GGGGCCAACAAACCAAGCA------AACCAAACCAAACACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAUAGGCAAAUUCUUGAUAUCAGGGAUUACAAAGAGUAA----
((.((...........)).------..))..........((....(((((((......))))))).....((((((..(((....))).)))))))).((((.....))))---- ( -20.50)
>DroSec_CAF1 14358 108 + 1
GGGGCCAAUAAACCAAGCA------AACCAAACCAAAAACCAACUUCAAGCGCUUUAUCGCUUGACACAACUGAUA-GCAAAUUCUUCAUAUCAGGGAUUACAAUGAGUAAUCCU
((.((...........)).------..))................(((((((......))))))).....((((((-............))))))(((((((.....))))))). ( -24.40)
>DroSim_CAF1 11311 108 + 1
GGGGCCAAUAAACCAAGCA------AACCAAACCAAAAACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAUA-GCAAAUUCUUCAUAUCAGGGAUUACAAUGAGUAAUCCU
((.((...........)).------..))................(((((((......))))))).....((((((-............))))))(((((((.....))))))). ( -24.40)
>DroYak_CAF1 18239 110 + 1
GGGGCCAAUAAACCAGGCAAAAAAAAACCAAACCAAAAACCAACUUCAA----CUUAUCGCUUGACACAACUGAUA-GCAAGUUCUUGAUAUCAGGGAUUACAAUAAAUAAGACU
...(((.........)))...............................----(((((...(((......((((((-.(((....))).))))))......)))...)))))... ( -15.00)
>consensus
GGGGCCAAUAAACCAAGCA______AACCAAACCAAAAACCAACUUCAAGCGCAUUAUCGCUUGACACAACUGAUA_GCAAAUUCUUCAUAUCAGGGAUUACAAUGAGUAAUCCU
.((.........))...............................(((((((......))))))).....((((((.............))))))(((((((.....))))))). (-13.10 = -15.35 +   2.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:42 2006