Locus 1291

Sequence ID	2R_DroMel_CAF1
Location	5,030,198 – 5,030,393
Length	195
Max. P	0.999849

overview

Window 2

Location	5,030,198 – 5,030,317
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	85.93
Mean single sequence MFE	-26.90
Consensus MFE	-18.92
Energy contribution	-19.44
Covariance contribution	0.52
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.70
SVM decision value	0.68
SVM RNA-class probability	0.820292
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5030198 119 + 20766785
GUAGAGAAACUGAAAAUAACUAAAUUAAGAGCGACUAAGUGUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUG
.((((((((........(((....(((((.(((......))).)))))..)))))))))))(((.(((.....))).)))..............(((((((((.....))))))))).. ( -27.10)
>DroSec_CAF1 10255 119 + 1
GUAGAGAAACUAAAAAUAACUAAAUUAAGAGCGACUAAGUGUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUG
.((((((((........(((....(((((.(((......))).)))))..)))))))))))(((.(((.....))).)))..............(((((((((.....))))))))).. ( -27.10)
>DroSim_CAF1 10281 119 + 1
GUAGAGAAACUGAAAAUAACUAAAUUAAGAGCGACUAAGUGUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUG
.((((((((........(((....(((((.(((......))).)))))..)))))))))))(((.(((.....))).)))..............(((((((((.....))))))))).. ( -27.10)
>DroEre_CAF1 10179 116 + 1
GUAGAGAAACUAAGAAUAACUAAAUUAGGAGCGAAU---AGGGCUCGAGAGUUUCUCUCUGUGCUUGCAACUUGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUG
..(((((((((........(((...)))((((....---...))))...)))))))))...(((.(((.....))).)))..............(((((((((.....))))))))).. ( -32.00)
>DroYak_CAF1 10421 98 + 1
------AAAUUAAGUGAAACUAAA---------------AGUUAUUAAGAGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUG
------..................---------------((((....((((.....))))(((((.......))))).............))))(((((((((.....))))))))).. ( -21.20)
>consensus
GUAGAGAAACUAAAAAUAACUAAAUUAAGAGCGACUAAGUGUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUG
..((((((((........................................))))))))...(((.(((.....))).)))..............(((((((((.....))))))))).. (-18.92 = -19.44 +   0.52)

alignment

secondary structure

dotplot

Window 3

Location	5,030,238 – 5,030,357
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	96.22
Mean single sequence MFE	-33.20
Consensus MFE	-29.76
Energy contribution	-30.64
Covariance contribution	0.88
Combinations/Pair	1.03
Mean z-score	-3.58
Structure conservation index	0.90
SVM decision value	4.25
SVM RNA-class probability	0.999849
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5030238 119 + 20766785
GUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACAC
((((..(((.......))).))))((((((((.((.(((((((...(((.....(((((((((.....))))))))))))..)))))))))....))))))))................ ( -33.70)
>DroSec_CAF1 10295 118 + 1
GUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAU-UCACACAC
((((..(((.......))).))))((((((((.((.(((((((...(((.....(((((((((.....))))))))))))..)))))))))....)))))))).......-........ ( -33.70)
>DroSim_CAF1 10321 119 + 1
GUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACAC
((((..(((.......))).))))((((((((.((.(((((((...(((.....(((((((((.....))))))))))))..)))))))))....))))))))................ ( -33.70)
>DroEre_CAF1 10216 119 + 1
GGGCUCGAGAGUUUCUCUCUGUGCUUGCAACUUGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACAC
.(((.((((((...))))).).)))(((((((((...((...(((((....((.(((((((((.....))))))))).))...))))).))..)))))))))................. ( -36.40)
>DroYak_CAF1 10440 119 + 1
GUUAUUAAGAGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUCUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACAC
.......((((.....))))....((((((((.((.(((((.....(((.....(((((((((.....))))))))))))....)))))))....))))))))................ ( -28.50)
>consensus
GUACUUGAGUGUUUUUCUCUGUGCUUGCAACUAGCACGCAAAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACAC
((((..(((.......))).))))((((((((.((.(((((((...(((.....(((((((((.....))))))))))))..)))))))))....))))))))................ (-29.76 = -30.64 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	5,030,238 – 5,030,357
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	96.22
Mean single sequence MFE	-29.32
Consensus MFE	-28.74
Energy contribution	-28.42
Covariance contribution	-0.32
Combinations/Pair	1.05
Mean z-score	-1.44
Structure conservation index	0.98
SVM decision value	1.61
SVM RNA-class probability	0.967611
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5030238 119 - 20766785
GUGUGUGAAAUUUAAUUUGCAACUCGAGGCCACAAAAGGACAGGCUAAACUAAAGAAGUUUAACCAGUUUUGUUUGUUUUGCGUGCUAGUUGCAAGCACAGAGAAAAACACUCAAGUAC
(.((((....(((..(((((((((.((.((.((((((((((.((.((((((.....)))))).)).))))).)))))...)).).).)))))))))...))).....)))).)...... ( -28.60)
>DroSec_CAF1 10295 118 - 1
GUGUGUGA-AUUUAAUUUGCAACUCGAGGCCACAAAAGGACAGGCUAAACUAAAGAAGUUUAACCAGUUUUGUUUGUUUUGCGUGCUAGUUGCAAGCACAGAGAAAAACACUCAAGUAC
.(((((..-.......((((((((.((.((.((((((((((.((.((((((.....)))))).)).))))).)))))...)).).).)))))))))))))(((.......)))...... ( -28.60)
>DroSim_CAF1 10321 119 - 1
GUGUGUGAAAUUUAAUUUGCAACUCGAGGCCACAAAAGGACAGGCUAAACUAAAGAAGUUUAACCAGUUUUGUUUGUUUUGCGUGCUAGUUGCAAGCACAGAGAAAAACACUCAAGUAC
(.((((....(((..(((((((((.((.((.((((((((((.((.((((((.....)))))).)).))))).)))))...)).).).)))))))))...))).....)))).)...... ( -28.60)
>DroEre_CAF1 10216 119 - 1
GUGUGUGAAAUUUAAUUUGCAACUCGAGGCCACAAAAGGACAGGCUAAACUAAAGAAGUUUAACCAGUUUUGUUUGUUUUGCGUGCAAGUUGCAAGCACAGAGAGAAACUCUCGAGCCC
.(((((......(((((((((.(.((((((.((((...(((.((.((((((.....)))))).)).)))))))..)))))).))))))))))...)))))(((((...)))))...... ( -32.40)
>DroYak_CAF1 10440 119 - 1
GUGUGUGAAAUUUAAUUUGCAACUCGAGGCCACAAGAGGACAGGCUAAACUAAAGAAGUUUAACCAGUUUUGUUUGUUUUGCGUGCUAGUUGCAAGCACAGAGAAAAACUCUUAAUAAC
.(((((..........((((((((.((.((.((((((((((.((.((((((.....)))))).)).))))).)))))...)).).).)))))))))))))(((.....)))........ ( -28.40)
>consensus
GUGUGUGAAAUUUAAUUUGCAACUCGAGGCCACAAAAGGACAGGCUAAACUAAAGAAGUUUAACCAGUUUUGUUUGUUUUGCGUGCUAGUUGCAAGCACAGAGAAAAACACUCAAGUAC
.(((((..........((((((((.((.((.((((((((((.((.((((((.....)))))).)).))))).)))))...)).).).)))))))))))))(((.......)))...... (-28.74 = -28.42 +  -0.32)

alignment

secondary structure

dotplot

Window 5

Location	5,030,278 – 5,030,393
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	97.39
Mean single sequence MFE	-25.32
Consensus MFE	-24.58
Energy contribution	-24.82
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.13
Structure conservation index	0.97
SVM decision value	3.41
SVM RNA-class probability	0.999173
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5030278 115 + 20766785
AAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACACACAGUGGCACAUAUCAGCGCACUCACACACACCAGG
...........((.(((((((((.....))))))))).))(((..((((.....((((.((.............(((.....)))((........))))))))...))))..))) ( -26.70)
>DroSec_CAF1 10335 114 + 1
AAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAU-UCACACACACAGUGGCACAUAUCAGCGCACUCACACACACCAGG
...........((.(((((((((.....))))))))).))(((..((((.....((((.((.........-...(((.....)))((........))))))))...))))..))) ( -26.70)
>DroSim_CAF1 10361 115 + 1
AAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACACACAGUGGCACAUAUCAGCGCACUCACACACACCAGG
...........((.(((((((((.....))))))))).))(((..((((.....((((.((.............(((.....)))((........))))))))...))))..))) ( -26.70)
>DroEre_CAF1 10256 115 + 1
AAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACACACAGUGGCACACAUCCGCGCACACACACACACCAGG
...........((.(((((((((.....))))))))).))(((..((((((........)).....................(((((.(......).)).)))...))))..))) ( -23.20)
>DroYak_CAF1 10480 115 + 1
AAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUCUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACACACCGUGGCACAUAUCAGCGCGCACACACACACCAGG
...........((.(((((((((.....))))))))).))(((..((((((........)).....................(((((.(......).)).)))...))))..))) ( -23.30)
>consensus
AAACAAACAAAACUGGUUAAACUUCUUUAGUUUAGCCUGUCCUUUUGUGGCCUCGAGUUGCAAAUUAAAUUUCACACACACAGUGGCACAUAUCAGCGCACUCACACACACCAGG
...........((.(((((((((.....))))))))).))(((..((((.....((((.((.............(((.....)))((........))))))))...))))..))) (-24.58 = -24.82 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:10 2006