Locus 1929

Sequence ID	3L_DroMel_CAF1
Location	5,385,302 – 5,385,551
Length	249
Max. P	0.826700

overview

Window 7

Location	5,385,302 – 5,385,393
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	93.16
Mean single sequence MFE	-28.70
Consensus MFE	-21.28
Energy contribution	-21.28
Covariance contribution	-0.00
Combinations/Pair	1.08
Mean z-score	-2.46
Structure conservation index	0.74
SVM decision value	0.70
SVM RNA-class probability	0.826700
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5385302 91 + 23771897
UGUGAAAAGCUUGCUUUGGGGGGGCUUAAUCCUUAUAGCCACUUGUGGCGUAAUUAAGGACAAAAAUCGGGGUUGAGCUCUUCUGUCAAUC
..(((((((....))))((((((((((((((((.((.((((....))))((........))....)).)))))))))))))))).)))... ( -30.40)
>DroSec_CAF1 34450 88 + 1
UGUGAAAAG-UGGCUUUGG--GGGCUUAAUCCUUAUAGCCACUUGUGGCGUAAUUAAGGACGAAAAUCGGGGUUGAACUCUUCUGUCAAUC
.((.(.(((-(((((.(((--(((.....)))))).)))))))).).)).........((((((....(((......)))))).))).... ( -25.10)
>DroSim_CAF1 32692 88 + 1
UGUGAAAAG-UGGCUUUGG--GGGCUUAAUCCUUAUAGCCACUUGUGGCGCAAUUAAGGACAAAAAUCGGGGUUGAGCUCUGCUGUCAAUC
((((..(((-(((((.(((--(((.....)))))).))))))))....))))......((((.....(((((.....))))).)))).... ( -29.70)
>DroEre_CAF1 34411 87 + 1
UGUGAAAAG-UGGCU-UAG--GGGCUUAAUCUUUAUAGCCACUUGUGGCGUAAUUAAGGACAAAAAUCGGGGUUGAGCUCUUCUGUCAAUC
.........-((((.-.((--(((((((((((..((.((((....))))((........))....))..)))))))))))))..))))... ( -27.80)
>DroYak_CAF1 33120 88 + 1
UGUGAAAAU-UGGCUCUGG--GGGCUUAAUCUUUAUAGCCACUUGUGGCGUAAUUAGGGACAAAAAUCGGGGUUGAGCUCCUCUGUCAAUC
.......((-((((...((--(((((((((((..((.((((....))))((........))....))..)))))))))))))..)))))). ( -30.50)
>consensus
UGUGAAAAG_UGGCUUUGG__GGGCUUAAUCCUUAUAGCCACUUGUGGCGUAAUUAAGGACAAAAAUCGGGGUUGAGCUCUUCUGUCAAUC
..........((((...((..((((((((((((....((((....)))).........((......))))))))))))))..))))))... (-21.28 = -21.28 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	5,385,331 – 5,385,432
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	93.39
Mean single sequence MFE	-24.02
Consensus MFE	-21.58
Energy contribution	-21.02
Covariance contribution	-0.56
Combinations/Pair	1.11
Mean z-score	-1.16
Structure conservation index	0.90
SVM decision value	0.12
SVM RNA-class probability	0.593480
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5385331 101 + 23771897
UCCUUAUAGCCACUUGUGGCGUAAUUAAGGACAAAAAUCGGGGUUGAGCUCUUCUGUCAAUCUCUUGGGACCACAUUUGAUCAGAAGAUAAAAUUAUAUAU
((((((..((((....)))).....))))))..........((((....(((((((((((.....((....))...)))).)))))))...))))...... ( -23.70)
>DroSec_CAF1 34476 99 + 1
UCCUUAUAGCCACUUGUGGCGUAAUUAAGGACGAAAAUCGGGGUUGAACUCUUCUGUCAAUCUCUUGGGACCACAUUUGAUCAGAAGAUAACAUUAU--AU
((((((..((((....)))).....))))))((.....))..((((...(((((((((((.....((....))...)))).))))))))))).....--.. ( -25.60)
>DroSim_CAF1 32718 99 + 1
UCCUUAUAGCCACUUGUGGCGCAAUUAAGGACAAAAAUCGGGGUUGAGCUCUGCUGUCAAUCUCUUGGGAGCACAUUUGAUCAGAAGAUAACAUUAU--AU
((((((..((((....)))).....)))))).....(((..(((..((...((((.((((....)))).))))..))..)))....)))........--.. ( -25.20)
>DroEre_CAF1 34436 99 + 1
UCUUUAUAGCCACUUGUGGCGUAAUUAAGGACAAAAAUCGGGGUUGAGCUCUUCUGUCAAUCUCUUGGGACAACAUUUGAUCAGGAGAUAACAUUAU--AU
........((((....))))(((((....((((......((((.....))))..)))).(((((((((..((.....)).)))))))))...)))))--.. ( -21.90)
>DroYak_CAF1 33146 99 + 1
UCUUUAUAGCCACUUGUGGCGUAAUUAGGGACAAAAAUCGGGGUUGAGCUCCUCUGUCAAUCUCGUGGGAGAACAUUUGAUCGGAAGAUAACAUUAU--AU
((((((..((((....)))).....)))))).....(((((((.....))))((((((((((((....))))....)))).)))).)))........--.. ( -23.70)
>consensus
UCCUUAUAGCCACUUGUGGCGUAAUUAAGGACAAAAAUCGGGGUUGAGCUCUUCUGUCAAUCUCUUGGGACCACAUUUGAUCAGAAGAUAACAUUAU__AU
((((((..((((....)))).....))))))((((....((((((((.(......))))))))).((......))))))(((....)))............ (-21.58 = -21.02 +  -0.56)

alignment

secondary structure

dotplot

Window 9

Location	5,385,432 – 5,385,551
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	90.76
Mean single sequence MFE	-32.69
Consensus MFE	-23.64
Energy contribution	-25.88
Covariance contribution	2.24
Combinations/Pair	1.09
Mean z-score	-1.94
Structure conservation index	0.72
SVM decision value	0.18
SVM RNA-class probability	0.621048
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5385432 119 + 23771897
GGCUAACAAUUUCACUCAAUUGGGAAGUGAUGGUUGGAAGUGAUUUUCCUUCCCACACGUUACUCACAUCCGUUUCGCAUUUCUUUGGAAUUUUCCCACCAUAUGUGAGGAUGACAACA
......((.((((((.....((((((((((((((.(((((.(.....)))))).)).)))))).....((((.............))))...))))))......)))))).))...... ( -30.62)
>DroSec_CAF1 34575 119 + 1
GGCUAACAAUUUCACUCAAUUGGGAAGUUAUGGUGGGAAGUGAUUUUCCUUCCCACACGUUACUCACAUCCGUUUCGCAUUUCUUUGGAAUUUUCCCACCAUAUGUGAGGAUGACAACA
(..((((((((((.(......).))))))...((((((((.(.....)))))))))..))))..).(((((...((((((......(((....)))......)))))))))))...... ( -34.30)
>DroSim_CAF1 32817 119 + 1
GGCUAACAAUUUCACUCAAUUGGGAAGUGCUGGUGGGAAGUGAUUUUCCUUUCCACACGGUACUCACAUCCGUUUCGCAUUUCUUCGGAAUUUUCCCACCAUAUGUGAGGAUGACAACA
......((.((((((.....((((((((((((((((((((.(.....))))))))).)))))).....((((.............))))...))))))......)))))).))...... ( -37.52)
>DroEre_CAF1 34535 119 + 1
GGCUAACAAUUUUACUCAAUUGCGAAGUGAUGGUGGGAAGUGAUUUUCAUCGCCACACGUUACUCACAUCCGUUUCGCAUUUCUUUGGAAUUUUCCCACCAUAUGUGCGGAUGACAACA
(..((((........((......)).(((.((((((((((....)))).)))))))))))))..).(((((((...((((......(((....)))......)))))))))))...... ( -30.00)
>DroYak_CAF1 33245 118 + 1
GGCUAACAAUUUUACUCAAUUGCGAAGUGAUGGUGGGAAGUAAUGGUGGGAA-GUGAUUUUACUCACAUCCGUUUCGCAUUUCUUUGGCAUUUUCCCACCAUAUGUGUGGAUGACAACA
...............(((.(..((.....(((((((((((........(((.-((((......)))).))).....((.........))..)))))))))))...))..).)))..... ( -31.00)
>consensus
GGCUAACAAUUUCACUCAAUUGGGAAGUGAUGGUGGGAAGUGAUUUUCCUUCCCACACGUUACUCACAUCCGUUUCGCAUUUCUUUGGAAUUUUCCCACCAUAUGUGAGGAUGACAACA
......(((((......))))).((.((((((((((((((........)))))))).)))))))).(((((....(((((......((......))......))))).)))))...... (-23.64 = -25.88 +   2.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:13 2006