Locus 7123

Sequence ID	2L_DroMel_CAF1
Location	19,975,034 – 19,975,319
Length	285
Max. P	0.994658

overview

Window 6

Location	19,975,034 – 19,975,141
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	91.53
Mean single sequence MFE	-31.33
Consensus MFE	-22.50
Energy contribution	-23.38
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-2.76
Structure conservation index	0.72
SVM decision value	0.80
SVM RNA-class probability	0.854209
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19975034 107 - 22407834
ACAGCGGAAGGCAUCCAAGGUCAUUAUCCUCCUCGCCGACUGCCUCAUCAUCAUCAAGUUAAUCAAAAUGCCAUUGGACAUUGGCCAUUGGCAUGGCUUGGCCAAAA
...((((..(((.....(((.......)))....)))..))))..........(((((((.......((((((.(((.......))).)))))))))))))...... ( -28.11)
>DroSec_CAF1 157914 107 - 1
ACAGCGGAAGGCAUCCCAGGUCAUUAUCCUCCUCGCCGACUGCCUCAUCAUCAUCAAGUUAAUCAAAAUGCCAUUGGCCAUUGGCCAUUGGCAUGGCUUGGCCAAAA
...((((..(((.....(((.......)))....)))..))))..........(((((((.......((((((.(((((...))))).)))))))))))))...... ( -33.71)
>DroSim_CAF1 160433 107 - 1
ACAGCGGAAGGCAUCCCAGGUCAUUAUCCUCCUCGCCGACUGCCUCAUCAUCAUCAAGUUAAUCAAAAUGCCAUUGGCCAUUGGCCAUUGGCAUGGCUUGGCCAAAA
...((((..(((.....(((.......)))....)))..))))..........(((((((.......((((((.(((((...))))).)))))))))))))...... ( -33.71)
>DroEre_CAF1 155980 100 - 1
ACAGCGGAAGGCACCCGAGGUCAUUAUCCUCCUCGCCGACUGCCUCAUCAUCAUCAAGUUAAUCAAAAUGCCAUUG-------GCCAUUGCCAUGGCAUGGCCAAAA
...((((..(((....((((.......))))...)))..))))..............................(((-------(((((.((....)))))))))).. ( -31.30)
>DroYak_CAF1 156927 100 - 1
ACAGCAGAAGGCACCCAAGGUCAUUAUCCUCCUCGCCAACUGCCUCAUCAUCAUCGAGUCAAUCAAAAUGCCAUUG-------GCCAUUGCCAUGGCAUGGCCGAAA
...((((..(((.....(((.......)))....)))..))))..........(((.((((.......((((((.(-------((....)))))))))))))))).. ( -29.81)
>consensus
ACAGCGGAAGGCAUCCAAGGUCAUUAUCCUCCUCGCCGACUGCCUCAUCAUCAUCAAGUUAAUCAAAAUGCCAUUGG_CAUUGGCCAUUGGCAUGGCUUGGCCAAAA
...((((..(((.....(((.......)))....)))..))))..............(((((.(...((((((.(((.......))).)))))).).)))))..... (-22.50 = -23.38 +   0.88)

alignment

secondary structure

dotplot

Window 7

Location	19,975,101 – 19,975,221
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-38.54
Consensus MFE	-35.02
Energy contribution	-34.14
Covariance contribution	-0.88
Combinations/Pair	1.15
Mean z-score	-1.16
Structure conservation index	0.91
SVM decision value	0.14
SVM RNA-class probability	0.603099
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19975101 120 - 22407834
GUUGGCCAUCUAACCGCAAUCAGGAGAUCGAAGGAAAUGCCACUUCGGAGGAAACGAGGAUGAGCCAACUGCCCACGUUGACAGCGGAAGGCAUCCAAGGUCAUUAUCCUCCUCGCCGAC
((((((.((((..((.......))))))(((((.........)))))(((((.....(((((((((...((((..(((.....)))...)))).....)))..))))))))))))))))) ( -36.70)
>DroSec_CAF1 157981 120 - 1
GUUGGCCAUUUAACCGCAAUCAGGAGAUCGAAGGAAAUGCCACUUCGGAGGAAACGAGGAUGAGCCAACUGCCCACGUUGACAGCGGAAGGCAUCCCAGGUCAUUAUCCUCCUCGCCGAC
((((((.......((.......)).((((((((.........)))))).(....)(((((((((((...((((..(((.....)))...)))).....)))..)))))))).)))))))) ( -36.60)
>DroSim_CAF1 160500 120 - 1
GUUGGCCAUCUAACCGCAAUCGGGAGAUCGAAGGAAAUGCCACUUCGGAGGAAACGAGGAUGAGCCAACUGCCCACGUUGACAGCGGAAGGCAUCCCAGGUCAUUAUCCUCCUCGCCGAC
((((((.......(((....)))(((.((((((.........)))))).(....)(((((((((((...((((..(((.....)))...)))).....)))..))))))))))))))))) ( -40.90)
>DroEre_CAF1 156040 119 - 1
GUUGGCCAUCUAACCGCAAUCAGGAGAUCGAAGGAAAUGCCACUUCGGAGGAAGCGAGGAUGAGCCAACUGC-CACAUUGACAGCGGAAGGCACCCGAGGUCAUUAUCCUCCUCGCCGAC
((((((..(((..((.......))...((((((.........)))))).)))((.(((((((((((..((((-..........))))..)))(((...)))..)))))))))).)))))) ( -36.50)
>DroYak_CAF1 156987 120 - 1
GUUGGCCAUCCAACCACAAUCAGGAGAUCGAAGGAAAUGCCACUUCGGUGGAAACGAGGAUGAGCCAACUGCCCACAUGGACAGCAGAAGGCACCCAAGGUCAUUAUCCUCCUCGCCAAC
((((((..(((..((.......))..(((((((.........))))))))))...(((((((((((..((((((....))...))))..)))(((...)))..))))))))...)))))) ( -42.00)
>consensus
GUUGGCCAUCUAACCGCAAUCAGGAGAUCGAAGGAAAUGCCACUUCGGAGGAAACGAGGAUGAGCCAACUGCCCACGUUGACAGCGGAAGGCAUCCAAGGUCAUUAUCCUCCUCGCCGAC
((((((..(((..((.......))...((((((.........)))))).)))...(((((((((((..((((...........))))..)))((.....))..))))))))...)))))) (-35.02 = -34.14 +  -0.88)

alignment

secondary structure

dotplot

Window 8

Location	19,975,221 – 19,975,319
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	92.65
Mean single sequence MFE	-36.76
Consensus MFE	-32.36
Energy contribution	-32.92
Covariance contribution	0.56
Combinations/Pair	1.15
Mean z-score	-2.02
Structure conservation index	0.88
SVM decision value	2.50
SVM RNA-class probability	0.994658
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19975221 98 - 22407834
GUUGGCUUGGCUGAGAGGCUCAUGGCCUCGCCAAAAGCGCAGUGAGCCGGAAUUUGCUUUCUCGGCCACGUUUAGUUCGAGGGGAUCUGGCUUAUUAA
....(((((((...(((((.....)))))))))..)))..(((((((((((......(..((((..(.......)..))))..).))))))))))).. ( -37.30)
>DroSec_CAF1 158101 98 - 1
GUUGGCUUGGCUGAGAAGCUCUUGGCUUCGCCAAAAGCCCAGUGAGCCGGAAUCCGCUUUCUCGGCCACGUUUAGUUCGAGGGGAUCUGGCUUAUUAA
.(((((..(((..((.....))..)))..)))))......(((((((((((.(((....(((((..(.......)..))))))))))))))))))).. ( -40.50)
>DroSim_CAF1 160620 98 - 1
GUUGGCUUGGCUGAGAAGCUCUUGGCUUCGCCAAAAGCGCAGUGAGCCGGAAUCCGCUUUCUCGGCCACGUUUAGUUCGAGGGGAUCUGGCUUAUUAA
.(((((..(((..((.....))..)))..)))))......(((((((((((.(((....(((((..(.......)..))))))))))))))))))).. ( -40.50)
>DroEre_CAF1 156159 97 - 1
GUUGGCUUGACGCU-CAGCUCAUGGCUUCGCCAAAAGCGCAGUGAGCCGGAAUCCGCUUUCUCGGCCACGUUUAGUUUGGGGGGAUCUGGCUUAUUAA
..((((.....)).-))(((..((((...))))..)))..(((((((((((.(((.(((.((..((...))..))...))).)))))))))))))).. ( -32.50)
>DroYak_CAF1 157107 97 - 1
GUUGGCUUGACUCU-CAGCUCAUGGCUUCGCCAAAAGCGCAGUGAGCCGGAAUUCGCUUUCUCGGCCACGUUUAGUUUGAGGGGAUCUGGCUUAUUAA
...((((.((((((-(((((..((((...))))..)))...(((.(((((((......))).)))))))........))))))..)).))))...... ( -33.00)
>consensus
GUUGGCUUGGCUGAGAAGCUCAUGGCUUCGCCAAAAGCGCAGUGAGCCGGAAUCCGCUUUCUCGGCCACGUUUAGUUCGAGGGGAUCUGGCUUAUUAA
.(((((..(((((((.....)))))))..)))))......(((((((((((.(((.(((.((..((...))..))...))).)))))))))))))).. (-32.36 = -32.92 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:59 2006