Locus 4181

Sequence ID	2L_DroMel_CAF1
Location	11,975,944 – 11,976,111
Length	167
Max. P	0.769765

overview

Window 8

Location	11,975,944 – 11,976,042
Length	98
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	78.43
Mean single sequence MFE	-28.72
Consensus MFE	-16.12
Energy contribution	-16.23
Covariance contribution	0.11
Combinations/Pair	1.24
Mean z-score	-1.66
Structure conservation index	0.56
SVM decision value	0.04
SVM RNA-class probability	0.553407
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11975944 98 + 22407834
GAGCCAACCGACAUGCAUGCAAUGUGGC---ACGGAUCUA-GGUCCAACU---UCGUUGUAAAAUGCAAACAGUUUUCCGCUG-UUGUGAGUGGAAAGCUGAGGAA
.......((....(((((((((((.((.---..((((...-.))))..))---.))))))...)))))..((((((((((((.-.....)))))))))))).)).. ( -35.20)
>DroSec_CAF1 195385 98 + 1
GAGCCAACCGACAUGCAUGCAAUGUGGC---ACGGAUCUA-GGUCCAACU---UCGUUGUAAAAUGCAAACAGUUUUCCGCUG-UUGAGAGUGGAAAGCCGAGGAA
.......((....(((((((((((.((.---..((((...-.))))..))---.))))))...)))))..(.((((((((((.-.....)))))))))).).)).. ( -30.60)
>DroSim_CAF1 161773 98 + 1
GAGCCAACCGACAUGCAUGCAAUGUGGC---ACGGAUCUA-GGUCCAACU---UCGUUGUAAAAUGCAAACAGUUUUCCGCUG-UUGAGAGUGGAAAGCCGAGGAA
.......((....(((((((((((.((.---..((((...-.))))..))---.))))))...)))))..(.((((((((((.-.....)))))))))).).)).. ( -30.60)
>DroEre_CAF1 169816 94 + 1
AAGCCAUCCAACAU----GCAAUGUGGC---ACGGAUCUA-GGUACAACU---UGGUUGUAAAAUGCAAACAGUUUUCCGCUG-CUGUGAGUGGAAAGCCGAGCAA
..(((((((....(----((......))---).))))...-)))(((((.---..)))))....(((...(.((((((((((.-.....)))))))))).).))). ( -23.90)
>DroYak_CAF1 166784 94 + 1
GAGCCAUUCAACAU----GCAAUGUGGC---ACGGAUCUG-GGUCCAACU---UCGUUGUAAAAUGCAAACAGUUUUCCGCUG-CUGUCAGUGGAAAAGCGAGGAA
..(((((.......----.....)))))---..((((...-.))))..((---(((((((.....))).....((((((((((-....)))))))))))))))).. ( -30.20)
>DroMoj_CAF1 187403 93 + 1
-------CAAAC----AUGCAAUAUGGCUGAACGGGUGGCUGCCUCAACACAGUCGACGGCACUUGAAAACA-UUUUCCGUUGCCUGCAAAUGGAAAAUUGUG-AA
-------.....----.(((....((((((...((((....)))).....))))))...))).......(((-(((((((((.......))))))))).))).-.. ( -21.80)
>consensus
GAGCCAACCAACAU__AUGCAAUGUGGC___ACGGAUCUA_GGUCCAACU___UCGUUGUAAAAUGCAAACAGUUUUCCGCUG_CUGUGAGUGGAAAGCCGAGGAA
........((((......((......)).....((((.....)))).........))))...........(.((((((((((.......)))))))))).)..... (-16.12 = -16.23 +   0.11)

alignment

secondary structure

dotplot

Window 9

Location	11,976,003 – 11,976,111
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.00
Mean single sequence MFE	-29.88
Consensus MFE	-13.62
Energy contribution	-13.43
Covariance contribution	-0.19
Combinations/Pair	1.21
Mean z-score	-2.01
Structure conservation index	0.46
SVM decision value	0.53
SVM RNA-class probability	0.769765
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11976003 108 + 22407834
CAAACAGUUUUCCGCUG-UUGUGAGUGGAAAGCUGAGGAAAAAUUAUGUGCUAAACACGCAGUCUGA-G----CG-AGUACAGUUAGCACAAAA--UAU-AAAGAACAUUCUCGUCCA--
....((((((((((((.-.....)))))))))))).(((...(((.((((((((((.(((.......-)----))-.))....)))))))).))--)..-...((......)).))).-- ( -34.10)
>DroVir_CAF1 177721 116 + 1
CAAACA-UUUUCCGCUGCCUGCAAAUGGAAAAUUGUG-AAAAAUGAUGUGCUAAACACGAAGCUUGCAACGGCUGUGGUACAGUUACUGCAAAAGGC--UGUACUCCAUUCUUCGCUUCC
.....(-(((((((.((....))..)))))))).(((-((.((((..((((.........((((((((..(((((.....)))))..))))...)))--)))))..)))).))))).... ( -28.70)
>DroSim_CAF1 161832 108 + 1
CAAACAGUUUUCCGCUG-UUGAGAGUGGAAAGCCGAGGAAAAAUUAUGUGCUAAACACGCAGUCUGA-G----CG-AGUACAGUUAGCACAAAA--UAU-AAAGCACAUUCUCGUCUA--
......((((((((((.-.....))))))))))((((((...(((.((((((((((.(((.......-)----))-.))....)))))))).))--)..-........))))))....-- ( -29.32)
>DroEre_CAF1 169871 108 + 1
CAAACAGUUUUCCGCUG-CUGUGAGUGGAAAGCCGAGCAAAAAUGAUGCGCUAAACACGCAGGCUGA-G----UG-AGUACAGUUAGCACAAGC--UAU-AAAGCACAUUCCCGUCUA--
....(.((((((((((.-.....)))))))))).).(((.......)))((.......))((((.((-(----((-.((.....((((....))--)).-...)).)))))..)))).-- ( -27.90)
>DroYak_CAF1 166839 110 + 1
CAAACAGUUUUCCGCUG-CUGUCAGUGGAAAAGCGAGGAAAAAUUAUGUGCUAAACACGCAGUCUGA-G----UG-GGUACAGUUAGCGCAAAAUAUAU-AAAGCACAUUCCCGUCUA--
.......((((((((((-....))))))))))(((.(((......(((((((......((.(.((((-.----((-....)).))))))).........-..)))))))))))))...-- ( -28.53)
>DroMoj_CAF1 187458 117 + 1
AAAACA-UUUUCCGUUGCCUGCAAAUGGAAAAUUGUG-AAAAGCUAUGUGCUAAACACGAAGCAUGCAACAGCUG-GGUACAGUUACUGCAAAAAGUCUCGAGCCACAUUCUUAGCUCAC
...(((-(((((((((.......))))))))).))).-....(((.((((.....)))).))).((((..(((((-....)))))..)))).........((((..........)))).. ( -30.70)
>consensus
CAAACAGUUUUCCGCUG_CUGUGAGUGGAAAACCGAGGAAAAAUUAUGUGCUAAACACGCAGUCUGA_G____UG_AGUACAGUUAGCACAAAA__UAU_AAAGCACAUUCUCGUCUA__
.......(((((((((.......)))))))))..............((((((((..((...................))....))))))))............................. (-13.62 = -13.43 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:46 2006