Locus 2070

Sequence ID	2L_DroMel_CAF1
Location	5,577,008 – 5,577,148
Length	140
Max. P	0.611108

overview

Window 4

Location	5,577,008 – 5,577,108
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.59
Mean single sequence MFE	-20.77
Consensus MFE	-14.50
Energy contribution	-14.18
Covariance contribution	-0.32
Combinations/Pair	1.11
Mean z-score	-1.71
Structure conservation index	0.70
SVM decision value	0.16
SVM RNA-class probability	0.611108
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5577008 100 - 22407834
UUCAACUAACCGUUCGAGUUUCAGUUUGCUUUCCGCUU----------------UUUUUU----UUUUGUUGCCACUCGAAGCAUUUCAAAAGAAGCACUUAAAAAUCGACACGGUAUGC
........(((((((((((........)).....((((----------------(((((.----...((((.........))))....))))))))).........)))).))))).... ( -20.20)
>DroSec_CAF1 21039 104 - 1
AUCAACUAACCGUUCGAGUUUCAGUUUGCUUUCCGCUU----------------CUUUUUUUUUUUUUUUUGCCACUCGAAGCAUUUCAAAAGAAGCACUUAAAAAUCGACACGGUAUGC
........(((((((((((........)).....((((----------------(((((...........(((........)))....))))))))).........)))).))))).... ( -19.86)
>DroSim_CAF1 22690 101 - 1
UUCAACUAACCGUUCGAGUUUCAGUUUGCUUUCCGCUU----------------CUUUUUU---UUGUUUUGCCACUCGAAGCAUUUCAAAAGAAGCUCUUAAAAAUCGACACGGUAUGC
........(((((((((((........)).....((((----------------(((((..---.(((((((.....)))))))....))))))))).........)))).))))).... ( -25.40)
>DroEre_CAF1 20961 117 - 1
UCCAACUUGCCGUUCGAGUUUCAGUUUGCUUUCCGCCUGGUUUUUACUUUUUUACUUUUUU---UUUUUUUGCCACACCGAGCAUUUCAAAAGAAGCACUUAAAAAUCGACACGGUAUGC
.......((((((((((...((((...((.....))))))........(((((((((((((---(.....(((........)))....))))))))....)))))))))).))))))... ( -20.00)
>DroYak_CAF1 20917 91 - 1
-CCAACUAACUGUUCGAGUUUCAGUUUGCUUUCCGC----------------------------UUUUUUUGCCACUGCUAGCAUUUCAAAAGAAGCACUUAAAAAUCGACACGGUAUGC
-.......(((((((((((........)).....((----------------------------((((((((....((....))...)))))))))).........)))).))))).... ( -18.40)
>consensus
UUCAACUAACCGUUCGAGUUUCAGUUUGCUUUCCGCUU________________CUUUUUU___UUUUUUUGCCACUCGAAGCAUUUCAAAAGAAGCACUUAAAAAUCGACACGGUAUGC
........((((((((((((((.....((.....))..................................(((........)))........))))).........)))).))))).... (-14.50 = -14.18 +  -0.32)

alignment

secondary structure

dotplot

Window 5

Location	5,577,048 – 5,577,148
Length	100
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	84.53
Mean single sequence MFE	-27.12
Consensus MFE	-20.88
Energy contribution	-22.25
Covariance contribution	1.38
Combinations/Pair	1.09
Mean z-score	-1.43
Structure conservation index	0.77
SVM decision value	-0.03
SVM RNA-class probability	0.516965
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5577048 100 + 22407834
UCGAGUGGCAACAAAA----AAAAAAAAGCGGAAAGCAAACUGAAACUCGAACGGUUAGUUGAAGGCGCUCGGGGUCGCGGCCUCUGCCCGAUCUCAAAUAGGC
..(((((.(..(((..----........((.....)).(((((.........)))))..)))..).)))))(((((((.(((....))))))))))........ ( -29.30)
>DroSec_CAF1 21079 104 + 1
UCGAGUGGCAAAAAAAAAAAAAAAAGAAGCGGAAAGCAAACUGAAACUCGAACGGUUAGUUGAUGGCGCUCGGGGUCGCGGCCUCUGCCCGAUCUCAAAUAGGC
..(((((.((..................((.....)).(((((.........)))))......)).)))))(((((((.(((....))))))))))........ ( -29.00)
>DroSim_CAF1 22730 101 + 1
UCGAGUGGCAAAACAA---AAAAAAGAAGCGGAAAGCAAACUGAAACUCGAACGGUUAGUUGAAGGCGCUCGGGGUCGCGGCCUCUGCCCGAUCUCAAAUAGGC
..(((((.(..(((..---.........((.....)).(((((.........))))).)))...).)))))(((((((.(((....))))))))))........ ( -29.40)
>DroYak_CAF1 20957 83 + 1
AGCAGUGGCAAAAAAA------------GCGGAAAGCAAACUGAAACUCGAACAGUUAGUUGG---------GGGUCGCGGCCCCUGCUCGAUCUCAAAUAGGC
(((((.(((.......------------((((..(((.(((((.........))))).)))..---------...)))).))).)))))............... ( -20.80)
>consensus
UCGAGUGGCAAAAAAA____AAAAAGAAGCGGAAAGCAAACUGAAACUCGAACGGUUAGUUGAAGGCGCUCGGGGUCGCGGCCUCUGCCCGAUCUCAAAUAGGC
..(((((.(...................((.....)).(((((.........))))).......).)))))(((((((.(((....))))))))))........ (-20.88 = -22.25 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:47 2006