Locus 210

Sequence ID	2L_DroMel_CAF1
Location	614,845 – 614,972
Length	127
Max. P	0.897115

overview

Window 3

Location	614,845 – 614,941
Length	96
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	80.59
Mean single sequence MFE	-25.20
Consensus MFE	-13.94
Energy contribution	-14.49
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.97
Structure conservation index	0.55
SVM decision value	0.09
SVM RNA-class probability	0.579140
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 614845 96 - 22407834
UUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUACACUUGGCUGAUGUUUAAUGCUUAAUGGCAUUAA
((((((((.((....))))))))))......((..((((...((((((....))))))......))))..))....((((((((....)))))))) ( -27.60)
>DroVir_CAF1 2600 78 - 1
UUUCGGUGUGGUCCCCCCCCCUACCC------------------CAGCGCCAGAGGUUAAUACACUUGCCUCAUGUUUAAUCCUAAAUGGCAUUAA
....((((.((.......)).)))).------------------....(((.(((((..........)))))..(((((....))))))))..... ( -17.00)
>DroSim_CAF1 3351 96 - 1
UUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUACACUUAGCUGAUGUUUAAUGCUUAAUGGCAUUAA
((((((((.((....)))))))))).......((((......)))).((((((((((......))))..)))))).((((((((....)))))))) ( -26.90)
>DroEre_CAF1 6044 96 - 1
UUUCGGUGUGGUCCCCCCACUGAAACACUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUACACUUGGCUGAUGUUUAAUGCUUAAUGGCAUUAA
((((((((.((....)))))))))).((...((..((((...((((((....))))))......))))..))..))((((((((....)))))))) ( -27.90)
>DroYak_CAF1 6579 96 - 1
UUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUACACUUGGCUGAUGUUUAAUGCUUAAUGGCAUUAA
((((((((.((....))))))))))......((..((((...((((((....))))))......))))..))....((((((((....)))))))) ( -27.60)
>DroMoj_CAF1 2349 78 - 1
UUUCGGUGUGGUCCCUCGCCUCACCG------------------CCCCGCCAGGGGUUAAUACACUUGCCUCAUGUUUAAUCCUAAAUGGCAUUAA
...(((((.(((.....))).)))))------------------....((((((((((((.(((.........)))))))))))...))))..... ( -24.20)
>consensus
UUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUACACUUGGCUGAUGUUUAAUGCUUAAUGGCAUUAA
....((((((...((((.............((......))............))))....))))))..........((((((((....)))))))) (-13.94 = -14.49 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	614,879 – 614,972
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	99.57
Mean single sequence MFE	-34.02
Consensus MFE	-33.52
Energy contribution	-33.72
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.34
Structure conservation index	0.99
SVM decision value	0.39
SVM RNA-class probability	0.716039
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 614879 93 + 22407834
UAUUAACCCCUGAUGGGAUCGAGCUUGAUCGCGAGGGUUUCAGUGGGGGGACCACACCGAAAUGGCUUGCUCAUGACCAGCGGCGAGGUCAGA
......(((((..((..(((..((......))...)))..))..)))))((((.(.(((...((((........).))).))).).))))... ( -34.20)
>DroSec_CAF1 4247 93 + 1
UAUUAACCCCUGAUGGGAUCGAGCUUGAUCGCGAGGGUUUCAGUGGGGGGACCACACCGAAAUGGCUUGCUCAUGACCAGCGGCGAGGUCAGA
......(((((..((..(((..((......))...)))..))..)))))((((.(.(((...((((........).))).))).).))))... ( -34.20)
>DroSim_CAF1 3385 93 + 1
UAUUAACCCCUGAUGGGAUCGAGCUUGAUCGCGAGGGUUUCAGUGGGGGGACCACACCGAAAUGGCUUGCUCAUGACCAGCGGCGAGGUCAGA
......(((((..((..(((..((......))...)))..))..)))))((((.(.(((...((((........).))).))).).))))... ( -34.20)
>DroEre_CAF1 6078 93 + 1
UAUUAACCCCUGAUGGGAUCGAGCUUGAUCGCGAGUGUUUCAGUGGGGGGACCACACCGAAAUGGCUUGCUCAUGACCAGCGGCGAGGUCAGA
.....(((((((.((((((((....)))))(((((((((((.(((((....)).))).))))).))))))......))).))).).))).... ( -33.30)
>DroYak_CAF1 6613 93 + 1
UAUUAACCCCUGAUGGGAUCGAGCUUGAUCGCGAGGGUUUCAGUGGGGGGACCACACCGAAAUGGCUUGCUCAUGACCAGCGGCGAGGUCAGA
......(((((..((..(((..((......))...)))..))..)))))((((.(.(((...((((........).))).))).).))))... ( -34.20)
>consensus
UAUUAACCCCUGAUGGGAUCGAGCUUGAUCGCGAGGGUUUCAGUGGGGGGACCACACCGAAAUGGCUUGCUCAUGACCAGCGGCGAGGUCAGA
......(((((..((..(((..((......))...)))..))..)))))((((.(.(((...((((........).))).))).).))))... (-33.52 = -33.72 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	614,879 – 614,972
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	99.57
Mean single sequence MFE	-29.40
Consensus MFE	-29.40
Energy contribution	-29.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	1.00
SVM decision value	1.00
SVM RNA-class probability	0.897115
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 614879 93 - 22407834
UCUGACCUCGCCGCUGGUCAUGAGCAAGCCAUUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUA
..(((((........))))).((((..((..((((((((.((....)))))))))).....))......))))((((((....)))))).... ( -29.40)
>DroSec_CAF1 4247 93 - 1
UCUGACCUCGCCGCUGGUCAUGAGCAAGCCAUUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUA
..(((((........))))).((((..((..((((((((.((....)))))))))).....))......))))((((((....)))))).... ( -29.40)
>DroSim_CAF1 3385 93 - 1
UCUGACCUCGCCGCUGGUCAUGAGCAAGCCAUUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUA
..(((((........))))).((((..((..((((((((.((....)))))))))).....))......))))((((((....)))))).... ( -29.40)
>DroEre_CAF1 6078 93 - 1
UCUGACCUCGCCGCUGGUCAUGAGCAAGCCAUUUCGGUGUGGUCCCCCCACUGAAACACUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUA
..(((((........))))).((((..((..((((((((.((....)))))))))).....))......))))((((((....)))))).... ( -29.40)
>DroYak_CAF1 6613 93 - 1
UCUGACCUCGCCGCUGGUCAUGAGCAAGCCAUUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUA
..(((((........))))).((((..((..((((((((.((....)))))))))).....))......))))((((((....)))))).... ( -29.40)
>consensus
UCUGACCUCGCCGCUGGUCAUGAGCAAGCCAUUUCGGUGUGGUCCCCCCACUGAAACCCUCGCGAUCAAGCUCGAUCCCAUCAGGGGUUAAUA
..(((((........))))).((((..((..((((((((.((....)))))))))).....))......))))((((((....)))))).... (-29.40 = -29.40 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:42 2006