Locus 1690

Sequence ID	2R_DroMel_CAF1
Location	6,414,476 – 6,414,676
Length	200
Max. P	0.762885

overview

Window 8

Location	6,414,476 – 6,414,596
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.42
Mean single sequence MFE	-41.76
Consensus MFE	-38.90
Energy contribution	-39.10
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-1.20
Structure conservation index	0.93
SVM decision value	0.51
SVM RNA-class probability	0.762885
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6414476 120 - 20766785
UCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUGGUGCAGGGCGGCAUGACGCCCUCCGCCAAGCAAUCGCUCGUAGAUAUGGCCCCCAAGUACAUCCUGGAACAGUUUCUCGA
.............((((((.......(((((((.(((.(((((.((((((......)))))).)))))))).(((.......))))))))))(((.(.....).)))....).))))).. ( -42.00)
>DroSec_CAF1 10222 120 - 1
CCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUGGUGCAGGGCGGCAUGACGCCCUCCGCCAAGCAAUCCCUCGUAGAUAUGGCCCCCAAGUACAUCCUGGAACAGUUCCUCGA
((.......))..((((((.......(((((((.(((.(((((.((((((......)))))).)))))))).(((.......))))))))))(((.(.....).)))....))).))).. ( -41.50)
>DroSim_CAF1 12316 120 - 1
CCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUGGUGCAGGGCGGCAUGACGCCCUCCGCCAAGCAAUCCCUCGUAGAUAUGGCCCCCAAGUACAUCCUGGAACAGUUCCUCGA
((.......))..((((((.......(((((((.(((.(((((.((((((......)))))).)))))))).(((.......))))))))))(((.(.....).)))....))).))).. ( -41.50)
>DroEre_CAF1 8983 120 - 1
CCGUAUGCAAGAAGAGAACAUCCACCGGGCCAUCGUUGUUGUUCAGGGCGGAAUGACGCCCUCCGCCAAACAAUCCCUCGUGGAUAUGGCUCCCAAGUACAUCCUGGAGCAGUUCCUCGA
.............((((((((((((.(((.....((((((((..((((((......))))))..))..)))))))))..))))))...(((((..((......))))))).))).))).. ( -39.90)
>DroYak_CAF1 9135 120 - 1
CCGUAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUGGUUCAGGGCGGAAUGACGCCCUCCGCCAAACAAUCUCUCGUGGAUAUGGCCCCCAAGUACAUCUUGGAGCAGUUCCUCGA
((.......))..((((((.......(((((((.(((.((((..((((((......))))))..))))))).((((.....)))))))))))(((((.....)))))....))).))).. ( -43.90)
>consensus
CCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUGGUGCAGGGCGGCAUGACGCCCUCCGCCAAGCAAUCCCUCGUAGAUAUGGCCCCCAAGUACAUCCUGGAACAGUUCCUCGA
.............((((((.......(((((((.(((.(((((.((((((......)))))).)))))))).(((.......))))))))))(((.(.....).)))....))).))).. (-38.90 = -39.10 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	6,414,556 – 6,414,676
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-38.00
Consensus MFE	-36.96
Energy contribution	-36.52
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-1.05
Structure conservation index	0.97
SVM decision value	-0.01
SVM RNA-class probability	0.526918
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6414556 120 - 20766785
GACGAUCCCACGGACCAGAUGUUCGUCUUCUUUCCCGAGGAGCCGAAGAUCGGCAUCAAGACAAUCAAGACGUACUGCACUCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUG
((((((.((.(((....(((((((.(((((.........((((((.....)))).)).................(((((......)))))))))))))))))..)))))..))))))... ( -39.80)
>DroSec_CAF1 10302 120 - 1
GACGAUCCCACGGACCAGAUGUUCGUCUUCUUUCCCGAGGAGCCGAAGAUCGGCAUCAAGACAAUCAAGACGUACUGCACCCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUG
((((((.((.(((....(((((((.(((((.........((((((.....)))).)).................(((((......)))))))))))))))))..)))))..))))))... ( -39.80)
>DroSim_CAF1 12396 120 - 1
GACGAUCCCACGGACCAGAUGUUCGUCUUCUUUCCCGAGGAGCCGAAGAUCGGCAUCAAGACAAUCAAGACGUACUGCACCCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUG
((((((.((.(((....(((((((.(((((.........((((((.....)))).)).................(((((......)))))))))))))))))..)))))..))))))... ( -39.80)
>DroEre_CAF1 9063 120 - 1
GACGAUCCCACGGACCAGAUGUUUGUCUUCUUCCCCGAGGAGCCGAAGAUCGGCAUCAAGACCAUCAAGACGUACUGCACCCGUAUGCAAGAAGAGAACAUCCACCGGGCCAUCGUUGUU
((((((.((.(((....(((((((.(((((((.......((((((.....)))).))...........(.(((((.......))))))))))))))))))))..)))))..))))))... ( -36.00)
>DroYak_CAF1 9215 120 - 1
GACGAUCCCACGGACCAGAUGUUUGUCUUCUUCCCCGAGGAGCCAAAGAUCGGCAUCAAGACCAUCAAGACGUACUGCACCCGUAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUG
((((((.((.(((....(((((((.(((((.(((....)))(((.......)))....................(((((......)))))))))))))))))..)))))..))))))... ( -34.60)
>consensus
GACGAUCCCACGGACCAGAUGUUCGUCUUCUUUCCCGAGGAGCCGAAGAUCGGCAUCAAGACAAUCAAGACGUACUGCACCCGCAUGCAGGAAGAGAACAUCCACCGGGCCAUCGUUGUG
((((((.((.(((....(((((((.(((((((.......((((((.....)))).))..............(((.(((....))))))))))))))))))))..)))))..))))))... (-36.96 = -36.52 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:46 2006