Locus 1219

Sequence ID	3R_DroMel_CAF1
Location	3,673,552 – 3,673,656
Length	104
Max. P	0.700023

overview

Window 1

Location	3,673,552 – 3,673,656
Length	104
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	89.29
Mean single sequence MFE	-47.90
Consensus MFE	-40.62
Energy contribution	-40.35
Covariance contribution	-0.27
Combinations/Pair	1.33
Mean z-score	-1.79
Structure conservation index	0.85
SVM decision value	0.35
SVM RNA-class probability	0.700023
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3673552 104 + 27905053
GUUGUGAGGCCGCCGACGCCGUUGCGCGGCGACUGCAUCAAGCCCACGGUAUCGCUCCUGCCGGUCUCCUCCGGCGGAGCCAUGACCGUGUCCAUGACCUGCUC
.......((.(((((.(((....)))))))).))((((((.(..((((((...(((((.(((((......))))))))))....))))))..).)))..))).. ( -48.80)
>DroSec_CAF1 32301 104 + 1
GUUGUGAGGCCGCCGACGCCGUUGCGCGGUGACUCCACCAAGCCCACGGUAUCGCUCCUGCCGGUCUCCUCCGGCGGAGCCAUGGCCGUGUCCAUGACCUGCUC
((..((.(((((((((..((((.((..((((....))))..))..))))..))(((((.(((((......))))))))))...)).)).)))))..))...... ( -49.30)
>DroSim_CAF1 34574 104 + 1
GUUGUGAGGCCGCCGACGCCGUUGCGCGGCGACUCCAUCAAGCCCACGGUAUCGCUCCUGCCGGUCUCCUCCGGCGGAGCCAUGGCCGUGUCCAUGACCUGCUC
..((.(((..(((((.(((....)))))))).)))))(((.(..((((((...(((((.(((((......))))))))))....))))))..).)))....... ( -50.10)
>DroEre_CAF1 31748 104 + 1
GUUGUGAGGCCGCCGACGCCGUUGCGCGGCGACUCCAUCAAGCCCACGGUAUCGCUCCUGCCGGUCUCCUCCGGCGGAGCCAUGGCCGUGUCCAUGACCUGCUC
..((.(((..(((((.(((....)))))))).)))))(((.(..((((((...(((((.(((((......))))))))))....))))))..).)))....... ( -50.10)
>DroYak_CAF1 23705 104 + 1
GUUGUGAGGCCGCCGACGCCGUUGCGCGGCGACUCCAUCAAGCCCACGGCAUCGCUCAUGCCGGUCUCCUCCGGCGGAGCCAUGGCCGUGUCCAUGAACUGCUC
..((.(((..(((((.(((....)))))))).)))))(((.(..((((((...((((.((((((......))))))))))....))))))..).)))....... ( -49.80)
>DroAna_CAF1 20596 104 + 1
GUUGUGCGCCCGCCGACGCCUUUGCGCGGCGAUUCAGUUAAGCCCUCGGGAUCUUUGCUGUUGGACGGCUCCGGUGGAGCUAUAUCCAUGGCGAUGGGAUGCUC
.....((((((((((.(((....)))))))(((((.(.........).))))).(((((((.(((.((((((...))))))...)))))))))).))).))).. ( -39.30)
>consensus
GUUGUGAGGCCGCCGACGCCGUUGCGCGGCGACUCCAUCAAGCCCACGGUAUCGCUCCUGCCGGUCUCCUCCGGCGGAGCCAUGGCCGUGUCCAUGACCUGCUC
((..((.((((((((.(((....))))))))..............(((((...(((((.(((((......))))))))))....))))))))))..))...... (-40.62 = -40.35 +  -0.27)

alignment

secondary structure

dotplot

Window 2

Location	3,673,552 – 3,673,656
Length	104
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	89.29
Mean single sequence MFE	-51.13
Consensus MFE	-40.28
Energy contribution	-42.50
Covariance contribution	2.22
Combinations/Pair	1.06
Mean z-score	-2.40
Structure conservation index	0.79
SVM decision value	0.14
SVM RNA-class probability	0.605145
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3673552 104 - 27905053
GAGCAGGUCAUGGACACGGUCAUGGCUCCGCCGGAGGAGACCGGCAGGAGCGAUACCGUGGGCUUGAUGCAGUCGCCGCGCAACGGCGUCGGCGGCCUCACAAC
(((...((((.(..((((((.((.((((((((((......))))).))))).))))))))..).))))...((((((((((....))).))))))))))..... ( -56.00)
>DroSec_CAF1 32301 104 - 1
GAGCAGGUCAUGGACACGGCCAUGGCUCCGCCGGAGGAGACCGGCAGGAGCGAUACCGUGGGCUUGGUGGAGUCACCGCGCAACGGCGUCGGCGGCCUCACAAC
...((((((.....(((((..((.((((((((((......))))).))))).)).)))))))))))(((..(((.((((((....))).))).)))..)))... ( -52.60)
>DroSim_CAF1 34574 104 - 1
GAGCAGGUCAUGGACACGGCCAUGGCUCCGCCGGAGGAGACCGGCAGGAGCGAUACCGUGGGCUUGAUGGAGUCGCCGCGCAACGGCGUCGGCGGCCUCACAAC
...((((((.....(((((..((.((((((((((......))))).))))).)).))))))))))).((..((((((((((....))).)))))))..)).... ( -54.20)
>DroEre_CAF1 31748 104 - 1
GAGCAGGUCAUGGACACGGCCAUGGCUCCGCCGGAGGAGACCGGCAGGAGCGAUACCGUGGGCUUGAUGGAGUCGCCGCGCAACGGCGUCGGCGGCCUCACAAC
...((((((.....(((((..((.((((((((((......))))).))))).)).))))))))))).((..((((((((((....))).)))))))..)).... ( -54.20)
>DroYak_CAF1 23705 104 - 1
GAGCAGUUCAUGGACACGGCCAUGGCUCCGCCGGAGGAGACCGGCAUGAGCGAUGCCGUGGGCUUGAUGGAGUCGCCGCGCAACGGCGUCGGCGGCCUCACAAC
.......(((.(..((((((.((.((((.(((((......)))))..)))).))))))))..).)))((..((((((((((....))).)))))))..)).... ( -52.80)
>DroAna_CAF1 20596 104 - 1
GAGCAUCCCAUCGCCAUGGAUAUAGCUCCACCGGAGCCGUCCAACAGCAAAGAUCCCGAGGGCUUAACUGAAUCGCCGCGCAAAGGCGUCGGCGGGCGCACAAC
...........((((.(((((...(((((...))))).))))).(((..(((.(((...))))))..)))...((((((((....))).)))))))))...... ( -37.00)
>consensus
GAGCAGGUCAUGGACACGGCCAUGGCUCCGCCGGAGGAGACCGGCAGGAGCGAUACCGUGGGCUUGAUGGAGUCGCCGCGCAACGGCGUCGGCGGCCUCACAAC
(((((((((.....(((((..((.((((((((((......))))).))))).)).))))))))))).....((((((((((....))).))))))))))..... (-40.28 = -42.50 +   2.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:54 2006