Locus 3460

Sequence ID	2R_DroMel_CAF1
Location	11,627,749 – 11,627,840
Length	91
Max. P	0.970385

overview

Window 5

Location	11,627,749 – 11,627,840
Length	91
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	80.14
Mean single sequence MFE	-32.20
Consensus MFE	-21.25
Energy contribution	-23.03
Covariance contribution	1.78
Combinations/Pair	1.22
Mean z-score	-3.24
Structure conservation index	0.66
SVM decision value	1.66
SVM RNA-class probability	0.970385
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11627749 91 + 20766785
AGCUGUAGAGAGUGAGGAGCAGGAUCAAGACCAGGCUGAUGAGGAGGAGCCCAAGGAAGA---GGGCUCCUCUUGGUUGGCAUCACGUAAGUAG
.(((.......((((......((.......))..((..((.(((((((((((........---))))))))))).))..)).))))...))).. ( -36.50)
>DroGri_CAF1 896 87 + 1
-----GCCAGAGCCA--AACAGCAGCAGGGCGAAGCGGCUGAGGAUAAGGAUGAGGAAGUCACAACAACAUCCUGGCUGGGCUCACGUAAGUAC
-----(((..((((.--..((((.((........)).))))......((((((..(.........)..)))))))))).)))..((....)).. ( -27.80)
>DroSec_CAF1 300 91 + 1
AGCAGUAGAGAGUGAGGAGCAGGAUCAGGACCAGGCUGAUGAGGAGGAGCCCAAGGAAGA---GGGCUCCUCUUGGUUGGCAUCACGUAAGUAG
...........((((......((.......))..((..((.(((((((((((........---))))))))))).))..)).))))........ ( -36.30)
>DroSim_CAF1 303 91 + 1
AGCAGUAGAGAGUGAGGAGCAGGAUCAAGACCAGGCUGAUGAGGAGGAGCCCAAGGAAGA---GGGCUCCUCUUGGUUGGCAUCCCGUAAGUAG
.............(.(((...((.......))..((..((.(((((((((((........---))))))))))).))..)).))))........ ( -34.60)
>DroEre_CAF1 284 91 + 1
UCCAGUAGAGAGUCAGGAGCAGGAUGGAGACCAGGAUGAUGAGGAGGAACCCAAAGAAGA---GGCCUCCUCUUGGUUGGCAUCACGUAAGUAG
(((............)))....((((..((((((((......(((((..(((......).---)))))))))))))))..))))((....)).. ( -25.00)
>DroYak_CAF1 295 91 + 1
ACCAGUAGAGAGUGAGGAGCAGGAUCAAGACCAGGAUGACGAGGAGGAGCCCAAAGAAGA---GGGCUCCUCUUGGUUGGCAUCACGUAAGUAG
...........((((...((.((.......)).....(((.(((((((((((........---))))))))))).))).)).))))........ ( -33.00)
>consensus
AGCAGUAGAGAGUGAGGAGCAGGAUCAAGACCAGGCUGAUGAGGAGGAGCCCAAGGAAGA___GGGCUCCUCUUGGUUGGCAUCACGUAAGUAG
...........((((......((.......))..((((((.(((((((((((...........))))))))))).)))))).))))........ (-21.25 = -23.03 +   1.78)

alignment

secondary structure

dotplot

Window 6

Location	11,627,749 – 11,627,840
Length	91
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	80.14
Mean single sequence MFE	-25.16
Consensus MFE	-14.07
Energy contribution	-14.58
Covariance contribution	0.51
Combinations/Pair	1.45
Mean z-score	-2.85
Structure conservation index	0.56
SVM decision value	1.28
SVM RNA-class probability	0.939611
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11627749 91 - 20766785
CUACUUACGUGAUGCCAACCAAGAGGAGCCC---UCUUCCUUGGGCUCCUCCUCAUCAGCCUGGUCUUGAUCCUGCUCCUCACUCUCUACAGCU
........((((..........(((((((((---........)))))))))......(((..((.......)).)))..))))........... ( -26.50)
>DroGri_CAF1 896 87 - 1
GUACUUACGUGAGCCCAGCCAGGAUGUUGUUGUGACUUCCUCAUCCUUAUCCUCAGCCGCUUCGCCCUGCUGCUGUU--UGGCUCUGGC-----
............(((.((((((((((.....((((.....))))...))))).((((.((........)).))))..--)))))..)))----- ( -24.10)
>DroSec_CAF1 300 91 - 1
CUACUUACGUGAUGCCAACCAAGAGGAGCCC---UCUUCCUUGGGCUCCUCCUCAUCAGCCUGGUCCUGAUCCUGCUCCUCACUCUCUACUGCU
........((((.((.......(((((((((---........)))))))))...(((((.......)))))...))...))))........... ( -27.20)
>DroSim_CAF1 303 91 - 1
CUACUUACGGGAUGCCAACCAAGAGGAGCCC---UCUUCCUUGGGCUCCUCCUCAUCAGCCUGGUCUUGAUCCUGCUCCUCACUCUCUACUGCU
.......((((((....((((.(((((((((---........)))))))))((....))..))))....))))))................... ( -27.90)
>DroEre_CAF1 284 91 - 1
CUACUUACGUGAUGCCAACCAAGAGGAGGCC---UCUUCUUUGGGUUCCUCCUCAUCAUCCUGGUCUCCAUCCUGCUCCUGACUCUCUACUGGA
..................(((.(((((((.(---((......)))..)))))))........((((..............))))......))). ( -19.94)
>DroYak_CAF1 295 91 - 1
CUACUUACGUGAUGCCAACCAAGAGGAGCCC---UCUUCUUUGGGCUCCUCCUCGUCAUCCUGGUCUUGAUCCUGCUCCUCACUCUCUACUGGU
........((((.((.......(((((((((---........)))))))))...((((.........))))...))...))))........... ( -25.30)
>consensus
CUACUUACGUGAUGCCAACCAAGAGGAGCCC___UCUUCCUUGGGCUCCUCCUCAUCAGCCUGGUCUUGAUCCUGCUCCUCACUCUCUACUGCU
........((((.((.......(((((((((...........)))))))))...(((((.......)))))...))...))))........... (-14.07 = -14.58 +   0.51)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:05 2006