Locus 6407

Sequence ID	X_DroMel_CAF1
Location	16,067,215 – 16,067,375
Length	160
Max. P	0.826621

overview

Window 4

Location	16,067,215 – 16,067,335
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.22
Mean single sequence MFE	-24.01
Consensus MFE	-19.77
Energy contribution	-19.40
Covariance contribution	-0.37
Combinations/Pair	1.09
Mean z-score	-1.75
Structure conservation index	0.82
SVM decision value	0.59
SVM RNA-class probability	0.792509
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16067215 120 + 22224390
CCUAAAUUGAUUCUACGUAAUGCGUAGAGACAACCCAUCCCCAUCCCCAUUCUCAUUCCCAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCAUUUUACUGUCUGGUGAUUCAAC
.((((.(((.(((((((.....))))))).))).........................(((.((.(.....).)).)))...))))..(((((...((......))..)))))....... ( -21.60)
>DroSec_CAF1 12964 114 + 1
CCCAAAUUGAUUCUACGUAAUGCGUAGAGACAACCCAUCCCCAU------UCCCACCCGCAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCAUUUUACUGUCUGGUGAUUCAAC
......(((.(((((((.....))))))).)))...........------...((((.(((..........((((.(((........)))))))..........)))..))))....... ( -23.35)
>DroEre_CAF1 12947 102 + 1
CCCCAAUUGAUUCUACGUAAUGCGUAGAGACAACCCCUCCC------------------CACCCCCCUCCGGUGGCUGGAGCUUAGAACACCACCCCAUUUGCCUGUCUGGUGGUUCAAC
......(((.(((((((.....))))))).)))...(((((------------------((((.......)))))..))))....((..((((((..((......))..))))))))... ( -29.70)
>DroYak_CAF1 9338 109 + 1
CCCAAAUUGAUUCUACGUAAUGCGUAGAGACAACCCAUCCCC-----------CAUCCUCAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCGUUUUACUGUCUGGUGAUUCAAC
......(((.(((((((.....))))))).))).........-----------..................((((.(((........)))))))...(..(((((....)))))..)... ( -21.40)
>consensus
CCCAAAUUGAUUCUACGUAAUGCGUAGAGACAACCCAUCCCC___________CAUCC_CAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCAUUUUACUGUCUGGUGAUUCAAC
......(((.(((((((.....))))))).)))..................................(((((...)))))........(((((...((......))..)))))....... (-19.77 = -19.40 +  -0.37)

alignment

secondary structure

dotplot

Window 5

Location	16,067,255 – 16,067,375
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.65
Mean single sequence MFE	-28.27
Consensus MFE	-26.74
Energy contribution	-26.18
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-1.53
Structure conservation index	0.95
SVM decision value	0.70
SVM RNA-class probability	0.826621
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16067255 120 + 22224390
CCAUCCCCAUUCUCAUUCCCAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCAUUUUACUGUCUGGUGAUUCAACUUUAGCUUCUGUCUGCCAGAAAGUGAACUUUGCUUUUGGC
.............................(((.((((((((.((..(.(((((...((......))..))))).)..)))))))))).)))...(((((((.(..(...)..)))))))) ( -26.00)
>DroSec_CAF1 13004 114 + 1
CCAU------UCCCACCCGCAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCAUUUUACUGUCUGGUGAUUCAACUUUAGCUGCUGUCUGCCAGAAAGUGAACUUUGCUUUUGGC
....------...................(((..(((((((.((..(.(((((...((......))..))))).)..)))))))))..)))...(((((((.(..(...)..)))))))) ( -29.40)
>DroEre_CAF1 12987 102 + 1
C------------------CACCCCCCUCCGGUGGCUGGAGCUUAGAACACCACCCCAUUUGCCUGUCUGGUGGUUCAACUUUGGCUUCUGUCUGCCAGAAAGUGAACUUUGCUUUUGGC
(------------------((((.......)))))(..((((..((...((((((..((......))..))))))(((..((((((........))))))...))).))..))))..).. ( -30.40)
>DroYak_CAF1 9378 109 + 1
CC-----------CAUCCUCAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCGUUUUACUGUCUGGUGAUUCAACUUUAGCUUCUGUCUGCCAGAAAGUGAACUUUGCUUUUGGC
..-----------................(((.((((((((.((..(.(((((..(.(.....).)..))))).)..)))))))))).)))...(((((((.(..(...)..)))))))) ( -27.30)
>consensus
CC___________CAUCC_CAUCCUCAUCCAGUGGCUGGAGCUUAGACCACCACCCCAUUUUACUGUCUGGUGAUUCAACUUUAGCUUCUGUCUGCCAGAAAGUGAACUUUGCUUUUGGC
.............................(((..(((((((.((..(.(((((...((......))..))))).)..)))))))))..)))...(((((((.(..(...)..)))))))) (-26.74 = -26.18 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:02 2006