Locus 2668

Sequence ID	3R_DroMel_CAF1
Location	7,157,824 – 7,157,923
Length	99
Max. P	0.853950

overview

Window 9

Location	7,157,824 – 7,157,923
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.86
Mean single sequence MFE	-40.28
Consensus MFE	-26.98
Energy contribution	-27.40
Covariance contribution	0.42
Combinations/Pair	1.20
Mean z-score	-1.27
Structure conservation index	0.67
SVM decision value	0.03
SVM RNA-class probability	0.551093
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7157824 99 + 27905053
UUUUUUUGGCGGCCGUCGAUG-AUGGG-------GUGCGAAGGGUUGGGGCG-----CGUGG-UGUGUUCCCCGGCCUGGUGGAGGCCAUGUACGCGUCGUCGUUUGCUAAAG-------
....((((((((....(((((-(((.(-------.((((..(((((((((.(-----((...-..))).)))))))))(((....))).))))).)))))))).)))))))).------- ( -41.20)
>DroSec_CAF1 90810 99 + 1
UUUUUUUGACGGCCGUCGAUG-GUGGC-------GUGCGAAGGGUUGGGGUG-----CGUGG-GGUGGUCCCCGGCCUGGUGGAGGCCAUGUACGCGUCGUCGUUUGCCAAAG-------
..........(((...(((((-..(.(-------(((((..(((((((((.(-----(....-....)))))))))))(((....))).)))))))..)))))...)))....------- ( -41.10)
>DroSim_CAF1 103984 99 + 1
UUUUUUUGGCGGCCGUCGAUG-AUGGG-------GUGCGAAGGGUUGGGGUG-----CGUGG-GGUGGUCCCCGGCCUGGCGGAGGCCAUGUACGCGUCGUCGUUUGCCAAAG-------
....((((((((....(((((-(((.(-------.((((..(((((((((.(-----(....-....)))))))))))(((....))).))))).)))))))).)))))))).------- ( -44.30)
>DroEre_CAF1 92524 99 + 1
UUUUUUUGGCGGCCGUCGAUG-AUGGG-------GUGCGAAGGGAUGGGGCG-----UGUAU-GGUGGUCCCCGGCCUGGUGGAGGCCAUGUACGCGUCGUCGUUUGCCAAAG-------
....((((((..(((((...)-)))).-------.....(((.(((((.(((-----(((((-(((..(((((.....)).))).))))))))))).))))).))))))))).------- ( -41.30)
>DroYak_CAF1 94596 104 + 1
UUU-UUUGGCGGCCGUCGAUGAAUGGG-------GUGCGAAGGGAUGGGGCGUGGGGUGUGU-GGUGGUCCCCGGCCUGGUGGAGGCCAUGUACGCGUCGUCGUUUGCCAAAG-------
...-((((((.(((.(((.....))).-------).)).(((.(((((.((((((((.....-......))))(((((.....)))))....)))).))))).))))))))).------- ( -41.20)
>DroAna_CAF1 99768 106 + 1
UUU-UUUGGCGGUUGUCGAUG-GAGGUGGACUCUGGGCGAUGGGUUAUGGGA-----AGGAUGGGUGGU-------UAGGUGCCAACCAUGUACGCGUCGUCGUUUGCUAGAGCCGUUCC
...-...(((((((.(.(..(-(((.....)))).(((((((.(((((((..-----........((((-------.....)))).))))).)).))))))).....).).))))))).. ( -32.60)
>consensus
UUUUUUUGGCGGCCGUCGAUG_AUGGG_______GUGCGAAGGGUUGGGGCG_____CGUGG_GGUGGUCCCCGGCCUGGUGGAGGCCAUGUACGCGUCGUCGUUUGCCAAAG_______
....((((((((.((.(((((.............(((((..(((..((((...................))))..)))(((....))).))))).))))).)).))))))))........ (-26.98 = -27.40 +   0.42)

alignment

secondary structure

dotplot

Window 0

Location	7,157,824 – 7,157,923
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.86
Mean single sequence MFE	-26.70
Consensus MFE	-17.42
Energy contribution	-18.56
Covariance contribution	1.14
Combinations/Pair	1.15
Mean z-score	-1.96
Structure conservation index	0.65
SVM decision value	0.80
SVM RNA-class probability	0.853950
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7157824 99 - 27905053
-------CUUUAGCAAACGACGACGCGUACAUGGCCUCCACCAGGCCGGGGAACACA-CCACG-----CGCCCCAACCCUUCGCAC-------CCCAU-CAUCGACGGCCGCCAAAAAAA
-------.....((...(((.((.(((.....(((((.....)))))((((..(...-....)-----..)))).......)))..-------....)-).)))...))........... ( -22.00)
>DroSec_CAF1 90810 99 - 1
-------CUUUGGCAAACGACGACGCGUACAUGGCCUCCACCAGGCCGGGGACCACC-CCACG-----CACCCCAACCCUUCGCAC-------GCCAC-CAUCGACGGCCGUCAAAAAAA
-------...........((((..((((....(((((.....)))))((((....))-)))))-----).................-------(((..-.......)))))))....... ( -30.30)
>DroSim_CAF1 103984 99 - 1
-------CUUUGGCAAACGACGACGCGUACAUGGCCUCCGCCAGGCCGGGGACCACC-CCACG-----CACCCCAACCCUUCGCAC-------CCCAU-CAUCGACGGCCGCCAAAAAAA
-------.((((((..........((((....(((((.....)))))((((....))-)))))-----)........((.(((...-------.....-...))).))..)))))).... ( -31.60)
>DroEre_CAF1 92524 99 - 1
-------CUUUGGCAAACGACGACGCGUACAUGGCCUCCACCAGGCCGGGGACCACC-AUACA-----CGCCCCAUCCCUUCGCAC-------CCCAU-CAUCGACGGCCGCCAAAAAAA
-------.((((((...((.(((.(((.....(((((.....)))))((((......-.....-----..)))).......)))..-------.....-..))).))...)))))).... ( -26.92)
>DroYak_CAF1 94596 104 - 1
-------CUUUGGCAAACGACGACGCGUACAUGGCCUCCACCAGGCCGGGGACCACC-ACACACCCCACGCCCCAUCCCUUCGCAC-------CCCAUUCAUCGACGGCCGCCAAA-AAA
-------.((((((..........((((....(((((.....)))))((((......-.....))))))))......((.(((...-------.........))).))..))))))-... ( -29.60)
>DroAna_CAF1 99768 106 - 1
GGAACGGCUCUAGCAAACGACGACGCGUACAUGGUUGGCACCUA-------ACCACCCAUCCU-----UCCCAUAACCCAUCGCCCAGAGUCCACCUC-CAUCGACAACCGCCAAA-AAA
(((..((((((.((..(((......)))...(((((((...)))-------))))........-----..............))..))))))....))-)................-... ( -19.80)
>consensus
_______CUUUGGCAAACGACGACGCGUACAUGGCCUCCACCAGGCCGGGGACCACC_ACACG_____CGCCCCAACCCUUCGCAC_______CCCAU_CAUCGACGGCCGCCAAAAAAA
........((((((...((.(((.........(((((.....)))))((((...................))))...........................))).))...)))))).... (-17.42 = -18.56 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:45 2006