Locus 2062

Sequence ID	3L_DroMel_CAF1
Location	5,676,122 – 5,676,216
Length	94
Max. P	0.930433

overview

Window 4

Location	5,676,122 – 5,676,216
Length	94
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.90
Mean single sequence MFE	-31.21
Consensus MFE	-15.98
Energy contribution	-15.79
Covariance contribution	-0.19
Combinations/Pair	1.19
Mean z-score	-2.47
Structure conservation index	0.51
SVM decision value	0.68
SVM RNA-class probability	0.819393
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5676122 94 + 23771897
---AGUUCCACUCGACAGUUUCCGCUCAGCU--UGAUGAU-UUCAUGGAAAACUUCAUUGAGCA-AGCGGAAACUAUUUCGUUUUGGCGCGGAGUG--------CAGGU-------
---.....(((((...((((((((((..(((--..(((((-(((...))))...))))..))).-))))))))))....(((......))))))))--------.....------- ( -33.20)
>DroVir_CAF1 61704 106 + 1
---AGUUCCGCUCGACAGCUUCCGUUCGGCU--UGAUGAU-UUCAUGGAAAACUUCAUUGAGCA-AGCGGAAACUAUUUCAUUU-GGC--GCUAUAAAUGUUGUCAGGUGUACUUU
---(((..(((..(((((((((((((..(((--..(((((-(((...))))...))))..))).-)))))))........((((-(..--....)))))))))))..))).))).. ( -31.10)
>DroPse_CAF1 50371 98 + 1
AACAGUUCCGCUCGACAGCUUCCGCUUGGCUGAUGAUGAUUUUCAUGGAAAACUUCAUUGAGCA-AGCGGAAACUAUUUCAUUUUGGU--GGAGUG--------CCAAU-------
........(((((.((((.(((((((((.(((((((.(.((((....)))).).))))).))))-))))))).))....(.....)))--.)))))--------.....------- ( -28.80)
>DroGri_CAF1 53532 109 + 1
ACCAGUUCCGCUCGACAGCUUCCGUUCGGCU--UGAUGAU-UUCAUGAAAAACUUCAUUGAGCA-AGCGGAAACUAUUUCAUUU-GGC--GCAAUAAAUGUUGUCAGUUGAAUGUU
....((((.(((.(((((((((((((..(((--..((((.-.............))))..))).-)))))))........((((-(..--....)))))))))))))).))))... ( -31.64)
>DroWil_CAF1 64342 93 + 1
AACAGUUCCGCUCGACAGCUUCCGCUUGGCU--UGAUGAU-UUCAUGGAAAACUUCAUUGAGCA-AGCGGAAACUAUUUCAUUUGGUC--AGAG----------CAGGA-------
......((((((((((((.(((((((((.((--..(((((-(((...))))...))))..))))-))))))).))....(....))))--.)))----------).)))------- ( -33.30)
>DroAna_CAF1 50140 98 + 1
AACAGUUCCGCUCGACAGCUUCCGCUCGGCU--UGAUGAU-UUCAUGGAAAACUUCAUUGAGUAAAGCGGAAACUAUUUCAUUUUGGU--GGAGUG-------CCAGGU------U
(((.....(((((.((((.(((((((..(((--..(((((-(((...))))...))))..)))..))))))).))....(.....)))--.)))))-------....))------) ( -29.20)
>consensus
AACAGUUCCGCUCGACAGCUUCCGCUCGGCU__UGAUGAU_UUCAUGGAAAACUUCAUUGAGCA_AGCGGAAACUAUUUCAUUUUGGC__GGAGUG________CAGGU_______
.....(((((((....)))((((((...(((...(((((...............))))).)))...))))))..................))))...................... (-15.98 = -15.79 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	5,676,122 – 5,676,216
Length	94
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.90
Mean single sequence MFE	-28.12
Consensus MFE	-17.96
Energy contribution	-18.18
Covariance contribution	0.22
Combinations/Pair	1.09
Mean z-score	-2.44
Structure conservation index	0.64
SVM decision value	1.21
SVM RNA-class probability	0.930433
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5676122 94 - 23771897
-------ACCUG--------CACUCCGCGCCAAAACGAAAUAGUUUCCGCU-UGCUCAAUGAAGUUUUCCAUGAA-AUCAUCA--AGCUGAGCGGAAACUGUCGAGUGGAACU---
-------.....--------(((((..((......))..((((((((((((-((((..((((..((......)).-.))))..--))).))))))))))))).))))).....--- ( -31.50)
>DroVir_CAF1 61704 106 - 1
AAAGUACACCUGACAACAUUUAUAGC--GCC-AAAUGAAAUAGUUUCCGCU-UGCUCAAUGAAGUUUUCCAUGAA-AUCAUCA--AGCCGAACGGAAGCUGUCGAGCGGAACU---
..(((.(..(((((..(((((.....--...-)))))....((((((((.(-((((..((((..((......)).-.))))..--)).))).))))))))))).))..).)))--- ( -23.80)
>DroPse_CAF1 50371 98 - 1
-------AUUGG--------CACUCC--ACCAAAAUGAAAUAGUUUCCGCU-UGCUCAAUGAAGUUUUCCAUGAAAAUCAUCAUCAGCCAAGCGGAAGCUGUCGAGCGGAACUGUU
-------.((((--------......--.)))).....(((((((.(((((-((((..((((.((((((...))))))..)))).)))..(((....)))...))))))))))))) ( -28.40)
>DroGri_CAF1 53532 109 - 1
AACAUUCAACUGACAACAUUUAUUGC--GCC-AAAUGAAAUAGUUUCCGCU-UGCUCAAUGAAGUUUUUCAUGAA-AUCAUCA--AGCCGAACGGAAGCUGUCGAGCGGAACUGGU
..(((((..(((((....((((((..--...-.))))))..((((((((.(-((((..((((..((......)).-.))))..--)).))).))))))))))).))..))).)).. ( -25.90)
>DroWil_CAF1 64342 93 - 1
-------UCCUG----------CUCU--GACCAAAUGAAAUAGUUUCCGCU-UGCUCAAUGAAGUUUUCCAUGAA-AUCAUCA--AGCCAAGCGGAAGCUGUCGAGCGGAACUGUU
-------..(((----------(((.--(((..........((((((((((-((((..((((..((......)).-.))))..--)).)))))))))))))))))))))....... ( -33.90)
>DroAna_CAF1 50140 98 - 1
A------ACCUGG-------CACUCC--ACCAAAAUGAAAUAGUUUCCGCUUUACUCAAUGAAGUUUUCCAUGAA-AUCAUCA--AGCCGAGCGGAAGCUGUCGAGCGGAACUGUU
.------.(((((-------......--.))).......(((((((((((((..((..((((..((......)).-.))))..--))..))))))))))))).....))....... ( -25.20)
>consensus
_______ACCUG________CACUCC__GCCAAAAUGAAAUAGUUUCCGCU_UGCUCAAUGAAGUUUUCCAUGAA_AUCAUCA__AGCCGAGCGGAAGCUGUCGAGCGGAACUGUU
.......................................((((((((((((..(((...(((.(..(((...)))...).)))..)))..)))))))))))).............. (-17.96 = -18.18 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:30 2006