Locus 3320

Sequence ID	X_DroMel_CAF1
Location	8,875,619 – 8,875,777
Length	158
Max. P	0.927056

overview

Window 9

Location	8,875,619 – 8,875,718
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	81.33
Mean single sequence MFE	-29.13
Consensus MFE	-18.36
Energy contribution	-19.50
Covariance contribution	1.14
Combinations/Pair	1.08
Mean z-score	-2.59
Structure conservation index	0.63
SVM decision value	0.90
SVM RNA-class probability	0.876701
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8875619 99 + 22224390
AUCUCUGCCUUUUGCUGGCGAGUGCUACAAUUGUCGCACGUAAUCGUGCUGGCAGUUACGCCUCAGAAAGCAGCCAAAAAAAAAAGAAAAAAAAACGCA
....((((.(((((..((((.(.....)((((((((((((....))))).))))))).)))).))))).)))).......................... ( -28.80)
>DroSec_CAF1 6093 87 + 1
AUC--UGCCUUUUGCUGGCGAGUGCUACAAUUGUCGCACGUAAUCGUGCUGGCAGUUACGCCUCAGAAAGCAGCCGAAAA----------AAAAACGCA
..(--(((.(((((..((((.(.....)((((((((((((....))))).))))))).)))).))))).)))).......----------......... ( -28.80)
>DroSim_CAF1 6442 88 + 1
AUC--UGCCUUUUGCUGGCGAGUGCUACAAUUGUCGCACGUAAUCGUGCUGGCAGUUACGCCUCAGAAAGCAGCCGAAAAA---------AAAAACGCA
..(--(((.(((((..((((.(.....)((((((((((((....))))).))))))).)))).))))).))))........---------......... ( -28.80)
>DroEre_CAF1 6099 83 + 1
AUC--UGCCUUUC---AGCGAGUGCUACAAUUGUCGCACGUAAUCGUGCUGGCAGUUACGGCUCAGAAAGCACCGAAAAAGCG--------UAGAU---
(((--(((((((.---..((.(((((..((((((((((((....))))).))))))).(......)..)))))))..)))).)--------)))))--- ( -30.20)
>DroYak_CAF1 6428 89 + 1
AUC--UGCCUUUUGCUGGCGAGUGCUACAAUUGUCGCACGUAAUCGUGCUGGCAGUUACGCCUCAGAAAGCAGCCGAAAAACG--------UAGAUACA
(((--(((.((((..(((((((.((...((((((((((((....))))).)))))))..))))).(....).)))).)))).)--------)))))... ( -31.80)
>DroAna_CAF1 10970 85 + 1
AUC--UGCCUG-CGGUGGCGAGUGUUACAGUUGUCGCACGUAAUAGCG----CAGUUACGCCUCAGAAAGCAGCCCGAAAAAGCU-------GAAGGCA
..(--((((((-(((((((((.((...)).))))))).)))...)).)----)))....((((.......((((........)))-------).)))). ( -26.40)
>consensus
AUC__UGCCUUUUGCUGGCGAGUGCUACAAUUGUCGCACGUAAUCGUGCUGGCAGUUACGCCUCAGAAAGCAGCCGAAAAA_G________AAAACGCA
.....(((.((((...((((.(.....)((((((((((((....))))).))))))).))))...)))))))........................... (-18.36 = -19.50 +   1.14)

alignment

secondary structure

dotplot

Window 0

Location	8,875,678 – 8,875,777
Length	99
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	78.12
Mean single sequence MFE	-28.01
Consensus MFE	-16.22
Energy contribution	-17.08
Covariance contribution	0.86
Combinations/Pair	1.22
Mean z-score	-2.22
Structure conservation index	0.58
SVM decision value	1.18
SVM RNA-class probability	0.927056
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8875678 99 - 22224390
CACACGACGAGUCAGCUGAGCGUAACGCAUG-----UGUUCGAGAUACUUUUGUAUCUUGUAUCUGCGUUUUUUUUUCUUUUUUUUUUGGCUGCUUUCUGAGGC
..((.((.(((.((((..((...((((((.(-----((..((((((((....))))))))))).))))))...............))..))))))))))).... ( -25.67)
>DroSec_CAF1 6150 89 - 1
CACACGACGAGUCAGCUGAGCGUAACGCAUG-----UGUUCGAGAUACUUUUGUAUCUUGUAUCUGCGUUUUU----------UUUUCGGCUGCUUUCUGAGGC
..((.((.(((.((((((((...((((((.(-----((..((((((((....))))))))))).))))))...----------..))))))))))))))).... ( -30.90)
>DroSim_CAF1 6499 90 - 1
CACACGACGAGUCAGCUGAGCGUAACGCAUG-----UGUUCGAGAUACUUUUGUAUCUUGUAUCUGCGUUUUU---------UUUUUCGGCUGCUUUCUGAGGC
..((.((.(((.((((((((...((((((.(-----((..((((((((....))))))))))).))))))...---------...))))))))))))))).... ( -30.30)
>DroEre_CAF1 6153 85 - 1
CACACGGCGAGUCAGCUGAGCGUAACGCAUG-----UGUUUGAGAUACUUUUGUAUCUUGU------AUCUA--------CGCUUUUUCGGUGCUUUCUGAGCC
.....(((.((..(((.((((((((((....-----)))..(((((((....)))))))..------...))--------))))).......)))..))..))) ( -22.40)
>DroYak_CAF1 6485 91 - 1
CACACGGCGAGUCAGCUGAGCGUAACGCAUG-----UGUUUGAGAUACUUUUGUGUCUUGUAUCUGUAUCUA--------CGUUUUUCGGCUGCUUUCUGAGGC
....(((.(((.((((((((((((..(((.(-----((..((((((((....))))))))))).)))...))--------)))...)))))))))).))).... ( -29.00)
>DroAna_CAF1 11022 89 - 1
CACCCAACG-----GACGAGCGUCACGCAUGAAGAGUGCCUCAGAUACUUUUGUAUCUCGG---UGCCUUC-------AGCUUUUUCGGGCUGCUUUCUGAGGC
..(((....-----(((....)))..((.(((((.(..((..((((((....)))))).))---..)))))-------)))......)))..((((....)))) ( -29.80)
>consensus
CACACGACGAGUCAGCUGAGCGUAACGCAUG_____UGUUCGAGAUACUUUUGUAUCUUGUAUCUGCGUUUU________C_UUUUUCGGCUGCUUUCUGAGGC
....((..(((.((((((((((...)))............((((((((....))))))))..........................))))))))))..)).... (-16.22 = -17.08 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:20 2006