Locus 5456

Sequence ID	3R_DroMel_CAF1
Location	14,412,396 – 14,412,541
Length	145
Max. P	0.650355

overview

Window 8

Location	14,412,396 – 14,412,501
Length	105
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.00
Mean single sequence MFE	-39.82
Consensus MFE	-20.43
Energy contribution	-24.13
Covariance contribution	3.70
Combinations/Pair	1.20
Mean z-score	-2.04
Structure conservation index	0.51
SVM decision value	0.24
SVM RNA-class probability	0.650355
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14412396 105 - 27905053
CCGCAGCUCCUGGUAAGGUUGCUGCA---CCAGCAACAUUAUUGCUAGACAGAUUGGCGGGUAUGGAGGUCAUGCUCCUGCUGCUUGCGGUUCCGUUUCCAGGUGCGA
.....((.(((((.((.(..((((((---.(((((........(((((.....)))))(((((((.....))))))).)))))..))))))..).)).))))).)).. ( -41.20)
>DroSec_CAF1 191018 102 - 1
GAGCAGCUCCUGGUAAGGUUGCUGCA---CCAGCAACAUUAUUGCUAGACAGAUUGGCGGGUAUGGAGGUCAUGCUCCU---GCUUGCGGUUCCGUUUCCAGCUGCGA
..((((((.(((((((.(((((((..---.)))))))....)))))))((.((.(.(((((((.((((......)))))---)))))).).)).))....)))))).. ( -43.10)
>DroSim_CAF1 183113 102 - 1
GCGCAGCUCCUGGUAAGGUUGCUGCA---CCAGCAACAUUAUUGCUAGACAGAUUGGCGGGUAUGGAGGUCAUGCUCCU---GCUUUCGGUUCCGUUUCCAGCUGCGA
.(((((((.(((((((.(((((((..---.)))))))....)))))))..........(((.((((((.(...((....---))....).)))))).)))))))))). ( -40.10)
>DroEre_CAF1 198720 102 - 1
CCGCAGCUCCUGGCAAGGUUGCUGCU---CCAGCAACAUUAUUGCUAGACAGAUUGGCGGGAAUGGAGGUCAUGCUCCU---GCUUGCGGUUCCGUUUCCAGCUGCGA
.(((((((.(((((((.(((((((..---.)))))))....)))))))..........((((((((((.(((.((....---)).)).).))))))))))))))))). ( -47.50)
>DroWil_CAF1 227697 90 - 1
CCACACCACCGGCGGCAGCUGCUGCAGCAGCAGCCACAUUAUUGCUGGACAAAUUGGCAGGUAUGGAGGUCAUGCUUCG---GGCUG------CGU---------UGG
.....(((.(.(((((....)))))....((((((.(((..((((..(.....)..))))..)))((((.....)))).---)))))------)).---------))) ( -33.40)
>DroAna_CAF1 175625 96 - 1
CGGCUGCUCCGGCGAGAUUUGCUGCU---CCAGCAACGUUGUUGCUGGACAGAUUGGCGGGUAUGGAGGUCAUGCUCCU---GGUUCCAGUUCCGUUUUCAG------
((((((.((((((((.(.((((((..---.))))))...).)))))))))))((..(.(((((((.....)))))))).---.)).......))).......------ ( -33.60)
>consensus
CCGCAGCUCCUGGUAAGGUUGCUGCA___CCAGCAACAUUAUUGCUAGACAGAUUGGCGGGUAUGGAGGUCAUGCUCCU___GCUUGCGGUUCCGUUUCCAGCUGCGA
.((((.((.(((((((.(((((((......)))))))....)))))))((.((.(.((((((..((((......))))....)))))).).)).))....)).)))). (-20.43 = -24.13 +   3.70)

alignment

secondary structure

dotplot

Window 9

Location	14,412,436 – 14,412,541
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	72.77
Mean single sequence MFE	-37.83
Consensus MFE	-14.90
Energy contribution	-15.71
Covariance contribution	0.81
Combinations/Pair	1.29
Mean z-score	-1.85
Structure conservation index	0.39
SVM decision value	-0.02
SVM RNA-class probability	0.525511
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14412436 105 + 27905053
CUCCAUACCCGCCAAUCUGUCUAGCAAUAAUGUUGCUGG---UGCAGCAACCUUA---CCAGGAGCUGC---------GGCACCGCCAGAGAAAUAUACAUGGCCGAACUCCAAGGACGA
.(((......(((.......((((((((...))))))))---.(((((..(((..---..))).)))))---------))).(.((((............)))).)........)))... ( -31.20)
>DroVir_CAF1 232504 108 + 1
UUCCAUACCUGCCACGCUGUCCAGCAAUAAUGUGGCUGG---CACUGCG---GCGACCGCUGGCGCUGCCCUAG------UGGCGCCCGAGAAGCAGCCAUGGCCCAAUUCCAAGGAUGA
...(((.((((((..(((....)))......(((((((.---(...(((---(...)))).(((((..(....)------..)))))......))))))))))).........)))))). ( -39.60)
>DroEre_CAF1 198757 105 + 1
CUCCAUUCCCGCCAAUCUGUCUAGCAAUAAUGUUGCUGG---AGCAGCAACCUUG---CCAGGAGCUGC---------GGCACCGCCAGAGAAACAGCCGUGGCCCAACUCCAAAGACGA
.................(((((((((((...))))))((---((..(((....))---)..((.((..(---------(((...............))))..))))..))))..))))). ( -31.66)
>DroWil_CAF1 227719 108 + 1
CUCCAUACCUGCCAAUUUGUCCAGCAAUAAUGUGGCUGCUGCUGCAGCAGCUGCC---GCCGGUGGUGU---------GGUCCCAGCAGAGAAGCAGCCGUGGCCCAACUCCAAGGAUGA
..(((((((.(((...(((.....)))....(((((.(((((....))))).)))---)).))))))))---------))(((..((......)).((....))..........)))... ( -38.30)
>DroMoj_CAF1 239507 117 + 1
UUCCAUACCUGCCACGCUGUCCAGCAACAAUGUUGCAGC---AACAGCAGCUGCAACGGCUGCAGCUGGAUUGGGCGCCACGGCGCCAGAGAAACAGCCCUGGCCCAACUCCAAGGACGA
.......(((((((.((((((((((..((.(((((((((---.......)))))))))..))..))))))...(((((....))))).......))))..)))).........))).... ( -48.50)
>DroAna_CAF1 175656 105 + 1
CUCCAUACCCGCCAAUCUGUCCAGCAACAACGUUGCUGG---AGCAGCAAAUCUC---GCCGGAGCAGC---------CGCUCCGCCAGAGAAGCAGCCAUGGCCCAACUCCAAAGACGA
..........((((.....(((((((((...))))))))---)((.((...((((---..((((((...---------.))))))...)))).)).))..))))................ ( -37.70)
>consensus
CUCCAUACCCGCCAAUCUGUCCAGCAAUAAUGUUGCUGG___AGCAGCAACUGCA___GCAGGAGCUGC_________GGCACCGCCAGAGAAACAGCCAUGGCCCAACUCCAAGGACGA
..........((((..((((((((((((...))))))))....(((((................)))))........................))))...))))................ (-14.90 = -15.71 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:09 2006