Locus 3018

Sequence ID	2R_DroMel_CAF1
Location	10,417,328 – 10,417,468
Length	140
Max. P	0.890969

overview

Window 7

Location	10,417,328 – 10,417,428
Length	100
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	79.48
Mean single sequence MFE	-34.20
Consensus MFE	-22.53
Energy contribution	-22.25
Covariance contribution	-0.28
Combinations/Pair	1.19
Mean z-score	-1.46
Structure conservation index	0.66
SVM decision value	0.29
SVM RNA-class probability	0.671411
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10417328 100 - 20766785
GACAGUCGUCGAGCGACUGUUCAAGAUGGCCGAUGUCAACAUACGGGCCAAGAAGGUAGGUAAGGGGCC---CCACCG-CCCAUGGAUCUCGAGCCCCGUAUGU--
((((((((.....)))))))).....((((....))))(((((((((.(..((.(((.......((((.---.....)-)))....)))))..).)))))))))-- ( -36.30)
>DroPse_CAF1 19458 99 - 1
GACAGUCGUGGAGCGACUGUUCAAGAUGGCCGAUGUCAACAUACGCGCCAAGAAGGUAGGUAAGGGGCC---GCACAACCCCAGAGACCACAGAUCCAGA--CA--
....(((.((((....((((......(((((((((....))).)).))))........(((..((((..---......))))....))))))).))))))--).-- ( -31.00)
>DroEre_CAF1 19673 99 - 1
AACAGUCGUCGAGCGACUGUUCAAGAUGGCCGACGUCAACAUACGGGCCAAGAAGGUAGGUAAGGGGC----CCAACG-CCCAGUGAUCCCGAGCCCAGUAUGA--
((((((((.....))))))))...((((.....))))..(((((((((......((..(((...((((----.....)-)))....)))))..)))).))))).-- ( -35.60)
>DroYak_CAF1 21333 100 - 1
AACAGUCGUCGAGCGACUGUUCAAGAUGGCCGAUGUCAACAUACGGGCCAAGAAGGUAGGUAAGGGGCC---CCAACG-CCCACUGAUCCCGAGCCCAGUUUGA--
.(((((((.....)))))))(((((..(((((..((((.(.(((..(((.....)))..))).)((((.---.....)-)))..))))..)).)))...)))))-- ( -34.90)
>DroMoj_CAF1 27529 103 - 1
GACAGUCGUGGAGCGACUGUUUCAGAUGGCCGAUGUCAACAUACGAGCCAAGAAGGUAGGUAAAGGCCUGUCACCUGG-UCGAUUGGCAUUGCAU-CACUC-AUAC
((((((((.....))))))))...((((..(((((((((....(((.(((.(..(..((((....))))..)..))))-))).))))))))))))-)....-.... ( -35.40)
>DroPer_CAF1 25535 99 - 1
GACAGUCGUGGAGCGACUGUUCAAGAUGGCCGAUGUCAACAUACGCGCCAAGAAGGUAGGUAAGGGGCC---GCACAACCCCAGAGACCACAGAUCCUGA--CA--
.(((((((.....)))))))(((.(((((((((((....))).)).)))......((.(((..((((..---......))))....)))))..))).)))--..-- ( -32.00)
>consensus
GACAGUCGUCGAGCGACUGUUCAAGAUGGCCGAUGUCAACAUACGGGCCAAGAAGGUAGGUAAGGGGCC___CCACCG_CCCAGUGACCACGAACCCAGU__GA__
((((((((.....)))))))).....(((((((((....))).)).))))....(((.(((...(((............)))....)))....))).......... (-22.53 = -22.25 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	10,417,355 – 10,417,468
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.44
Mean single sequence MFE	-43.78
Consensus MFE	-33.68
Energy contribution	-33.80
Covariance contribution	0.12
Combinations/Pair	1.32
Mean z-score	-2.21
Structure conservation index	0.77
SVM decision value	0.96
SVM RNA-class probability	0.890969
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10417355 113 - 20766785
UGCUCGUAUCGUUGGCCAAGCUGAAGCAGCCCGCCCAUCGGACAGUCGUCGAGCGACUGUUCAAGAUGGCCGAUGUCAACAUACGGGCCAAGAAGGUAGGUAAGGGGCC---CCAC----
.((((((((.((((((...((((...)))).((.((((((((((((((.....)))))))))..))))).))..))))))))))))))......((..(((.....)))---))..---- ( -46.90)
>DroVir_CAF1 29048 116 - 1
UGCUCGUUUCUUUGGCCAAGCUGAAGCAAGCGGCGCAUCGGACAGUCGUGGAGCGACUGUUUCAGAUGGCCGAUGUCAACAUACGAGCAAAAAAGGUAGGUAAAGGCACGUCAUAG----
(((((((....(((((...(((......)))(((.((((.((((((((.....))))))))...)))))))...)))))...)))))))...........................---- ( -40.90)
>DroGri_CAF1 16570 113 - 1
UGCUCGUAUCGUUGGCCAAGCUGAAGCAAGUGGCACAUCGGACGGUCGUGGAGCGACUGUUCCAGAUGGCCGAUGUCAACAUACGGGCCAAGAAGGUAGGUAAAGGCAC---ACCC----
.((((((((.((((((((.((....))...))))(((((((.(.(((.((((((....))))))))).))))))))))))))))))))......(((..((....))..---))).---- ( -48.30)
>DroWil_CAF1 37277 116 - 1
UGCUCGUCUCGUUGGCGAAAUUGAAACAACCGUCACAUCGUACAGUCGUUGAGCGACUGUUUCAGAUGGCUGAUGUCAAUAUACGAGCCAAAAAGGUAGGUAAGGUGCUGCCCCCA----
.((((((.(((....))).(((((..((.(((((.......(((((((.....)))))))....))))).))...)))))..))))))......(((((........)))))....---- ( -36.50)
>DroMoj_CAF1 27556 116 - 1
UGCUCGUCUCGUUGGCCAAGCUGAAGCAAGCGGCGCAUCGGACAGUCGUGGAGCGACUGUUUCAGAUGGCCGAUGUCAACAUACGAGCCAAGAAGGUAGGUAAAGGCCUGUCACCU----
.((((((...((((((...(((......)))(((.((((.((((((((.....))))))))...)))))))...))))))..))))))......(..((((....))))..)....---- ( -48.90)
>DroAna_CAF1 25608 117 - 1
UGUUGGUGUCGCUGGCCAAGCUGAAGCAGCCCGCCCAUCGAACAGUCGUCCAGCGACUCUUCAAGAUGGCCGACGUCAACUUGCGCGCCAAGAAGGUAGGUAAGGGCCU---CCAAAAAG
(.((((((.(((((((...((((...)))).((.((((((((.(((((.....))))).)))..))))).))..))))....))))))))).).((.((((....))))---))...... ( -41.20)
>consensus
UGCUCGUAUCGUUGGCCAAGCUGAAGCAACCGGCACAUCGGACAGUCGUGGAGCGACUGUUCCAGAUGGCCGAUGUCAACAUACGAGCCAAGAAGGUAGGUAAAGGCCC___ACAA____
.((((((...((((((...((....))...((((.(((((((((((((.....)))))))))..))))))))..))))))..))))))................................ (-33.68 = -33.80 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:20 2006