Locus 5408

Sequence ID	3R_DroMel_CAF1
Location	14,225,491 – 14,225,592
Length	101
Max. P	0.939095

overview

Window 3

Location	14,225,491 – 14,225,592
Length	101
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	68.08
Mean single sequence MFE	-34.55
Consensus MFE	-15.45
Energy contribution	-15.57
Covariance contribution	0.12
Combinations/Pair	1.44
Mean z-score	-1.73
Structure conservation index	0.45
SVM decision value	0.60
SVM RNA-class probability	0.796346
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14225491 101 + 27905053
UAUUAAAAGCUG--------UUACC-AAAUUAUGUCCUACGCCGGCUAUAGCCAGCUGCCCAGCGGCA---GCGACCAGGAGCGCAGGCAGGCGCAGCUCGCGGCCAGCACCU
........((((--------.....-......((.(((.(((((((....))).((((((....))))---))......).))).)))))(.(((.....))).))))).... ( -35.90)
>DroVir_CAF1 104473 112 + 1
UAAUCCUAUUUUACAGCCCAAAGCC-GCAGUAUGUCCUAUAAUGGGUACACCCAACUGCCUAGCGGUAGCAUCGACUACGAGCGCCGCCAGCAACAGGUGGUGGCCAACACCU
.........................-((.(((.(((......((((....)))).(((((....)))))....))))))..))(((((((.(....).)))))))........ ( -32.50)
>DroPse_CAF1 106136 90 + 1
UGUCAA--------------------AAAACAUGUCAUACGCCGGCUAUAGCCAGCUGCCCAGCGGCA---GCGACCACGAGCAGCGCCAGCAGCAGCUGGCUGCGAACACUU
..((..--------------------.......(((.......(((....))).((((((....))))---))))).....(((..((((((....)))))))))))...... ( -33.70)
>DroYak_CAF1 97931 102 + 1
UGUUGGAAAUUC--------UUAACAAAAUUAUGUCGUAUGCCGGCUAUAGCCAGCUGCCCAGUGGCA---GCGACCAGGAGCGCAGACAGGCGCAGCUCGCGGCCAGCACCU
((((((......--------...(((......)))(((..((.(((....))).((((((....))))---))........((((......)))).))..))).))))))... ( -34.20)
>DroAna_CAF1 90576 104 + 1
UACUCUAAAUUU--------AUCUG-AAAGGAUGUCCAACGCCGGCUACAGCCAGCUGCCCAUUGGCAGUGGCGACCACGAGCGACGACAGGCUCAGUUGGUGGCCAACACCU
...........(--------((((.-...))))).....(((((((....))).((((((....)))))))))).....((((........))))....((((.....)))). ( -37.30)
>DroPer_CAF1 112018 90 + 1
UGUCAA--------------------AAAACAUGUCAUACGCCGGCUACAGCCAGCUGCCCAGCGGCA---GCGACCACGAGCAGCGCCAGCAGCAGCUGGCUGCGAACACUU
..((..--------------------.......(((.......(((....))).((((((....))))---))))).....(((..((((((....)))))))))))...... ( -33.70)
>consensus
UAUUAAAA_UU__________U__C_AAAAUAUGUCCUACGCCGGCUACAGCCAGCUGCCCAGCGGCA___GCGACCACGAGCGCCGCCAGCAGCAGCUGGCGGCCAACACCU
................................(((....((((((((.......(((((...)))))....((........))............))))))))....)))... (-15.45 = -15.57 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	14,225,491 – 14,225,592
Length	101
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	68.08
Mean single sequence MFE	-40.40
Consensus MFE	-20.08
Energy contribution	-19.53
Covariance contribution	-0.55
Combinations/Pair	1.30
Mean z-score	-1.89
Structure conservation index	0.50
SVM decision value	1.30
SVM RNA-class probability	0.939095
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14225491 101 - 27905053
AGGUGCUGGCCGCGAGCUGCGCCUGCCUGCGCUCCUGGUCGC---UGCCGCUGGGCAGCUGGCUAUAGCCGGCGUAGGACAUAAUUU-GGUAA--------CAGCUUUUAAUA
....((((((((((.....))).((((((((((.......((---((((....)))))).(((....))))))))))).))......-)))..--------))))........ ( -41.30)
>DroVir_CAF1 104473 112 - 1
AGGUGUUGGCCACCACCUGUUGCUGGCGGCGCUCGUAGUCGAUGCUACCGCUAGGCAGUUGGGUGUACCCAUUAUAGGACAUACUGC-GGCUUUGGGCUGUAAAAUAGGAUUA
.((((.....)))).((((((.(((((((.(((((....))).))..)))))))(((((((((....))))...........)))))-(((.....)))....)))))).... ( -39.10)
>DroPse_CAF1 106136 90 - 1
AAGUGUUCGCAGCCAGCUGCUGCUGGCGCUGCUCGUGGUCGC---UGCCGCUGGGCAGCUGGCUAUAGCCGGCGUAUGACAUGUUUU--------------------UUGACA
..((((((((.((((((....))))))((((((((((((...---.))))).)))))))((((....)))))))...)))))(((..--------------------..))). ( -42.70)
>DroYak_CAF1 97931 102 - 1
AGGUGCUGGCCGCGAGCUGCGCCUGUCUGCGCUCCUGGUCGC---UGCCACUGGGCAGCUGGCUAUAGCCGGCAUACGACAUAAUUUUGUUAA--------GAAUUUCCAACA
..((((((((...((((.(((......))))))).(((((((---((((....)))))).)))))..))))))))..((((......))))..--------............ ( -39.10)
>DroAna_CAF1 90576 104 - 1
AGGUGUUGGCCACCAACUGAGCCUGUCGUCGCUCGUGGUCGCCACUGCCAAUGGGCAGCUGGCUGUAGCCGGCGUUGGACAUCCUUU-CAGAU--------AAAUUUAGAGUA
.(((((((((.((((...((((........)))).)))).)))..((((....))))((((((....))))))....))))))....-.....--------............ ( -37.50)
>DroPer_CAF1 112018 90 - 1
AAGUGUUCGCAGCCAGCUGCUGCUGGCGCUGCUCGUGGUCGC---UGCCGCUGGGCAGCUGGCUGUAGCCGGCGUAUGACAUGUUUU--------------------UUGACA
..((((((((.((((((....))))))((((((((((((...---.))))).)))))))((((....)))))))...)))))(((..--------------------..))). ( -42.70)
>consensus
AGGUGUUGGCCGCCAGCUGCGCCUGGCGGCGCUCGUGGUCGC___UGCCGCUGGGCAGCUGGCUAUAGCCGGCGUAGGACAUAAUUU_G__A__________AA_UUUUAACA
.((((.(((.(((.....))).)))....))))....(((.....((((....))))((((((....))))))....)))................................. (-20.08 = -19.53 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:58 2006