Locus 7903

Sequence ID	3R_DroMel_CAF1
Location	21,210,073 – 21,210,200
Length	127
Max. P	0.982061

overview

Window 7

Location	21,210,073 – 21,210,166
Length	93
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	63.84
Mean single sequence MFE	-45.40
Consensus MFE	-18.26
Energy contribution	-18.14
Covariance contribution	-0.12
Combinations/Pair	1.55
Mean z-score	-2.25
Structure conservation index	0.40
SVM decision value	1.65
SVM RNA-class probability	0.970162
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21210073 93 + 27905053
CCCAUUCCUGUGUCUGGACCUCC---------AGGUCCGCCGGGCCCACCAGGUCCACCAGGACAGCGGGGACCUGCAGGACCCCCAGGUCCACGGGGU---------CCA
...............((((((((---------((((((.(((((....))..((((....))))..))))))))))..(((((....)))))..)))))---------)). ( -45.70)
>DroVir_CAF1 50825 102 + 1
CCGAUACCAGUGCCAGGUCCACC---------AGGUCCACCGGGUCCACCGGGGCCUCCAGGACCGCGCGGACUAACCGGACCAAUGGGGCCACGAGGUAGGGAUGGUCCA
.........((((..(((((...---------(((.((.((((.....)))))))))...)))))))))((((((.((..(((..((....))...)))..)).)))))). ( -44.90)
>DroGri_CAF1 46635 111 + 1
CCGAUACCAGUGCCUGGUCCCCCGGGACCACCAGGACCACCUGGACCACGUGGACUGCCUGGACCACGUGGUCCAACGGGUCCAACUGGACCACGGGGCAGGGAGGGUCCA
.....(((..(.((((...(((((((.(((...(((((...((((((((((((.((....)).))))))))))))...)))))...))).)).))))))))).).)))... ( -59.60)
>DroWil_CAF1 38866 93 + 1
CCCAUUCCAGUUCCAGGGCCCCC---------GGGGCCACCAGGACCACCUGGCCCACCUGGUUUACGUGGCGCCACCGGACCAGUUGGCCCACGCGGA---------CAC
.....(((.((.(((((((((..---------.))))).(((((....))))).....))))...))((((.((((.(......).))))))))..)))---------... ( -40.00)
>DroYak_CAF1 38683 84 + 1
CCCAUUCCAGUGCCCGGUCCUCC---------UGGUCCGC---------CAGGUCCACCAGGCCAGCGGGGACCUGCAGGUCCGCCAGGUCCUCGGGGU---------CCA
(((......(.(((.(((...((---------(((....)---------))))...))).))))..(((((((((((......).))))))))))))).---------... ( -41.50)
>DroAna_CAF1 35573 93 + 1
CCUAUUCCAGUGCCCGGACCUCC---------GGGCCCACCCGGUCCCCCAGGGCCGCCUGGUAUGCGAGGACCUAUUGGACCCACUGGACCACGGGGC---------CAG
(((..((((((((((((....))---------))))(((...(((((((((((....))))).....).)))))...)))....))))))....)))..---------... ( -40.70)
>consensus
CCCAUUCCAGUGCCAGGUCCUCC_________AGGUCCACCGGGACCACCAGGGCCACCAGGACAGCGGGGACCUACAGGACCAACUGGACCACGGGGU_________CCA
...........(((((((((.............(((((.((.((....)).)).((....)).......))))).............)))))...))))............ (-18.26 = -18.14 +  -0.12)

alignment

secondary structure

dotplot

Window 8

Location	21,210,096 – 21,210,200
Length	104
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	72.77
Mean single sequence MFE	-53.35
Consensus MFE	-26.97
Energy contribution	-30.00
Covariance contribution	3.03
Combinations/Pair	1.17
Mean z-score	-2.26
Structure conservation index	0.51
SVM decision value	1.84
SVM RNA-class probability	0.979551
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21210096 104 + 27905053
AGGUCCGCCGGGCCCACCAGGUCCACCAGGACAGCGGGGACCUGCAGGACCCCCAGGUCCACGGGGU---------CCACGAGGUCCUGCCGGUGAGUCUGGCGUUAUUUCAU
.....((((((((.((((((((((.((........))))))))((((((((....((.((....)).---------))....)))))))).)))).))))))))......... ( -55.10)
>DroVir_CAF1 50848 110 + 1
AGGUCCACCGGGUCCACCGGGGCCUCCAGGACCGCGCGGACUAACCGGACCAAUGGGGCCACGAGGUAGGGAUGGUCCACGCGGACCACCCGGAAACGCAGGU---AUUACAG
.(((((.((((.....))))((((....)).))(((.((((((.((..(((..((....))...)))..)).)))))).))))))))(((((....))..)))---....... ( -49.70)
>DroSec_CAF1 36818 104 + 1
UGGCCCGCCGGGCCCACCAGGUCCACCAGGGCAGCGGGGACCUGCAGGACCACCAGGUCCACGGGGU---------CCCCGAGGUCCUGCCGGCGAGUCUGGCGUUAUUUCAG
.(((.(((((((((.....)))))..((((((..(((((((((...(((((....)))))...))))---------)))))..))))))..)))).))).............. ( -59.00)
>DroSim_CAF1 38454 104 + 1
UGGCCCGCCGGGCCCACCAGGUCCACCAGGGCAGCGGGGACCUGCAGGACCACCAGGUCCACGGGGU---------CCCCGAGGUCCUGCCGGCGAGUCUGGCGUUAUUUCAG
.(((.(((((((((.....)))))..((((((..(((((((((...(((((....)))))...))))---------)))))..))))))..)))).))).............. ( -59.00)
>DroEre_CAF1 38274 95 + 1
UGGCCCGC---------CAGGUCCACCAGGACAGCGGGGACCUGCUGGUCCGCCAGGUCCUCGGGGU---------CCACGAGGUCCUGCCGGUGAGUCUGGCAUUAUUUCAG
......((---------((((..((((.(((((((((....))))).))))(.((((.((((((...---------.).))))).)))).)))))..)))))).......... ( -51.20)
>DroAna_CAF1 35596 104 + 1
GGGCCCACCCGGUCCCCCAGGGCCGCCUGGUAUGCGAGGACCUAUUGGACCCACUGGACCACGGGGC---------CAGCGAGGACCUCCAGGUGAGCCAGGUGCGUCCCCAG
(((((.....)))))....((((((((((((.(((((((.((....)).(((.((((.((....)))---------))).).)).))))...))).)))))))).)))).... ( -46.10)
>consensus
UGGCCCGCCGGGCCCACCAGGUCCACCAGGACAGCGGGGACCUGCAGGACCACCAGGUCCACGGGGU_________CCACGAGGUCCUGCCGGUGAGUCUGGCGUUAUUUCAG
.(((.((((((..((..(((((((.((........)))))))))..)).....((((.((.((.((..........)).)).)).)))))))))).))).............. (-26.97 = -30.00 +   3.03)

alignment

secondary structure

dotplot

Window 9

Location	21,210,096 – 21,210,200
Length	104
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	72.77
Mean single sequence MFE	-54.18
Consensus MFE	-29.75
Energy contribution	-31.70
Covariance contribution	1.95
Combinations/Pair	1.17
Mean z-score	-2.20
Structure conservation index	0.55
SVM decision value	1.90
SVM RNA-class probability	0.982061
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21210096 104 - 27905053
AUGAAAUAACGCCAGACUCACCGGCAGGACCUCGUGG---------ACCCCGUGGACCUGGGGGUCCUGCAGGUCCCCGCUGUCCUGGUGGACCUGGUGGGCCCGGCGGACCU
.........((((.(.((((((.((((((((((..((---------.((....)).))..))))))))))(((((((((......))).)))))))))))).).))))..... ( -55.10)
>DroVir_CAF1 50848 110 - 1
CUGUAAU---ACCUGCGUUUCCGGGUGGUCCGCGUGGACCAUCCCUACCUCGUGGCCCCAUUGGUCCGGUUAGUCCGCGCGGUCCUGGAGGCCCCGGUGGACCCGGUGGACCU
..(((..---...)))...((((((....((((((((((...((..(((..(((....))).)))..))...)))))))))).))))))((((((((.....)))).)).)). ( -49.90)
>DroSec_CAF1 36818 104 - 1
CUGAAAUAACGCCAGACUCGCCGGCAGGACCUCGGGG---------ACCCCGUGGACCUGGUGGUCCUGCAGGUCCCCGCUGCCCUGGUGGACCUGGUGGGCCCGGCGGGCCA
.........((((((..((((((((((.....(((((---------(((..(((((((....))))).)).)))))))))))))..)))))..))))))(((((...))))). ( -59.80)
>DroSim_CAF1 38454 104 - 1
CUGAAAUAACGCCAGACUCGCCGGCAGGACCUCGGGG---------ACCCCGUGGACCUGGUGGUCCUGCAGGUCCCCGCUGCCCUGGUGGACCUGGUGGGCCCGGCGGGCCA
.........((((((..((((((((((.....(((((---------(((..(((((((....))))).)).)))))))))))))..)))))..))))))(((((...))))). ( -59.80)
>DroEre_CAF1 38274 95 - 1
CUGAAAUAAUGCCAGACUCACCGGCAGGACCUCGUGG---------ACCCCGAGGACCUGGCGGACCAGCAGGUCCCCGCUGUCCUGGUGGACCUG---------GCGGGCCA
.........((((((..((((((.((((.(((((.(.---------...)))))).)))).)((((.(((.(....).))))))).)))))..)))---------)))..... ( -45.30)
>DroAna_CAF1 35596 104 - 1
CUGGGGACGCACCUGGCUCACCUGGAGGUCCUCGCUG---------GCCCCGUGGUCCAGUGGGUCCAAUAGGUCCUCGCAUACCAGGCGGCCCUGGGGGACCGGGUGGGCCC
..(((......)))(((((((((...(((((((.(.(---------(((((.((((...(((((.((....)).)).)))..)))))).))))..))))))))))))))))). ( -55.20)
>consensus
CUGAAAUAACGCCAGACUCACCGGCAGGACCUCGUGG_________ACCCCGUGGACCUGGUGGUCCUGCAGGUCCCCGCUGUCCUGGUGGACCUGGUGGGCCCGGCGGGCCA
.........((((...........((((.((.((.((..........)).)).)).))))..(((((..((((((((((......))).)))))))..))))).))))..... (-29.75 = -31.70 +   1.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:39 2006