Locus 446

Sequence ID	3R_DroMel_CAF1
Location	1,704,409 – 1,704,561
Length	152
Max. P	0.598610

overview

Window 3

Location	1,704,409 – 1,704,529
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.15
Mean single sequence MFE	-43.92
Consensus MFE	-29.26
Energy contribution	-29.90
Covariance contribution	0.64
Combinations/Pair	1.30
Mean z-score	-1.41
Structure conservation index	0.67
SVM decision value	0.04
SVM RNA-class probability	0.552565
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1704409 120 - 27905053
UGAUCUACACGCCCAAAGGCGAGCGAGACUACGGAACAUUGGCCUGUUACGGCCGGAAUGCCAUUGGAAAACAGUCGGAUCCGUGUGUGUUCCAAGUGGUGCCAGCAGGUGAGUUCCACU
...(((...((((....))))....)))....(((((..(.(((((((..(((......((((((((((.(((..((....))..))).)))).)))))))))))))))).))))))... ( -42.20)
>DroVir_CAF1 17984 116 - 1
UGAUCUAUACGCCGAAGGGCGAACGGGACUAUGGCACGCUGGCGUGUUGGGGCCGGAAUGCGAUUGGCAAACAGUCGGAGCCGUGUCUAUUUCAGGUGGUGCCAGCGGGUGAGUGU----
...(((...((((....))))....))).......(((((.((.((((((.(((....(.((((((.....)))))).)(((.((.......)))))))).)))))).)).)))))---- ( -45.40)
>DroGri_CAF1 17489 116 - 1
UGAUCUAUACUCCCAAGGGGGAGAGGGACUAUGGAACGUUGGCUUGCUGGGGACGCAAUGCGAUUGGCAAACAGUCAGAGCCUUGUCUAUUCCAGGUGGUGCCAGCGGGUGAGUUU----
...((((((.((((..........)))).)))))).((((((((..((.((((.((((.((..(((((.....))))).)).))))...)))).))..).))))))).........---- ( -40.70)
>DroWil_CAF1 11393 120 - 1
UGAUCUAUACGCCCAAGGGUGAACGAGACUAUGGUACACUGGCUUGCUGGGGUCGAAAUGCCAUUGGCAAGCAGUCGGAGCCAUGUCUGUUUCAGGUGGUGCCAGCAGGUAAGUUCCUUU
.........((((....))))(((.((((.(((((.(((((.(((((..((((......))).)..))))))))).)..))))))))))))..(((...((((....))))....))).. ( -41.10)
>DroMoj_CAF1 17933 116 - 1
UGAUCUAUACGCCCAAGGGCGAGCGAGACUACGGCACGCUGGCUUGCUGGGGCCGCAAUGCGAUUGGCAAACAGUCGGAGCCUUGUCUGUUCCAGGUGGUGCCGGCGGGUGAGUGU----
.........(((((..((((.((((.(.(....)).)))).))))(((((.(((((.....(((((.....)))))(((((.......)))))..))))).)))))))))).....---- ( -53.50)
>DroAna_CAF1 11177 120 - 1
UGAUAUACACUCCGAAAGGCGAAAGGGACUACGGAACGUUGGCCUGUUAUGGCCGAAAUGCGAUUGGAAAGCAGUCGGAUCCGUGUGUUUUUCAGGUGGUGCCAGCAGGUAAUUAUUCCU
.......((((((....)).((((((.((.(((((.(.((((((......))))))....((((((.....))))))).))))))).)))))).)))).((((....))))......... ( -40.60)
>consensus
UGAUCUAUACGCCCAAGGGCGAACGAGACUACGGAACGCUGGCUUGCUGGGGCCGAAAUGCGAUUGGCAAACAGUCGGAGCCGUGUCUGUUCCAGGUGGUGCCAGCAGGUGAGUUU____
...(((...((((....))))....))).........(((.(((((((((.(((......((((((.....))))))..(((.((.......)))))))).))))))))).)))...... (-29.26 = -29.90 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	1,704,449 – 1,704,561
Length	112
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	79.62
Mean single sequence MFE	-39.73
Consensus MFE	-22.84
Energy contribution	-21.85
Covariance contribution	-0.99
Combinations/Pair	1.45
Mean z-score	-1.75
Structure conservation index	0.57
SVM decision value	0.13
SVM RNA-class probability	0.598610
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1704449 112 - 27905053
CCAUGUAC------UUACAGUGGAAACCGUCAGCGAGCUGAUCUACACGCCCAAAGGCGAGCGAGACUACGGAACAUUGGCCUGUUACGGCCGGAAUGCCAUUGGAAAACAGUCGGAU
((.(((..------...((((((...(((((((....))))(((...((((....))))....)))...)))....((((((......))))))....))))))....)))...)).. ( -33.10)
>DroVir_CAF1 18020 112 - 1
UUUUUUUC------UCGCAGUGGAAACUGUUAGUGAGCUGAUCUAUACGCCGAAGGGCGAACGGGACUAUGGCACGCUGGCGUGUUGGGGCCGGAAUGCGAUUGGCAAACAGUCGGAG
.......(------(((((((....)))))..((..((..(((....((((....))))..(((..(((..(((((....))))))))..)))......)))..))..)).....))) ( -41.10)
>DroPse_CAF1 11416 112 - 1
UUUUUUUG------GCACAGUGGAAACGGUCAGCGAAUUGAUCUAUACACCCAAGGGUGAGCGGGACUACGGGACGCUGGCCUGUUACGGCCGGAAUGCCAUUGGCAAGCAAUCGGAC
...(((((------((...((((....((((((((......(((...((((....))))....)))(....)..))))))))..)))).)))))))((((...))))........... ( -37.60)
>DroGri_CAF1 17525 115 - 1
AAUUUUUG---CCAUUGCAGUGGAAACAGUCAGUGAGCUGAUCUAUACUCCCAAGGGGGAGAGGGACUAUGGAACGUUGGCUUGCUGGGGACGCAAUGCGAUUGGCAAACAGUCAGAG
....((((---((((((((.((....)).((((..(((..(((((((.((((..........)))).))))))...)..)))..))))........))))).)))))))......... ( -41.90)
>DroWil_CAF1 11433 112 - 1
UUCUUUCA------UUACAGUGGAAACAGUCAGCGAACUGAUCUAUACGCCCAAGGGUGAACGAGACUAUGGUACACUGGCUUGCUGGGGUCGAAAUGCCAUUGGCAAGCAGUCGGAG
.(((..(.------...(((((....(((((((....))))).....((((....))))..........))...)))))((((((..((((......))).)..)))))).)..))). ( -34.40)
>DroMoj_CAF1 17969 118 - 1
AUUUUUUGUUGUGGUUACAGUGGAAACAGUUAGUGAGCUGAUCUAUACGCCCAAGGGCGAGCGAGACUACGGCACGCUGGCUUGCUGGGGCCGCAAUGCGAUUGGCAAACAGUCGGAG
.......((((((((..(((((....)((((((((.((((.(((...((((....))))....)))...)))).)))))))).))))..)))))))).((((((.....))))))... ( -50.30)
>consensus
UUUUUUUG______UUACAGUGGAAACAGUCAGCGAGCUGAUCUAUACGCCCAAGGGCGAGCGAGACUACGGAACGCUGGCUUGCUGGGGCCGGAAUGCCAUUGGCAAACAGUCGGAG
...................((((......((((....))))(((...((((....))))....)))))))......(((((.((((...(((((.......))))).))))))))).. (-22.84 = -21.85 +  -0.99)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:23 2006