Locus 5988

Sequence ID	3R_DroMel_CAF1
Location	15,776,960 – 15,777,110
Length	150
Max. P	0.999527

overview

Window 9

Location	15,776,960 – 15,777,070
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	91.64
Mean single sequence MFE	-29.16
Consensus MFE	-24.66
Energy contribution	-24.54
Covariance contribution	-0.12
Combinations/Pair	1.15
Mean z-score	-3.12
Structure conservation index	0.85
SVM decision value	3.69
SVM RNA-class probability	0.999527
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15776960 110 + 27905053
GAAAGAUUGUGAAUGCGGUAUUUUACGUCGGUAUCGUGUUUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUACUG
....(((((((..(((((((((((.((((((((...(((....)))...))))((((((....)))))).......))))..))))))))))).)))))))......... ( -32.10)
>DroSim_CAF1 2651 110 + 1
GAAAGAUUGUGAAUGCGGUAUUUUACGUCGGUAUCGUGUUUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUGCUG
....(((((((..(((((((((((.((((((((...(((....)))...))))((((((....)))))).......))))..))))))))))).)))))))......... ( -32.10)
>DroEre_CAF1 2619 110 + 1
CAAAGAUUGUUUAAGCACUGUUUCACGUCGGUAUCGUGUUUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAACGCUG
..(((.((((((((((((.((.((.....)).)).)))))))))))))))(((((((((....))))))).((((((.((((.......)))).))))))......)).. ( -28.60)
>DroYak_CAF1 19650 110 + 1
GAAAGAUUGUGAAAGCGGUAUUUUACGUCGGUAUCGUGUUUAGACAAUUUGCCUUAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUGCUG
....(((((((...((((((((((.((((((((...(((....)))...))))((((((....)))))).......))))..))))))))))..)))))))......... ( -28.70)
>DroAna_CAF1 18481 110 + 1
GAAAGAUUGUUGUGGCUGUAUUUUAUGUCCAUUUCAUGUUUAGACAACUUGCUUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAGCAUAAUCAAAAUGCUG
....((((((.((.((.(((((((.((((.............))))...(((.((((((.((((....)))))))))).)))))))))).)).))))))))......... ( -24.32)
>consensus
GAAAGAUUGUGAAAGCGGUAUUUUACGUCGGUAUCGUGUUUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUGCUG
....(((((((...(((((((((((((.......))))..........((((.((((((.((((....)))))))))).)))))))))))))..)))))))......... (-24.66 = -24.54 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	15,776,960 – 15,777,070
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	91.64
Mean single sequence MFE	-20.00
Consensus MFE	-17.14
Energy contribution	-17.06
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-1.51
Structure conservation index	0.86
SVM decision value	0.81
SVM RNA-class probability	0.855887
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15776960 110 - 27905053
CAGUAUUUUGAUUAUGUUGCAGCAUUUUUGCAUCAUAAUACUCAUAAAUAUUUAUGAGGCAAGUUGUCUAAACACGAUACCGACGUAAAAUACCGCAUUCACAAUCUUUC
..((((((((((((((.(((((.....))))).)))))).(((((((....)))))))....(((((......))))).......))))))))................. ( -21.60)
>DroSim_CAF1 2651 110 - 1
CAGCAUUUUGAUUAUGUUGCAGCAUUUUUGCAUCAUAAUACUCAUAAAUAUUUAUGAGGCAAGUUGUCUAAACACGAUACCGACGUAAAAUACCGCAUUCACAAUCUUUC
..((...(((((((((.(((((.....))))).)))))).(((((((....))))))).)))(((((......)))))................)).............. ( -19.70)
>DroEre_CAF1 2619 110 - 1
CAGCGUUUUGAUUAUGUUGCAGCAUUUUUGCAUCAUAAUACUCAUAAAUAUUUAUGAGGCAAGUUGUCUAAACACGAUACCGACGUGAAACAGUGCUUAAACAAUCUUUG
..((......((((((.(((((.....))))).)))))).(((((((....)))))))))..(((((.(((.(((..(((....))).....))).))).)))))..... ( -23.10)
>DroYak_CAF1 19650 110 - 1
CAGCAUUUUGAUUAUGUUGCAGCAUUUUUGCAUCAUAAUACUCAUAAAUAUUUAUAAGGCAAAUUGUCUAAACACGAUACCGACGUAAAAUACCGCUUUCACAAUCUUUC
.(((......((((((.(((((.....))))).))))))...........(((((..((...(((((......))))).))...))))).....)))............. ( -15.50)
>DroAna_CAF1 18481 110 - 1
CAGCAUUUUGAUUAUGCUGCAGCAUUUUUGCAUCAUAAUACUCAUAAAUAUUUAUGAAGCAAGUUGUCUAAACAUGAAAUGGACAUAAAAUACAGCCACAACAAUCUUUC
((((((.......))))))..((...(((((.((((((.............)))))).))))).((((((.........)))))).........)).............. ( -20.12)
>consensus
CAGCAUUUUGAUUAUGUUGCAGCAUUUUUGCAUCAUAAUACUCAUAAAUAUUUAUGAGGCAAGUUGUCUAAACACGAUACCGACGUAAAAUACCGCAUUCACAAUCUUUC
..((..((((((((((.(((((.....))))).)))))).(((((((....))))))).)))).((((.............)))).........)).............. (-17.14 = -17.06 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	15,776,999 – 15,777,110
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	88.02
Mean single sequence MFE	-21.18
Consensus MFE	-15.00
Energy contribution	-15.00
Covariance contribution	0.00
Combinations/Pair	1.18
Mean z-score	-1.64
Structure conservation index	0.71
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15776999 111 + 27905053
UUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUACUGAACGGAGCGAACGAAAAUGUAGGGAGGACAAAGAAAACGA
........(((.((((....((((((.(.((((((.(((((((.......))))......))).)))))).).((.......)).))))))...))))...)))....... ( -18.80)
>DroSim_CAF1 2690 111 + 1
UUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUGCUGAACGGAGCGAACGAAAAUACAGGGAGGACAAAAAAAACGA
.........(((((((.....(((((.((.(.((((((.((((.......)))).)))))))....((((......))))..)).)))))....)))).)))......... ( -20.10)
>DroEre_CAF1 2658 111 + 1
UUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAACGCUGAACGGAGCCAACGAAAAUGCAGGGAGGACAGAGAAAACGA
.....(..((((((((((((....))))))).((((((.((((.......)))).))))))......(((......)))..........)))))..).............. ( -20.90)
>DroYak_CAF1 19689 111 + 1
UUAGACAAUUUGCCUUAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUGCUGAACGGAGCGAACGAAAAUGCAGGGAGGACAAAGAAAACGA
........((((((((.....(((((.((.(.((((((.((((.......)))).)))))))....((((......))))..)).)))))....)))).))))........ ( -19.10)
>DroAna_CAF1 18520 104 + 1
UUAGACAACUUGCUUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAGCAUAAUCAAAAUGCUGAGUAGG-UGGCCG-GGGUGGCGGCAAAACAAAAAA-----
.........((((.((((((.((((....)))))))))).))))...((((.((((((.......)))))))))).(-(.((((-......))))...))......----- ( -27.00)
>consensus
UUAGACAACUUGCCUCAUAAAUAUUUAUGAGUAUUAUGAUGCAAAAAUGCUGCAACAUAAUCAAAAUGCUGAACGGAGCGAACGAAAAUGCAGGGAGGACAAAGAAAACGA
........((((((((((((....))))))).((((((.((((.......)))).))))))............................)))))................. (-15.00 = -15.00 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:56 2006