Locus 5422

Sequence ID	3R_DroMel_CAF1
Location	14,286,005 – 14,286,101
Length	96
Max. P	0.597247

overview

Window 3

Location	14,286,005 – 14,286,101
Length	96
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	92.52
Mean single sequence MFE	-22.72
Consensus MFE	-19.38
Energy contribution	-19.88
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.56
Structure conservation index	0.85
SVM decision value	0.13
SVM RNA-class probability	0.597247
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14286005 96 + 27905053
UUGAAAUAAAUCAACGAUUAUCGCUCACGCAAAUCUCGGCUAUCGGCUAUCGUCGAUGGCCAAAAAGACGCGCUGCUCACACCUAGAAUGAAAAAG
((((......))))........((...(((...(((.((((((((((....))))))))))....))).)))..)).................... ( -22.00)
>DroSec_CAF1 65309 95 + 1
UUGAAAUAAAUCAACGAUUAUCGCUCACGCAAAUCUCGGCUAUCGGCUAUCGUCGAUGGCCAA-AAGACGCGCUGCUCACACCUAGAAUGAAAAAG
((((......))))........((...(((...(((.((((((((((....))))))))))..-.))).)))..)).................... ( -22.60)
>DroSim_CAF1 57057 95 + 1
UUGAAAUAAAUCAACGAUUAUCGCUCACGCAAAUCUCGGCUAUCGGCUAUCGUCGAUGGCCAA-AAGACGCGCUGCUCACACCUAGAAUGAAAAAG
((((......))))........((...(((...(((.((((((((((....))))))))))..-.))).)))..)).................... ( -22.60)
>DroEre_CAF1 67241 95 + 1
UUGAAAUAAAUCAGCGAUUAUCGCUCACGCAAAUCUCGGCUAUCGGCUAUCGUCGAUGGCCAA-AAGACGCGCUGCUCACACCUAGAAUGAAAAAG
...........(((((....((((....)).......((((((((((....))))))))))..-..))..)))))..................... ( -26.30)
>DroYak_CAF1 62375 95 + 1
UUGAAAUAAAUCAGCGAUUAUCGCUCACGCAAAUCUCGGCUAUCGGCUAUCGUCGAUGGCCAA-AAGACGCGCUGCUCACACCUAGAAUGAAAAAU
...........(((((....((((....)).......((((((((((....))))))))))..-..))..)))))..................... ( -26.30)
>DroAna_CAF1 57299 90 + 1
GGCAAAUAAAUCAAAGUUUAUCGCUCACGCAAAUCUCGGCUAUCGACCAU---CGAUGACCA--AAGACGCGUUGCUCACACCUAGAACGGAGAU-
(((..((((((....)))))).))).......(((((((.(((((.....---))))).)).--......((((.((.......)))))))))))- ( -16.50)
>consensus
UUGAAAUAAAUCAACGAUUAUCGCUCACGCAAAUCUCGGCUAUCGGCUAUCGUCGAUGGCCAA_AAGACGCGCUGCUCACACCUAGAAUGAAAAAG
......................((...(((...(((.((((((((((....))))))))))....))).)))..)).................... (-19.38 = -19.88 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	14,286,005 – 14,286,101
Length	96
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	92.52
Mean single sequence MFE	-27.07
Consensus MFE	-24.11
Energy contribution	-23.95
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.24
Structure conservation index	0.89
SVM decision value	0.12
SVM RNA-class probability	0.594986
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14286005 96 - 27905053
CUUUUUCAUUCUAGGUGUGAGCAGCGCGUCUUUUUGGCCAUCGACGAUAGCCGAUAGCCGAGAUUUGCGUGAGCGAUAAUCGUUGAUUUAUUUCAA
.............((.((((((((((.(((.(((((((.((((.(....).)))).)))))))...((....)))))...))))).))))).)).. ( -26.90)
>DroSec_CAF1 65309 95 - 1
CUUUUUCAUUCUAGGUGUGAGCAGCGCGUCUU-UUGGCCAUCGACGAUAGCCGAUAGCCGAGAUUUGCGUGAGCGAUAAUCGUUGAUUUAUUUCAA
.............(((....((.(((((..((-(((((.((((.(....).)))).)))))))..)))))..))....))).((((......)))) ( -27.00)
>DroSim_CAF1 57057 95 - 1
CUUUUUCAUUCUAGGUGUGAGCAGCGCGUCUU-UUGGCCAUCGACGAUAGCCGAUAGCCGAGAUUUGCGUGAGCGAUAAUCGUUGAUUUAUUUCAA
.............(((....((.(((((..((-(((((.((((.(....).)))).)))))))..)))))..))....))).((((......)))) ( -27.00)
>DroEre_CAF1 67241 95 - 1
CUUUUUCAUUCUAGGUGUGAGCAGCGCGUCUU-UUGGCCAUCGACGAUAGCCGAUAGCCGAGAUUUGCGUGAGCGAUAAUCGCUGAUUUAUUUCAA
.............((.((((((((((.(((((-(((((.((((.(....).)))).)))))))...((....)))))...))))).))))).)).. ( -29.20)
>DroYak_CAF1 62375 95 - 1
AUUUUUCAUUCUAGGUGUGAGCAGCGCGUCUU-UUGGCCAUCGACGAUAGCCGAUAGCCGAGAUUUGCGUGAGCGAUAAUCGCUGAUUUAUUUCAA
.............((.((((((((((.(((((-(((((.((((.(....).)))).)))))))...((....)))))...))))).))))).)).. ( -29.20)
>DroAna_CAF1 57299 90 - 1
-AUCUCCGUUCUAGGUGUGAGCAACGCGUCUU--UGGUCAUCG---AUGGUCGAUAGCCGAGAUUUGCGUGAGCGAUAAACUUUGAUUUAUUUGCC
-........((.((((....((.(((((..((--(((..((((---.....))))..)))))...)))))..)).....)))).)).......... ( -23.10)
>consensus
CUUUUUCAUUCUAGGUGUGAGCAGCGCGUCUU_UUGGCCAUCGACGAUAGCCGAUAGCCGAGAUUUGCGUGAGCGAUAAUCGUUGAUUUAUUUCAA
.............((.((((((((((.(((((...(((.((((........)))).))))))))((((....))))....))))).))))).)).. (-24.11 = -23.95 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:17 2006