Locus 7216

Sequence ID	3R_DroMel_CAF1
Location	18,993,276 – 18,993,409
Length	133
Max. P	0.997377

overview

Window 7

Location	18,993,276 – 18,993,369
Length	93
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	86.15
Mean single sequence MFE	-32.98
Consensus MFE	-28.10
Energy contribution	-27.54
Covariance contribution	-0.56
Combinations/Pair	1.08
Mean z-score	-2.21
Structure conservation index	0.85
SVM decision value	1.82
SVM RNA-class probability	0.978732
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18993276 93 + 27905053
GG--------GGUGUUACUAUGGUCGAAACCAUUGUUGUCAAUUUAAGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCUCACGAAA
.(--------((((..((.(((((....))))).))...)...........((((..(((((((((.((....)).)))))))))---))))..))))...... ( -29.30)
>DroSec_CAF1 6949 94 + 1
GGG-------GGUGUUACUAUGGUCGAAACCAUUGUUGUCAAUUCACGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCUCACGAAA
...-------.(((...(((((((....)))))((((((......))))))((((..(((((((((.((....)).)))))))))---))))))...))).... ( -29.80)
>DroSim_CAF1 6941 93 + 1
AC--------UAUGGUACUAUGGUCGAAACCAUUGUUGUCAAUUUACGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCUCACGAAA
((--------((((....)))))).((..((..((((((......))))))((((..(((((((((.((....)).)))))))))---))))))..))...... ( -30.40)
>DroEre_CAF1 8089 98 + 1
GGGA------GGAGUUACUAUGGUCGAAACCAUUGUUGUCAGUUUACGAUACUGCCACCGCUGCCAUUUGAUUGAUUGGCAGCGGGCGGCAGUGGCCCAUGGAU
(((.------.((...((.(((((....))))).))..)).........(((((((.(((((((((.((....)).)))))))))..))))))).)))...... ( -41.90)
>DroYak_CAF1 7293 101 + 1
GGGGGUGGGGGAUGUUACUAUGGUCGCAACCAUUGUUGUCAAUUUACGAUACUGCUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCGCGCGAAA
....(((.(((.(((.((....)).))).))..((((((......))))))((((..(((((((((.((....)).)))))))))---))))...).))).... ( -33.50)
>consensus
GGG_______GGUGUUACUAUGGUCGAAACCAUUGUUGUCAAUUUACGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG___GCAGGGGCUCACGAAA
................((.(((((....))))).))((((.......))))((((..(((((((((.((....)).)))))))))...))))............ (-28.10 = -27.54 +  -0.56)

alignment

secondary structure

dotplot

Window 8

Location	18,993,276 – 18,993,369
Length	93
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	86.15
Mean single sequence MFE	-28.12
Consensus MFE	-22.90
Energy contribution	-22.58
Covariance contribution	-0.32
Combinations/Pair	1.17
Mean z-score	-3.01
Structure conservation index	0.81
SVM decision value	2.85
SVM RNA-class probability	0.997377
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18993276 93 - 27905053
UUUCGUGAGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCUUAAAUUGACAACAAUGGUUUCGACCAUAGUAACACC--------CC
....(((.....(((.---(((((((((..........)))))))))...)))...............((.(((((....))))).))..))).--------.. ( -24.40)
>DroSec_CAF1 6949 94 - 1
UUUCGUGAGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCGUGAAUUGACAACAAUGGUUUCGACCAUAGUAACACC-------CCC
.(((((((....(((.---(((((((((..........)))))))))...)))..)))))))......((.(((((....))))).))......-------... ( -26.00)
>DroSim_CAF1 6941 93 - 1
UUUCGUGAGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCGUAAAUUGACAACAAUGGUUUCGACCAUAGUACCAUA--------GU
.((..(((....(((.---(((((((((..........)))))))))...)))..)))..))......((.(((((....))))).))......--------.. ( -23.60)
>DroEre_CAF1 8089 98 - 1
AUCCAUGGGCCACUGCCGCCCGCUGCCAAUCAAUCAAAUGGCAGCGGUGGCAGUAUCGUAAACUGACAACAAUGGUUUCGACCAUAGUAACUCC------UCCC
....((((...(((((((((.(((((((..........)))))))))))))))).(((.(((((.........)))))))))))).........------.... ( -37.90)
>DroYak_CAF1 7293 101 - 1
UUUCGCGCGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAGCAGUAUCGUAAAUUGACAACAAUGGUUGCGACCAUAGUAACAUCCCCCACCCCC
..(((((.(((.((((---(((((((((..........)))))))))..))))........((((....))))))))))))....................... ( -28.70)
>consensus
UUUCGUGAGCCCCUGC___CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCGUAAAUUGACAACAAUGGUUUCGACCAUAGUAACACC_______CCC
....((((....(((....(((((((((..........)))))))))...)))..)))).........((.(((((....))))).))................ (-22.90 = -22.58 +  -0.32)

alignment

secondary structure

dotplot

Window 9

Location	18,993,302 – 18,993,409
Length	107
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	79.67
Mean single sequence MFE	-33.18
Consensus MFE	-24.66
Energy contribution	-24.30
Covariance contribution	-0.36
Combinations/Pair	1.15
Mean z-score	-2.19
Structure conservation index	0.74
SVM decision value	1.59
SVM RNA-class probability	0.965838
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18993302 107 + 27905053
GUUGUCAAUUUAAGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCUCACGAAAAGGGAUGGAACUGAUUUGGAGCUAGUUUACUUUCAUUUUU
..((((.......))))((((..(((((((((.((....)).)))))))))---)))).(((((.((((..((.......))..)))))))))................. ( -32.20)
>DroSec_CAF1 6976 107 + 1
GUUGUCAAUUCACGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCUCACGAAAAGGGAUUGAACUAAGUUGAAGCUACUUUACUUUAGUUUUU
....(((((((......((((..(((((((((.((....)).)))))))))---))))(......)......)))))))((((((.(((((...))))).)))))).... ( -31.50)
>DroSim_CAF1 6967 106 + 1
GUUGUCAAUUUACGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCUCACGAAAAGGGGUUGAACUGAUUUAAAGCUACUUUACUUUA-UUUUU
...((((.(((......((((..(((((((((.((....)).)))))))))---)))).(((((.(.....))))))))).)))).(((((........)))))-..... ( -27.30)
>DroEre_CAF1 8117 92 + 1
GUUGUCAGUUUACGAUACUGCCACCGCUGCCAUUUGAUUGAUUGGCAGCGGGCGGCAGUGGCCCAUGGAUAGGGAUUCAACUGGCUUAAAGC------------------
...(((((((.....(((((((.(((((((((.((....)).)))))))))..))))))).(((.......)))....))))))).......------------------ ( -42.70)
>DroYak_CAF1 7327 104 + 1
GUUGUCAAUUUACGAUACUGCUACUGCUGCCAUUUGAUUGAUUGGCAGCAG---GCAGGGGCGCGCGAAAGGGGAUUCAACAGGCUUGCAGCUCC--UAGUUUA-CUUCU
(((((......))))).((((..(((((((((.((....)).)))))))))---))))(((.((((((....(.......)....)))).)).))--)......-..... ( -32.20)
>consensus
GUUGUCAAUUUACGAUACUGUUACUGCUGCCAUUUGAUUGAUUGGCAGCAG___GCAGGGGCUCACGAAAAGGGAUUGAACUGACUUGAAGCUACUUUACUUUA_UUUUU
..((((.......))))((((..(((((((((.((....)).)))))))))...)))).(((...(((..((........))...)))..)))................. (-24.66 = -24.30 +  -0.36)

alignment

secondary structure

dotplot

Window 0

Location	18,993,302 – 18,993,409
Length	107
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	79.67
Mean single sequence MFE	-26.84
Consensus MFE	-17.72
Energy contribution	-17.28
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-2.43
Structure conservation index	0.66
SVM decision value	1.79
SVM RNA-class probability	0.977406
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18993302 107 - 27905053
AAAAAUGAAAGUAAACUAGCUCCAAAUCAGUUCCAUCCCUUUUCGUGAGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCUUAAAUUGACAAC
....(((((((......((((.......)))).......)))))))(((...(((.---(((((((((..........)))))))))...)))...)))........... ( -20.52)
>DroSec_CAF1 6976 107 - 1
AAAAACUAAAGUAAAGUAGCUUCAACUUAGUUCAAUCCCUUUUCGUGAGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCGUGAAUUGACAAC
...(((((((((......))).....))))))......(..(((((((....(((.---(((((((((..........)))))))))...)))..)))))))..)..... ( -23.80)
>DroSim_CAF1 6967 106 - 1
AAAAA-UAAAGUAAAGUAGCUUUAAAUCAGUUCAACCCCUUUUCGUGAGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCGUAAAUUGACAAC
.....-((((((......))))))..((((((...........(....)...(((.---(((((((((..........)))))))))...))).......)))))).... ( -23.30)
>DroEre_CAF1 8117 92 - 1
------------------GCUUUAAGCCAGUUGAAUCCCUAUCCAUGGGCCACUGCCGCCCGCUGCCAAUCAAUCAAAUGGCAGCGGUGGCAGUAUCGUAAACUGACAAC
------------------((.....))(((((....(((.......)))..(((((((((.(((((((..........))))))))))))))))......)))))..... ( -37.70)
>DroYak_CAF1 7327 104 - 1
AGAAG-UAAACUA--GGAGCUGCAAGCCUGUUGAAUCCCCUUUCGCGCGCCCCUGC---CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAGCAGUAUCGUAAAUUGACAAC
....(-(....((--.(((((((..((.(((.(((......)))))).))......---(((((((((..........)))))))))..))))).)).)).....))... ( -28.90)
>consensus
AAAAA_UAAAGUAAAGUAGCUUCAAAUCAGUUCAAUCCCUUUUCGUGAGCCCCUGC___CUGCUGCCAAUCAAUCAAAUGGCAGCAGUAACAGUAUCGUAAAUUGACAAC
...........................(((((...........(....)...(((....(((((((((..........)))))))))...))).......)))))..... (-17.72 = -17.28 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:26 2006