Locus 6405

Sequence ID	3L_DroMel_CAF1
Location	17,166,323 – 17,166,470
Length	147
Max. P	0.784064

overview

Window 0

Location	17,166,323 – 17,166,430
Length	107
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	68.98
Mean single sequence MFE	-21.52
Consensus MFE	-8.60
Energy contribution	-10.28
Covariance contribution	1.68
Combinations/Pair	1.20
Mean z-score	-1.72
Structure conservation index	0.40
SVM decision value	0.09
SVM RNA-class probability	0.577796
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17166323 107 + 23771897
AAAUCUGUUUACUGAC-------AAAAU---UCUUGAUCUCUAGCUGAUUUCAUUUACACAAUAGACAUUGAUGUCGAUAUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCA
......((((((((.(-------((((.---((.(((..((.....))..)))...........((((....))))))...)))))))))))))(((((((....)))))))..... ( -26.50)
>DroSec_CAF1 50732 92 + 1
AAAUCUGUUCACUGAC-------AAAAUAGAUA--GAUCUCUAGCUGAUUUCAUUUACACAAU----------------AUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCA
......((((((((.(-------((((((((((--((((.......))))).)))))......----------------..)))))))))))))(((((((....)))))))..... ( -24.20)
>DroSim_CAF1 42750 110 + 1
AAAUCUGUUUACUGAC-------AAAAUAGAUCCUAAUCUCUAGCUGAUUUCAUUUACACAAUAGACAAUGAUGUCGACAUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCA
......((((((((.(-------(((((((((...((((.......))))..))))).......((((....)))).....)))))))))))))(((((((....)))))))..... ( -25.50)
>DroEre_CAF1 52900 92 + 1
ACAUCUGUGAACUUAC-------UAAGU---AGUUGAAUUCUAG--------------AUAAUAGACAUUGAUAUCGAUUU-UUUCCAGUGAGCCUGCAGUUACCAUUGCAGUUGCA
......(..(.(((((-------(....---.((..(..((((.--------------....))))..)..))...((...-..)).)))))).(((((((....))))))))..). ( -16.10)
>DroYak_CAF1 53907 104 + 1
AGAACUCCUACCUUACAAAUAAAUAAAU---ACCCGAACUCUAG----------UUACAUAAGAGAUAUUGAUAUCGAUUUUUUUCCAGUGCACCUGCAGUUACCAUUGCAGUUGCA
............................---.............----------........((((.((((....))))...))))...((((.(((((((....))))))).)))) ( -15.30)
>consensus
AAAUCUGUUAACUGAC_______AAAAU___UCCUGAUCUCUAGCUGAUUUCAUUUACACAAUAGACAUUGAUAUCGAUAUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCA
......((((((((.....................(....).......................((((....))))..........))))))))(((((((....)))))))..... ( -8.60 = -10.28 +   1.68)

alignment

secondary structure

dotplot

Window 1

Location	17,166,353 – 17,166,470
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	82.33
Mean single sequence MFE	-27.23
Consensus MFE	-21.58
Energy contribution	-21.90
Covariance contribution	0.32
Combinations/Pair	1.08
Mean z-score	-1.72
Structure conservation index	0.79
SVM decision value	0.48
SVM RNA-class probability	0.753277
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17166353 117 + 23771897
CUAGCUGAUUUCAUUUACACAAUAGACAUUGAUGUCGAUAUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCACUUGCAUUUGCAAUUUGCAUUUCGGACGCUCAGGCAAUUA
........................((((....)))).......((((..((((((((((((....))))))).((((.((((....))))..))))........))))).))))... ( -29.10)
>DroSec_CAF1 50763 101 + 1
CUAGCUGAUUUCAUUUACACAAU----------------AUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCACUUGCAUUUGCAAUUUGCAUUUCGGACGCUCAGGCAAUUA
.......................----------------....((((..((((((((((((....))))))).((((.((((....))))..))))........))))).))))... ( -25.80)
>DroSim_CAF1 42783 117 + 1
CUAGCUGAUUUCAUUUACACAAUAGACAAUGAUGUCGACAUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCACUUGCAUUUGCAAUUUGCAUUUCGGACGCUCAGGCAAUUA
...(.((((.(((((............))))).)))).)....((((..((((((((((((....))))))).((((.((((....))))..))))........))))).))))... ( -30.00)
>DroEre_CAF1 52930 102 + 1
CUAG--------------AUAAUAGACAUUGAUAUCGAUUU-UUUCCAGUGAGCCUGCAGUUACCAUUGCAGUUGCACUUGCAUUUGCAAUUUGCAUUUCGGACGCUCAGGCAAUUA
....--------------........(((((..........-....))))).(((((.(((..((..((((((((((........))))).)))))....))..))))))))..... ( -24.94)
>DroYak_CAF1 53944 107 + 1
CUAG----------UUACAUAAGAGAUAUUGAUAUCGAUUUUUUUCCAGUGCACCUGCAGUUACCAUUGCAGUUGCACUUGCAUUUGCAAUUUGCAUUUCGGACGCUCAGGCAAUUA
....----------........((((.((((....)))).))))(((((((((.(((((((....))))))).))))))((((.........))))....))).((....))..... ( -26.30)
>consensus
CUAGCUGAUUUCAUUUACACAAUAGACAUUGAUAUCGAUAUUUUUGCAGUGAGCCUGCAAUUCCCGUUGCAGUUGCACUUGCAUUUGCAAUUUGCAUUUCGGACGCUCAGGCAAUUA
...........................................((((..((((((((((((....))))))).((((.((((....))))..))))........))))).))))... (-21.58 = -21.90 +   0.32)

alignment

secondary structure

dotplot

Window 2

Location	17,166,353 – 17,166,470
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	82.33
Mean single sequence MFE	-27.20
Consensus MFE	-21.86
Energy contribution	-22.62
Covariance contribution	0.76
Combinations/Pair	1.11
Mean z-score	-1.75
Structure conservation index	0.80
SVM decision value	0.57
SVM RNA-class probability	0.784064
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17166353 117 - 23771897
UAAUUGCCUGAGCGUCCGAAAUGCAAAUUGCAAAUGCAAGUGCAACUGCAACGGGAAUUGCAGGCUCACUGCAAAAAUAUCGACAUCAAUGUCUAUUGUGUAAAUGAAAUCAGCUAG
...((((.(((((........((((..((((....)))).)))).((((((......)))))))))))..)))).......((((....))))........................ ( -28.70)
>DroSec_CAF1 50763 101 - 1
UAAUUGCCUGAGCGUCCGAAAUGCAAAUUGCAAAUGCAAGUGCAACUGCAACGGGAAUUGCAGGCUCACUGCAAAAAU----------------AUUGUGUAAAUGAAAUCAGCUAG
...((((.(((((........((((..((((....)))).)))).((((((......)))))))))))..))))....----------------....................... ( -25.80)
>DroSim_CAF1 42783 117 - 1
UAAUUGCCUGAGCGUCCGAAAUGCAAAUUGCAAAUGCAAGUGCAACUGCAACGGGAAUUGCAGGCUCACUGCAAAAAUGUCGACAUCAUUGUCUAUUGUGUAAAUGAAAUCAGCUAG
...((((.(((((........((((..((((....)))).)))).((((((......)))))))))))..)))).......((((....))))........................ ( -29.50)
>DroEre_CAF1 52930 102 - 1
UAAUUGCCUGAGCGUCCGAAAUGCAAAUUGCAAAUGCAAGUGCAACUGCAAUGGUAACUGCAGGCUCACUGGAAA-AAAUCGAUAUCAAUGUCUAUUAU--------------CUAG
........(((((........((((..((((....)))).)))).(((((........))))))))))(((((..-.(((.((((....)))).))).)--------------)))) ( -25.60)
>DroYak_CAF1 53944 107 - 1
UAAUUGCCUGAGCGUCCGAAAUGCAAAUUGCAAAUGCAAGUGCAACUGCAAUGGUAACUGCAGGUGCACUGGAAAAAAAUCGAUAUCAAUAUCUCUUAUGUAA----------CUAG
...((((.((((..(((....(((.....)))......((((((.(((((........))))).)))))))))........((((....)))).)))).))))----------.... ( -26.40)
>consensus
UAAUUGCCUGAGCGUCCGAAAUGCAAAUUGCAAAUGCAAGUGCAACUGCAACGGGAAUUGCAGGCUCACUGCAAAAAUAUCGACAUCAAUGUCUAUUGUGUAAAUGAAAUCAGCUAG
...((((.(((((........((((..((((....)))).)))).((((((......)))))))))))..)))).......((((....))))........................ (-21.86 = -22.62 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:40 2006