Locus 4549

Sequence ID	X_DroMel_CAF1
Location	11,968,222 – 11,968,328
Length	106
Max. P	0.872594

overview

Window 0

Location	11,968,222 – 11,968,328
Length	106
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	86.19
Mean single sequence MFE	-33.15
Consensus MFE	-24.96
Energy contribution	-26.90
Covariance contribution	1.94
Combinations/Pair	1.09
Mean z-score	-2.06
Structure conservation index	0.75
SVM decision value	0.88
SVM RNA-class probability	0.872594
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11968222 106 + 22224390
CAGCACGCCAGGGUAAUUUAUCGAUAGCAUUGGGCAUAUCGAUUACUGUGGCUGCAGCGUCAGCUAAAUUGAUUGCUUGCACA----------ACUGUACUAAGAAGUGCAUCAAU
..(((.((((.((((....(((((((((.....)).))))))))))).)))))))(((....)))......((((..(((((.----------.((......))..))))).)))) ( -36.00)
>DroSec_CAF1 7584 106 + 1
CAGCACGCCAGGGUAAUUUAUCGAUAGCAUUGGGCAUAUCGAUUACUGUGGCUGCAGUGUCAUCUAAAUUGAUUCCUAGCACA----------ACUGUACUAAGAAGUGCAUCAAU
..(((.((((.((((....(((((((((.....)).))))))))))).)))))))((.((((.......))))..)).((((.----------.((......))..))))...... ( -32.50)
>DroSim_CAF1 7640 106 + 1
CAGCGCGCCAGGGUAAUUUAUCGAUAGCAUUGGGCAUAUCGAUUACUGGGGCUGCAGUGUCAGCUAAAUUGAUUGCUAGCACA----------ACUGUACUAAGAAGUGCAUCAAU
..(((.(((..((((....(((((((((.....)).)))))))))))..)))))).(((..(((..........)))..))).----------..((((((....))))))..... ( -33.70)
>DroEre_CAF1 7883 116 + 1
CAGCACGCCAUGGAAAUUUAUCGAUAGCAUGGGGCAUAUCGAUUAUUGCGGCUUGAGUGCCAGUUAAGUUGAUUCCUCGCACAAACUUGCGUAACUGUACUGAGGAGGGCAUCGAU
......(((.....((((((((((((((.....)).)))))).......(((......)))...))))))..(((((((((......)))(((....))).)))))))))...... ( -30.40)
>consensus
CAGCACGCCAGGGUAAUUUAUCGAUAGCAUUGGGCAUAUCGAUUACUGUGGCUGCAGUGUCAGCUAAAUUGAUUCCUAGCACA__________ACUGUACUAAGAAGUGCAUCAAU
..(((.((((.((((....(((((((((.....)).))))))))))).))))))).((((.(((..........))).)))).............((((((....))))))..... (-24.96 = -26.90 +   1.94)

alignment

secondary structure

dotplot

Window 1

Location	11,968,222 – 11,968,328
Length	106
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	86.19
Mean single sequence MFE	-30.95
Consensus MFE	-19.88
Energy contribution	-22.50
Covariance contribution	2.62
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.64
SVM decision value	0.44
SVM RNA-class probability	0.738595
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11968222 106 - 22224390
AUUGAUGCACUUCUUAGUACAGU----------UGUGCAAGCAAUCAAUUUAGCUGACGCUGCAGCCACAGUAAUCGAUAUGCCCAAUGCUAUCGAUAAAUUACCCUGGCGUGCUG
.....(((((..((......)).----------.)))))((((.......((((....))))..((((..((((((((((.((.....)))))))))....)))..)))).)))). ( -28.70)
>DroSec_CAF1 7584 106 - 1
AUUGAUGCACUUCUUAGUACAGU----------UGUGCUAGGAAUCAAUUUAGAUGACACUGCAGCCACAGUAAUCGAUAUGCCCAAUGCUAUCGAUAAAUUACCCUGGCGUGCUG
......((((((((((((((...----------.))))))))))....................((((..((((((((((.((.....)))))))))....)))..)))))))).. ( -32.90)
>DroSim_CAF1 7640 106 - 1
AUUGAUGCACUUCUUAGUACAGU----------UGUGCUAGCAAUCAAUUUAGCUGACACUGCAGCCCCAGUAAUCGAUAUGCCCAAUGCUAUCGAUAAAUUACCCUGGCGCGCUG
...................((((----------.(((((((...........((((......)))).......(((((((.((.....)))))))))........))))))))))) ( -26.00)
>DroEre_CAF1 7883 116 - 1
AUCGAUGCCCUCCUCAGUACAGUUACGCAAGUUUGUGCGAGGAAUCAACUUAACUGGCACUCAAGCCGCAAUAAUCGAUAUGCCCCAUGCUAUCGAUAAAUUUCCAUGGCGUGCUG
((((((((..(((((.((((((..((....)))))))))))))............(((......))))))....)))))......((((((((.((......)).))))))))... ( -36.20)
>consensus
AUUGAUGCACUUCUUAGUACAGU__________UGUGCUAGCAAUCAAUUUAGCUGACACUGCAGCCACAGUAAUCGAUAUGCCCAAUGCUAUCGAUAAAUUACCCUGGCGUGCUG
......(((((((((((((((............)))))))))))....................((((..((((((((((.((.....)))))))))....)))..)))))))).. (-19.88 = -22.50 +   2.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:53 2006