Locus 3420

Sequence ID	2R_DroMel_CAF1
Location	11,573,261 – 11,573,409
Length	148
Max. P	0.965225

overview

Window 8

Location	11,573,261 – 11,573,369
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	99.44
Mean single sequence MFE	-23.75
Consensus MFE	-23.75
Energy contribution	-23.75
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	1.00
SVM decision value	0.84
SVM RNA-class probability	0.864320
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11573261 108 + 20766785
GCUUGUCAUUUCCUGUUUUAUUUUCACUCUGCCUUCAAAUUCCCUGCAUAUUUCAGAUGUCGAAACAAAUCAGGGACGCAAGCAGCCGACAACAUCGAGCAUAAAUGA
((((((...((((((.(((.((((.((((((......................)))).)).)))).))).)))))).)))))).(((((.....))).))........ ( -23.75)
>DroSec_CAF1 9739 108 + 1
GCUUGUCAUUUCCUGUUUUAUUUUCACUCUGCCUUCAAAUUCCCUGCAUAUUUCAGAUGUCGAAACAAAUCAGGGACGCAAGCAGCCGACAACAUCGAGCAUAAAUGA
((((((...((((((.(((.((((.((((((......................)))).)).)))).))).)))))).)))))).(((((.....))).))........ ( -23.75)
>DroSim_CAF1 10020 108 + 1
GCUUGUCAUUUCCUGUUUUAUUUUCACUCUGCCUUCAAAUUCCCUGCAUAUUUCAGAUGUCGAAACAAAUCAGGGACGCAAGCAGCCGACAACAUCGAGCAUAAAUGA
((((((...((((((.(((.((((.((((((......................)))).)).)))).))).)))))).)))))).(((((.....))).))........ ( -23.75)
>DroEre_CAF1 10003 108 + 1
GCUUGUCAUUUCCUGUUUUAUUUUCACUCUGCCUUCAAAUUCCCUGCAUAUUUCAGAUGUCGAAACAAAUCAGGGACGCAAGCAGCCGACAACAUCGGGCAUAAAUGA
((((((...((((((.(((.((((.((((((......................)))).)).)))).))).)))))).))))))..((((.....)))).......... ( -23.75)
>DroYak_CAF1 10131 108 + 1
GCUUGUCAUUUCCUGUUUUAUUUUCACUCUGCCUUCAAAUUCCCUGCAUAUUUCAGAUGUCGAAACAAAUCAGGGACGCAAGCAGCCGACAACAUCGGGCAUAAAUGA
((((((...((((((.(((.((((.((((((......................)))).)).)))).))).)))))).))))))..((((.....)))).......... ( -23.75)
>consensus
GCUUGUCAUUUCCUGUUUUAUUUUCACUCUGCCUUCAAAUUCCCUGCAUAUUUCAGAUGUCGAAACAAAUCAGGGACGCAAGCAGCCGACAACAUCGAGCAUAAAUGA
((((((...((((((.(((.((((.((((((......................)))).)).)))).))).)))))).)))))).(((((.....))).))........ (-23.75 = -23.75 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	11,573,261 – 11,573,369
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-30.26
Consensus MFE	-30.10
Energy contribution	-29.86
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-1.68
Structure conservation index	0.99
SVM decision value	1.58
SVM RNA-class probability	0.965225
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11573261 108 - 20766785
UCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUUGAAGGCAGAGUGAAAAUAAAACAGGAAAUGACAAGC
((((((........((((.(((.((((((...((((((...(((((((.....)))))))..))))))......))))))..))).)))).......))))))..... ( -29.56)
>DroSec_CAF1 9739 108 - 1
UCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUUGAAGGCAGAGUGAAAAUAAAACAGGAAAUGACAAGC
((((((........((((.(((.((((((...((((((...(((((((.....)))))))..))))))......))))))..))).)))).......))))))..... ( -29.56)
>DroSim_CAF1 10020 108 - 1
UCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUUGAAGGCAGAGUGAAAAUAAAACAGGAAAUGACAAGC
((((((........((((.(((.((((((...((((((...(((((((.....)))))))..))))))......))))))..))).)))).......))))))..... ( -29.56)
>DroEre_CAF1 10003 108 - 1
UCAUUUAUGCCCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUUGAAGGCAGAGUGAAAAUAAAACAGGAAAUGACAAGC
((((((.((.(((((...)))))((((((...((((((...(((((((.....)))))))..))))))......)))))).............))..))))))..... ( -31.30)
>DroYak_CAF1 10131 108 - 1
UCAUUUAUGCCCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUUGAAGGCAGAGUGAAAAUAAAACAGGAAAUGACAAGC
((((((.((.(((((...)))))((((((...((((((...(((((((.....)))))))..))))))......)))))).............))..))))))..... ( -31.30)
>consensus
UCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUUGAAGGCAGAGUGAAAAUAAAACAGGAAAUGACAAGC
((((((.((.(((((...)))))((((((...((((((...(((((((.....)))))))..))))))......)))))).............))..))))))..... (-30.10 = -29.86 +  -0.24)

alignment

secondary structure

dotplot

Window 0

Location	11,573,297 – 11,573,409
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	97.86
Mean single sequence MFE	-33.62
Consensus MFE	-33.26
Energy contribution	-33.18
Covariance contribution	-0.08
Combinations/Pair	1.06
Mean z-score	-1.46
Structure conservation index	0.99
SVM decision value	1.39
SVM RNA-class probability	0.949503
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11573297 112 - 20766785
GGGCUUGUCCUGAGCUCCUUCCGCUCCCGUUGCUACUGCAUCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUU
((((((.....))))))....(((....((.(((((.(((((..........))))).)).))).))..)))((((((...(((((((.....)))))))..)))))).... ( -34.40)
>DroSec_CAF1 9775 112 - 1
GGGCUUGUCCUGAGCUCCUUCCGCUCCCGUUGCUACUGCAUCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUU
((((((.....))))))....(((....((.(((((.(((((..........))))).)).))).))..)))((((((...(((((((.....)))))))..)))))).... ( -34.40)
>DroSim_CAF1 10056 112 - 1
GGGCUUGUCCUGAGCUCCUUCCGCUCCCGUUGCUACUGCAUCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUU
((((((.....))))))....(((....((.(((((.(((((..........))))).)).))).))..)))((((((...(((((((.....)))))))..)))))).... ( -34.40)
>DroEre_CAF1 10039 112 - 1
GGGCUUGUCCUGAGCUGCUUCCGCUCCCGUUGCUACUGCAUCAUUUAUGCCCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUU
.(((((.....))))).....(((....((.(((((.(((((..........))))).)).))).))..)))((((((...(((((((.....)))))))..)))))).... ( -32.70)
>DroYak_CAF1 10167 112 - 1
GGACUCGUCCUGAGUUGCUUCCGCUCCCGUUGCUACUGCAUCAUUUAUGCCCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUU
.(((((.....))))).....(((....((.(((((.(((((..........))))).)).))).))..)))((((((...(((((((.....)))))))..)))))).... ( -32.20)
>consensus
GGGCUUGUCCUGAGCUCCUUCCGCUCCCGUUGCUACUGCAUCAUUUAUGCUCGAUGUUGUCGGCUGCUUGCGUCCCUGAUUUGUUUCGACAUCUGAAAUAUGCAGGGAAUUU
((((((.....))))))....(((....((.(((((.(((((..........))))).)).))).))..)))((((((...(((((((.....)))))))..)))))).... (-33.26 = -33.18 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:02 2006