Locus 6121

Sequence ID	3L_DroMel_CAF1
Location	16,216,971 – 16,217,171
Length	200
Max. P	0.976123

overview

Window 2

Location	16,216,971 – 16,217,091
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.08
Mean single sequence MFE	-52.70
Consensus MFE	-45.48
Energy contribution	-46.16
Covariance contribution	0.68
Combinations/Pair	1.03
Mean z-score	-1.37
Structure conservation index	0.86
SVM decision value	0.25
SVM RNA-class probability	0.655332
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16216971 120 - 23771897
GCUUCGGCCUGAGGUCGCAGGAUGACCUAGUUCACUCGGAUGACGCAGCCAGCGUUGCAACAUCGAGGAGCGGCGGAGGCGGCUGUGGAGGUGGAGUAGCCGGGGUCACUCUCCAGGAGG
(((((.(((..((((((.....)))))).((((.((((.(((..(((((....)))))..)))))))))))))).)))))((((.(((..(.....)..))).)))).(((.....))). ( -51.40)
>DroSec_CAF1 35730 120 - 1
GCUUCGGCCUGAGGUCGCAAGAUGACCUAGUUCACUCGGAUGACGCAGCCAGCGUUGCAACAUCGAGGAGCGGCGGAGGCGGCUGUGGCGGUGGAGUAGCCGGGGUCACUCUCCAGGAGG
(((((.(((..((((((.....)))))).((((.((((.(((..(((((....)))))..)))))))))))))).)))))((((.((((.........)))).)))).(((.....))). ( -55.50)
>DroSim_CAF1 37327 120 - 1
GCUUCGGCCUGAGGUCGCAGGAUGACCUAGUUCACUCGGAUGACGCAGCCAGCGUUGCAACAUCGAGGAGCGGCGGAGGCGGCUGUGGCGGUGGAGUAGCCGGGGUCACUCUCCAGGAGG
(((((.(((..((((((.....)))))).((((.((((.(((..(((((....)))))..)))))))))))))).)))))((((.((((.........)))).)))).(((.....))). ( -55.50)
>DroEre_CAF1 35225 120 - 1
GCUUCGGCCUGAGGUCGCAGGAUGACCUAGUUCACUCGGAUGACGCAGCCAGCGUUGCAACAUCGAGGAGCGGAGGAGGCGGAUGUGGAGGGGGAGUAGCCGGGGUCACUCUCCAGGAGG
(((((..((..((((((.....)))))).((((.((((.(((..(((((....)))))..)))))))))))))..)))))..........(((((((..(....)..)))))))...... ( -49.60)
>DroYak_CAF1 72211 120 - 1
GCUUCGGCCUGAGGUCGCAGGAUGACCUAGUUCACUCGGAUGACGCAGCCAGCGUUGCAACAUCAAGGAGCAGUGCAGGCGGAAGCGGAGGUGGAGUAGCCGGGGUCACUCUCCAGGAGG
(((((.(((((((((((.....)))))).((((.((..((((..(((((....)))))..)))).))))))....))))).)))))...((.(((((..(....)..)))))))...... ( -51.50)
>consensus
GCUUCGGCCUGAGGUCGCAGGAUGACCUAGUUCACUCGGAUGACGCAGCCAGCGUUGCAACAUCGAGGAGCGGCGGAGGCGGCUGUGGAGGUGGAGUAGCCGGGGUCACUCUCCAGGAGG
(((((.(((..((((((.....)))))).((((.((((.(((..(((((....)))))..)))))))))))))).))))).........((.(((((..(....)..)))))))...... (-45.48 = -46.16 +   0.68)

alignment

secondary structure

dotplot

Window 3

Location	16,217,051 – 16,217,171
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.75
Mean single sequence MFE	-52.28
Consensus MFE	-51.78
Energy contribution	-52.38
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.99
SVM decision value	1.76
SVM RNA-class probability	0.976123
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16217051 120 + 23771897
UCCGAGUGAACUAGGUCAUCCUGCGACCUCAGGCCGAAGCGGCGGCUCAGCUGCCGAAAAAAGCCCAGAUUGCGUUCGUAGCGCGGUGUUGGCGAAACGCUUAGACUGCCGCCCGGCGAU
..........(((((((.......))))).))((((..(((((((((.(((((((((.....(((......((((.....))))))).))))))....))).)).))))))).))))... ( -45.20)
>DroSec_CAF1 35810 120 + 1
UCCGAGUGAACUAGGUCAUCUUGCGACCUCAGGCCGAAGCGGCGGCUCAGCUGCCGAAAGAAGCCCAGAUUGCGUUCGUAGCGCGGUGUUGGCGAAACGCUCAGACUGCCGCCCGGCGAU
..........(((((((.......))))).))((((..(((((((((.(((...(....)..(((.(.(((((((.....))))))).).))).....))).)).))))))).))))... ( -49.40)
>DroSim_CAF1 37407 120 + 1
UCCGAGUGAACUAGGUCAUCCUGCGACCUCAGGCCGAAGCGGCGGCUCAGCUGCCGAAAGAAGCCCAGAUUGCGUUCGUAGCGCGGUGUUGGCGAAACGCUGAGACUGCCGCCCGGCGAU
..........(((((((.......))))).))((((..(((((((((((((...(....)..(((.(.(((((((.....))))))).).))).....)))))).))))))).))))... ( -55.60)
>DroEre_CAF1 35305 120 + 1
UCCGAGUGAACUAGGUCAUCCUGCGACCUCAGGCCGAAGCGGCGGCUCAGCUGCCGAAAGAAGCCCAGAUUGCGUUCGUAGCGCGGUGUUGGCGAAACGCUGAGACUGCCGCCCGGCGAU
..........(((((((.......))))).))((((..(((((((((((((...(....)..(((.(.(((((((.....))))))).).))).....)))))).))))))).))))... ( -55.60)
>DroYak_CAF1 72291 120 + 1
UCCGAGUGAACUAGGUCAUCCUGCGACCUCAGGCCGAAGCGGCGGCUCAGCUGCCGAAAGAAGCCCAGAUUGCGUUCGUAGCGCGGUGUUGGCGAAACGCUGAGACUGCCGCCCGGCGAU
..........(((((((.......))))).))((((..(((((((((((((...(....)..(((.(.(((((((.....))))))).).))).....)))))).))))))).))))... ( -55.60)
>consensus
UCCGAGUGAACUAGGUCAUCCUGCGACCUCAGGCCGAAGCGGCGGCUCAGCUGCCGAAAGAAGCCCAGAUUGCGUUCGUAGCGCGGUGUUGGCGAAACGCUGAGACUGCCGCCCGGCGAU
..........(((((((.......))))).))((((..(((((((((((((...(....)..(((.(.(((((((.....))))))).).))).....)))))).))))))).))))... (-51.78 = -52.38 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:36 2006