Locus 1653

Sequence ID 3R_DroMel_CAF1
Location 4,784,517 – 4,784,672
Length 155
Max. P 0.762040
window2725 window2726

overview

Window 5

Location 4,784,517 – 4,784,632
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 85.48
Mean single sequence MFE -23.42
Consensus MFE -15.05
Energy contribution -16.22
Covariance contribution 1.17
Combinations/Pair 1.17
Mean z-score -2.36
Structure conservation index 0.64
SVM decision value 0.50
SVM RNA-class probability 0.762040
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4784517 115 - 27905053
AUAAAAACACAAGAGUUUAAUGAAAGAUUAAGCAGAUGUGUGGAGCGAAAGAUACACGAAUAUCUAGAGUAGGGGUAAAGCAGAGGGACUAACCUGUUUAUAUCUGCAAAGAAUU
......((.(.((((((((((.....)))))))...((((((...(....).))))))....))).).)).........(((((.((((......))))...)))))........ ( -24.50)
>DroSec_CAF1 19756 98 - 1
AUAAAACCGCAAGAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAAAGAU-----------------AGGGGCAAAGCAGAGAGACUAACCUGUUUAUAUCUGAAAAGAAUU
......(((((...(((((((.....))))))).....)))))......((((-----------------(((...................)))))))...(((....)))... ( -18.21)
>DroSim_CAF1 15201 115 - 1
AUAAAACCACAAGAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAAAGAUACACGAAUAUCUAGAGUAGGGGCAAAGCAGGGAGACUAACCUGUUUAUAUCUGCAAAGAAUU
..............(((((((.....)))))))(((((((((...(....)...)))..))))))...(((((....(((((((........)))))))...)))))........ ( -27.90)
>DroEre_CAF1 19994 115 - 1
AUAAAACCACAACAUUUUAAUGAAAGAUUAAACAGAUGUGGGGAGCGAAGGAUGCAAGAAUAUCUAGAGUCGGGGUAAAGCAGAAUGAAUAACCUGUUUAUAUCUGCAAAGAAUU
......(((((.(..((((((.....))))))..).)))))....(((.(((((......)))))....))).......(((((((((((.....)))))).)))))........ ( -21.90)
>DroYak_CAF1 20299 115 - 1
AUAAAACCACAACAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAGAGAUGCAAGAAUAUCUGGUGUAGUGGUAAAGCAGAACGAAGAACCUGUUUAUAUCAGCAAAGAAUU
.....(((((.((((((((((.....)))))))((((((.((.(.(....).).))...))))))..))).))))).((((((..........))))))................ ( -24.60)
>consensus
AUAAAACCACAAGAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAAAGAUACAAGAAUAUCUAGAGUAGGGGUAAAGCAGAGAGACUAACCUGUUUAUAUCUGCAAAGAAUU
......(((((...(((((((.....))))))).....))))).((...(((((......))))).......(((((((((((..........)))))).)))))))........ (-15.05 = -16.22 +   1.17)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,784,552 – 4,784,672
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.58
Mean single sequence MFE -26.62
Consensus MFE -20.37
Energy contribution -20.34
Covariance contribution -0.03
Combinations/Pair 1.21
Mean z-score -1.81
Structure conservation index 0.77
SVM decision value 0.50
SVM RNA-class probability 0.759462
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4784552 120 - 27905053
GUGCCAGAAGUUCAUUCAUGGCUAAAACAAACCGCCGACGAUAAAAACACAAGAGUUUAAUGAAAGAUUAAGCAGAUGUGUGGAGCGAAAGAUACACGAAUAUCUAGAGUAGGGGUAAAG
..(((((((.....))).))))........(((.((.((...............(((((((.....)))))))(((((((((...(....)...)))..))))))...)).))))).... ( -27.90)
>DroSec_CAF1 19791 103 - 1
GUGCCAGAAGUUCAUUCAUGGCUAAAACAAACCGCCGACGAUAAAACCGCAAGAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAAAGAU-----------------AGGGGCAAAG
..(((((((.....))).))))...........(((..........(((((...(((((((.....))))))).....)))))..(....)..-----------------...))).... ( -24.20)
>DroSim_CAF1 15236 120 - 1
GUGCCAGAAGUUCAUUCAUGGCUUAAACAAACCGCCGACGAUAAAACCACAAGAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAAAGAUACACGAAUAUCUAGAGUAGGGGCAAAG
..(((((((.....))).))))...........(((..........(((((...(((((((.....))))))).....))))).((...(((((......)))))...))...))).... ( -26.70)
>DroEre_CAF1 20029 120 - 1
GUGCCAGAAGUUCAUUCAUGGCCGAAACAAACAGCCAGCGAUAAAACCACAACAUUUUAAUGAAAGAUUAAACAGAUGUGGGGAGCGAAGGAUGCAAGAAUAUCUAGAGUCGGGGUAAAG
(.(((((((.....))).)))))..........(((..((((....(((((.(..((((((.....))))))..).)))))........(((((......)))))...)))).))).... ( -24.80)
>DroYak_CAF1 20334 120 - 1
GUGCCACAAGUUCAUUCAUGGCUAAAACAAACAGCCAACGAUAAAACCACAACAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAGAGAUGCAAGAAUAUCUGGUGUAGUGGUAAAG
.((((((...........(((((.........))))).........(((((...(((((((.....))))))).....))))).(((..(((((......)))))..))).))))))... ( -29.50)
>consensus
GUGCCAGAAGUUCAUUCAUGGCUAAAACAAACCGCCGACGAUAAAACCACAAGAGUUUAAUGAAAGAUUAAACAGAUGUGUGGAGCGAAAGAUACAAGAAUAUCUAGAGUAGGGGUAAAG
.((((....((((.....((((...........))))..........((((...(((((((.....)))))))...))))..))))...(((((......)))))........))))... (-20.37 = -20.34 +  -0.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:57 2006