Locus 4332

Sequence ID 3R_DroMel_CAF1
Location 11,454,798 – 11,454,997
Length 199
Max. P 0.766379
window7079 window7080 window7081

overview

Window 9

Location 11,454,798 – 11,454,917
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.00
Mean single sequence MFE -28.82
Consensus MFE -22.94
Energy contribution -22.30
Covariance contribution -0.64
Combinations/Pair 1.14
Mean z-score -1.65
Structure conservation index 0.80
SVM decision value 0.52
SVM RNA-class probability 0.766379
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11454798 119 + 27905053
GCUGUCUUUGAUUUUUUUCUAAAAGCAUUUGCACUGAGUUCCUUUUU-GGGGGACGAAUUUCGUUGGAAAGUGAAUUUGGUGAGGUUUCCUGUUUUAAAAUUAGUGAUUGUGACUAAUUA
((.(((.((((((((...(...((((.....(((..((((((((((.-.(.(((.....))).)..))))).)))))..)))..))))...)....)))))))).))).))......... ( -28.60)
>DroSec_CAF1 187309 118 + 1
GCUGUCUUUGAUUU-UUUCUAAAAGCAUUUACACUGAGUUCCUUUUU-GGGGGACGAAUUUCGUUGGAAAGUGAAUUUGGUGAGGUUUCCUGUUUGAAAAUUAGUGAUUGUGACUAAUUA
((.(((.(((((((-((.....((((.....(((..((((((((((.-.(.(((.....))).)..))))).)))))..)))(((...)))))))))))))))).))).))......... ( -29.40)
>DroSim_CAF1 182361 118 + 1
GCUGUCUUUGAUUU-UUUCUAAAAGCAUUUACACUGAGUUCCUUUUU-GGGGGACGAAUUUCGUUGGAAAGUGAAUUUGGUGAGGUUUCCUGUUUGAAAAUUAGUGAUUGUGACUAAUUA
((.(((.(((((((-((.....((((.....(((..((((((((((.-.(.(((.....))).)..))))).)))))..)))(((...)))))))))))))))).))).))......... ( -29.40)
>DroEre_CAF1 176632 112 + 1
---GUCUUUGGUU---UUCUAAAAGCAUU-UCUCCGAGUCCCUUUUU-GGGAGGCGAAUUUCGUUGGAAAGUGAAUUUGGAGAGGCUUCCUGUUUAAAAAUUAGUGAUUGUGACUAAUUA
---......(.((---(((((((..((((-(.(((...((((.....-))))((((.....))))))))))))..))))))))).)............(((((((.......))))))). ( -28.30)
>DroYak_CAF1 180381 118 + 1
GCUGUCUUUGGUU--UUUCUAAAAGCAUUUUCCCCGAGUUCCUUUUUCGGGAGACGAAUUUCGUUGGAAAGUGAAUUCGGUGAGGUUUCCUGUUUAAAAAUUAGUGAUUGUGACUAAUUA
..((..(((((..--...)))))..)).((((.(((((((((((((.((..(......)..))...))))).)))))))).)))).............(((((((.......))))))). ( -28.40)
>consensus
GCUGUCUUUGAUUU_UUUCUAAAAGCAUUUACACUGAGUUCCUUUUU_GGGGGACGAAUUUCGUUGGAAAGUGAAUUUGGUGAGGUUUCCUGUUUAAAAAUUAGUGAUUGUGACUAAUUA
......................((((.....((((((((((((((((.(.((((....)))).).)))))).))))))))))(((...)))))))...(((((((.......))))))). (-22.94 = -22.30 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,454,838 – 11,454,957
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.64
Mean single sequence MFE -18.74
Consensus MFE -17.38
Energy contribution -17.18
Covariance contribution -0.20
Combinations/Pair 1.09
Mean z-score -1.10
Structure conservation index 0.93
SVM decision value 0.09
SVM RNA-class probability 0.578924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11454838 119 - 27905053
AGCAAAUCCCACUAAUUAUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUAAAACAGGAAACCUCACCAAAUUCACUUUCCAACGAAAUUCGUCCCCC-AAAAAGG
........((.........((((((((((............(((((((.......)))))))........(....)....))))))))))......(((.....))).....-.....)) ( -18.60)
>DroSec_CAF1 187348 119 - 1
GGCAAAUCCCACUAAUUGUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUCAAACAGGAAACCUCACCAAAUUCACUUUCCAACGAAAUUCGUCCCCC-AAAAAGG
(((.......(((((((((((....(((....)))..)))))))))))......................(((((...............)))))..........)))....-....... ( -18.96)
>DroSim_CAF1 182400 119 - 1
GGCAAAUCCAACUAAUUGUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUCAAACAGGAAACCUCACCAAAUUCACUUUCCAACGAAAUUCGUCCCCC-AAAAAGG
(((.......(((((((((((....(((....)))..)))))))))))......................(((((...............)))))..........)))....-....... ( -18.96)
>DroEre_CAF1 176665 118 - 1
U-CCAAUCCCACUAAUUAUGUGCGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUUAAACAGGAAGCCUCUCCAAAUUCACUUUCCAACGAAAUUCGCCUCCC-AAAAAGG
.-......(((((((((((((..(((.(....)))).)))))))))))......................(((......)))..............................-.....)) ( -18.00)
>DroYak_CAF1 180419 120 - 1
AGCAAAUCCCACUAAUUAUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUUAAACAGGAAACCUCACCGAAUUCACUUUCCAACGAAAUUCGUCUCCCGAAAAAGG
........(((((((((((((....(((....)))..)))))))))))............(((((.....(((((...............))))).(((.....))).....))))).)) ( -19.16)
>consensus
AGCAAAUCCCACUAAUUAUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUCAAACAGGAAACCUCACCAAAUUCACUUUCCAACGAAAUUCGUCCCCC_AAAAAGG
..........(((((((((((....(((....)))..)))))))))))......................(((((...............))))).(((.....)))............. (-17.38 = -17.18 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,454,877 – 11,454,997
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.00
Mean single sequence MFE -18.82
Consensus MFE -14.64
Energy contribution -14.40
Covariance contribution -0.24
Combinations/Pair 1.07
Mean z-score -1.49
Structure conservation index 0.78
SVM decision value 0.05
SVM RNA-class probability 0.559189
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11454877 120 - 27905053
CGUAUCGAGCUUACUCCACAUCAAAGCAAAUUACUCCACAAGCAAAUCCCACUAAUUAUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUAAAACAGGAAACCUCA
......(((.((..(((........((..............)).......(((((((((((....(((....)))..)))))))))))......................))))).))). ( -19.54)
>DroSec_CAF1 187387 120 - 1
CGUAUCGAGCUUACUCCACAUCAAAGCAAAUUACUCCACAGGCAAAUCCCACUAAUUGUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUCAAACAGGAAACCUCA
.(((....((((...........))))....)))(((...((......))(((((((((((....(((....)))..)))))))))))......................)))....... ( -21.00)
>DroSim_CAF1 182439 120 - 1
CGUAUCGAGCUUACUCCACAUCAAAGCAAAUUACUCCACAGGCAAAUCCAACUAAUUGUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUCAAACAGGAAACCUCA
.(((....((((...........))))....)))(((...((.....)).(((((((((((....(((....)))..)))))))))))......................)))....... ( -20.60)
>DroEre_CAF1 176704 101 - 1
------------------CAUCAAAGCAAAGUACUCCACCU-CCAAUCCCACUAAUUAUGUGCGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUUAAACAGGAAGCCUCU
------------------.......((..............-........(((((((((((..(((.(....)))).)))))))))))............(((((....))))))).... ( -14.70)
>DroYak_CAF1 180459 120 - 1
CAGAUCCAGCGCCCUCCACAUCAAAGCAAAUUACUCCACAAGCAAAUCCCACUAAUUAUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUUAAACAGGAAACCUCA
....(((.((...............)).......................(((((((((((....(((....)))..)))))))))))......................)))....... ( -18.26)
>consensus
CGUAUCGAGCUUACUCCACAUCAAAGCAAAUUACUCCACAAGCAAAUCCCACUAAUUAUGUGAGUUUGGCAACGACAGCAUAAUUAGUCACAAUCACUAAUUUUCAAACAGGAAACCUCA
..................................................(((((((((((....(((....)))..)))))))))))......................(....).... (-14.64 = -14.40 +  -0.24)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:29 2006