Locus 994

Sequence ID 3L_DroMel_CAF1
Location 2,963,330 – 2,963,543
Length 213
Max. P 0.998392
window1534 window1535 window1536 window1537

overview

Window 4

Location 2,963,330 – 2,963,424
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 96.70
Mean single sequence MFE -26.14
Consensus MFE -24.96
Energy contribution -24.76
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -1.99
Structure conservation index 0.95
SVM decision value 3.09
SVM RNA-class probability 0.998392
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963330 94 - 23771897
AAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCGAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCGCGCAUUUUAAAGAC
...((((((..(((.(((((((....)))))))))).((.(((((.....)))))(((((((.((...)).)))))))))..))))))...... ( -27.20)
>DroSec_CAF1 191974 94 - 1
AAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCUCGCAUUUUAAAGAG
.((((.((((.(((.(((((((....))))))))))....(((((.....)))))(((((((.((...)).))))))).)))).))))...... ( -28.40)
>DroSim_CAF1 178093 94 - 1
AAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCUCGCAUUUUAAAGAC
.((((.((((.(((.(((((((....))))))))))....(((((.....)))))(((((((.((...)).))))))).)))).))))...... ( -28.40)
>DroEre_CAF1 200074 94 - 1
AAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCUGCUCGCAUUUUAAAGAG
.....((..(((((.(((((((....))))))))))(((..((((.....)))))))........))..))..(((.....))).......... ( -23.90)
>DroYak_CAF1 204290 94 - 1
AAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCUCCCCGUAUUUUAAAGAC
.....((....(((.(((((((....))))))))))))..(((((.....)))))(((((((.((...)).)))))))................ ( -22.80)
>consensus
AAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCUCGCAUUUUAAAGAC
...((((((..(((.(((((((....))))))))))....(((((.....)))))(((((((.((...)).)))))))....))))))...... (-24.96 = -24.76 +  -0.20)

alignment

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secondary structure

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Window 5

Location 2,963,344 – 2,963,464
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.75
Mean single sequence MFE -35.08
Consensus MFE -32.70
Energy contribution -32.50
Covariance contribution -0.20
Combinations/Pair 1.06
Mean z-score -1.39
Structure conservation index 0.93
SVM decision value 0.96
SVM RNA-class probability 0.891001
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963344 120 - 23771897
CUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUUGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCGAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCG
...........((((......(((((.....((....))......)))))..((.(((((((....))))))))))))).(((((.....)))))(((((((.((...)).))))))).. ( -34.90)
>DroSec_CAF1 191988 120 - 1
CUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUGGUCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCU
...((((((....(((((..(((.....)))....))))).....))))))(((.(((((((....))))))))))....(((((.....)))))(((((((.((...)).))))))).. ( -35.60)
>DroSim_CAF1 178107 120 - 1
CUGUUUAUCCACGGACCGAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCU
............(((((......((((((...)).))))......)))...(((.(((((((....))))))))))))..(((((.....)))))(((((((.((...)).))))))).. ( -35.70)
>DroEre_CAF1 200088 120 - 1
CUGUUUAUCCACGGACCGAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCUGCU
....((((((..(((((......((((((...)).))))......)))...(((.(((((((....))))))))))))..(((((.....)))))))))))..((...((....)).)). ( -33.90)
>DroYak_CAF1 204304 120 - 1
CUGUUUAUCUACGGACCAAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCUCCC
((((......)))).............(((.((.(((((....((((..(.(((.(((((((....))))))))))(((..((((.....)))))))....)..))))))))).))))). ( -35.30)
>consensus
CUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAAAUCGAACAAAUCGAUGGGUAAUUGCUUUGCCAUUGCCCCU
............(((......(((((.....((....))......)))))..((.(((((((....))))))))))))..(((((.....)))))(((((((.((...)).))))))).. (-32.70 = -32.50 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,963,384 – 2,963,503
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.99
Mean single sequence MFE -29.46
Consensus MFE -26.53
Energy contribution -26.41
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.67
Structure conservation index 0.90
SVM decision value 1.44
SVM RNA-class probability 0.954481
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963384 119 - 23771897
GGGCAAACAAAUAAACGCCACGCAAAUGCAAACAA-AACGCUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUUGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCGA
((..(((((.......((...))....((......-...)))))))..)).((((......(((((.....((....))......)))))..((.(((((((....))))))))))))). ( -28.80)
>DroSec_CAF1 192028 119 - 1
GGGCAAACAAAUUAACGCCACGCAAAUGCAAACAA-AACGCUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUGGUCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAA
((.............((((..((....))(((((.-.....))))).......(((((..(((.....)))....))))).....))))..(((.(((((((....)))))))))))).. ( -30.30)
>DroSim_CAF1 178147 118 - 1
G-GCAAACAAAUAAACGCCACGCAAAUGCAAACAA-AACGCUGUUUAUCCACGGACCGAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAA
(-((............)))..((....))(((((.-.....)))))......(((((......((((((...)).))))......)))...(((.(((((((....)))))))))))).. ( -29.20)
>DroEre_CAF1 200128 120 - 1
GGGCAAACAAAUAAACGCCACGCAAAUGCAAACAAAAACGCUGUUUAUCCACGGACCGAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAA
((.............((((..((....))..........(((((.(((((..((..((....)))).)))))..)))))......))))..(((.(((((((....)))))))))))).. ( -30.10)
>DroYak_CAF1 204344 120 - 1
GGGCAAACAAAUAAACGCCACGCAAAUGCAAACAAAAACGCUGUUUAUCUACGGACCAAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAA
((.............((((..((....))...........((((......)))).........((((((...)).))))......))))..(((.(((((((....)))))))))))).. ( -28.90)
>consensus
GGGCAAACAAAUAAACGCCACGCAAAUGCAAACAA_AACGCUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUGGCCAAAAAGGUGAAAGGACGCUUAAGCACUUGAGCGCCUCCAA
((..(((((............((....))............)))))..))..(((......(((((.....((....))......)))))..((.(((((((....)))))))))))).. (-26.53 = -26.41 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,963,424 – 2,963,543
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.60
Mean single sequence MFE -25.86
Consensus MFE -19.66
Energy contribution -20.34
Covariance contribution 0.68
Combinations/Pair 1.09
Mean z-score -2.00
Structure conservation index 0.76
SVM decision value 0.67
SVM RNA-class probability 0.816757
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963424 119 - 23771897
GUCCAAGCUCCAAGCUCCUCGACCAGCAGACAUCAACAGCGGGCAAACAAAUAAACGCCACGCAAAUGCAAACAA-AACGCUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUUGCC
(((..(((.....)))....)))..((((.....((((((((((............)))..((....))......-..)))))))(((((..((..........)).)))))...)))). ( -25.30)
>DroSec_CAF1 192068 112 - 1
GUCCAA-------ACUCAUCGACCAGCAGACAUCAACAGCGGGCAAACAAAUUAACGCCACGCAAAUGCAAACAA-AACGCUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUGGUC
......-------.......((((((((..(...((((((((((............)))..((....))......-..))))))).......((..........)).)..)))..))))) ( -26.00)
>DroSim_CAF1 178187 111 - 1
GUCCAA-------ACUCCUCGACCAGCAGACAUCAACAGCG-GCAAACAAAUAAACGCCACGCAAAUGCAAACAA-AACGCUGUUUAUCCACGGACCGAAAUCGCCAGGAUGCCAUGGCC
((((..-------.((.((.....)).)).....(((((((-((............)))..((....))......-...)))))).......)))).......((((((...)).)))). ( -24.20)
>DroEre_CAF1 200168 113 - 1
UCCCAA-------ACUCCUCCACCAGCAGACAUCAGCAGCGGGCAAACAAAUAAACGCCACGCAAAUGCAAACAAAAACGCUGUUUAUCCACGGACCGAAAUCGCCAGGAUGCCAUGGCC
......-------.........((((((..(...((((((((((............)))..((....)).........))))))).......((..((....)))).)..)))..))).. ( -23.30)
>DroYak_CAF1 204384 113 - 1
GCCCAA-------AUUCUGCGACCAGCAGACAUCAACAGCGGGCAAACAAAUAAACGCCACGCAAAUGCAAACAAAAACGCUGUUUAUCUACGGACCAAAAUCGCCAGGAUGCCAUGGCC
(((...-------..(((((.....)))))((((((((((((((............)))..((....)).........)))))))..((....)).............))))....))). ( -30.50)
>consensus
GUCCAA_______ACUCCUCGACCAGCAGACAUCAACAGCGGGCAAACAAAUAAACGCCACGCAAAUGCAAACAA_AACGCUGUUUAUCCACGGACCAAAAUCGCCAGGAUGCCAUGGCC
((((........................(....)((((((((((............)))..((....)).........))))))).......)))).......((((((...)).)))). (-19.66 = -20.34 +   0.68)

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 09:56:23 2006