Locus 4200

Sequence ID 3L_DroMel_CAF1
Location 12,267,701 – 12,267,831
Length 130
Max. P 0.993156
window6510 window6511 window6512

overview

Window 0

Location 12,267,701 – 12,267,805
Length 104
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 82.38
Mean single sequence MFE -25.01
Consensus MFE -15.26
Energy contribution -15.22
Covariance contribution -0.04
Combinations/Pair 1.16
Mean z-score -1.80
Structure conservation index 0.61
SVM decision value 0.00
SVM RNA-class probability 0.533886
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12267701 104 - 23771897
GGCAAUUAAAUGCAGUCCAAUUAAAUGUACUGAGAGCUGCAAUCGACUAUUUUCGCAUUUAU-------UUGUCAUUUGGCAGAACAAACUGAGUGCAAGCUGGUCUAGAG
..........(((((..(...............)..)))))...(((((.(((.((((((((-------(((((....))))))......)))))))))).)))))..... ( -22.76)
>DroSec_CAF1 2736 104 - 1
GGCAAUUAAAUGCAGUCCAAUUAAAUGUACUGAGAGCUGCAAUCGACUAUUUUCGCAUUUAU-------UUGCCAUGUGGCAGAACAAACUGAGUGCAAGCUGUUCUAAAG
............((((.((......)).))))(((((.((....((......))((((((((-------(((((....))))))......)))))))..)).))))).... ( -24.60)
>DroSim_CAF1 2685 89 - 1
GGCAAUUAAAUGCAGUCCAAUUAAAUGUACUG---------------UAUUUUCGCAUUUAU-------UUGCCAUUGGGCAGAACAAACUGAGUGCAAGCUGUUCUAAAG
(((....(((((((((.((......)).))))---------------)))))..((((((((-------(((((....))))))......)))))))..)))......... ( -24.40)
>DroEre_CAF1 2779 103 - 1
GGCAAUUAAAUGCAGUCCAAUUAAAUGCACUCACAACGGCAAUUGACUAUUUUCGCAUUUAU-------UUGCCAUUCGGCUGAACGAGACAAGUGCAAGCUGA-CUAAAG
(((((.(((((((((((.(((....(((.(.......)))))))))))......))))))).-------)))))..((((((..((.......))...))))))-...... ( -26.50)
>DroYak_CAF1 2890 110 - 1
GGCAAUUAAAUGCAGUCCAAUUAAAUGCACUCAGAACUGCAAUCGACUAAUUUCGCAUUUAUUUACGAUUUGCCAUUUGGCUGAAUAAAAUAAGUGCAAGCUGA-GUAAAG
.(((.((((.((.....)).)))).)))((((((..........((......))((((((((((...(((((((....))).)))).))))))))))...))))-)).... ( -26.80)
>consensus
GGCAAUUAAAUGCAGUCCAAUUAAAUGUACUGAGAACUGCAAUCGACUAUUUUCGCAUUUAU_______UUGCCAUUUGGCAGAACAAACUGAGUGCAAGCUGAUCUAAAG
(((.......((((...........)))).........................(((((((........(((((....))))).......)))))))..)))......... (-15.26 = -15.22 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,267,733 – 12,267,831
Length 98
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 82.09
Mean single sequence MFE -24.07
Consensus MFE -15.98
Energy contribution -16.86
Covariance contribution 0.88
Combinations/Pair 1.04
Mean z-score -3.12
Structure conservation index 0.66
SVM decision value 2.38
SVM RNA-class probability 0.993156
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12267733 98 + 23771897
CAAAUGACAA-------AUAAAUGCGAAAAUAGUCGAUUGCAGCUCUCAGUACAUUUAAUUGGACUGCAUUUAAUUGCCAUUUGGAUAUAGAAAAACUAUGCAGA-
((((((.(((-------.(((((.(((......)))...((((.((.((((.......))))))))))))))).))).))))))(.(((((.....))))))...- ( -20.10)
>DroSec_CAF1 2768 99 + 1
CACAUGGCAA-------AUAAAUGCGAAAAUAGUCGAUUGCAGCUCUCAGUACAUUUAAUUGGACUGCAUUUAAUUGCCAUUUGGAAAUGGAAAAACUAUGCAGAA
((.(((((((-------.(((((.(((......)))...((((.((.((((.......))))))))))))))).))))))).))...((((.....))))...... ( -22.50)
>DroSim_CAF1 2717 84 + 1
CCAAUGGCAA-------AUAAAUGCGAAAAUA---------------CAGUACAUUUAAUUGGACUGCAUUUAAUUGCCAUUUGGAUGCAGAAAAACUAUGCUAAA
((((((((((-------.((((((((......---------------((((.......))))...)))))))).)))))).))))..(((.........))).... ( -22.50)
>DroEre_CAF1 2810 97 + 1
CGAAUGGCAA-------AUAAAUGCGAAAAUAGUCAAUUGCCGUUGUGAGUGCAUUUAAUUGGACUGCAUUUAAUUGCCAUUUGAAUAUAGAAAAAGUAUGCA--A
((((((((((-------.((((((((....((((.((.((((.......).))).)).))))...)))))))).))))))))))...................--. ( -26.30)
>DroYak_CAF1 2921 104 + 1
CAAAUGGCAAAUCGUAAAUAAAUGCGAAAUUAGUCGAUUGCAGUUCUGAGUGCAUUUAAUUGGACUGCAUUUAAUUGCCAUUUGAAUGUAGAAAAACUAUGCA--A
((((((((((.(((((......)))))........((.((((((((...............)))))))).))..))))))))))..((((.........))))--. ( -28.96)
>consensus
CAAAUGGCAA_______AUAAAUGCGAAAAUAGUCGAUUGCAGCUCUCAGUACAUUUAAUUGGACUGCAUUUAAUUGCCAUUUGGAUAUAGAAAAACUAUGCA_AA
((((((((((........(((((((((......)).............(((.((......)).)))))))))).))))))))))...................... (-15.98 = -16.86 +   0.88)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,267,733 – 12,267,831
Length 98
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 82.09
Mean single sequence MFE -21.30
Consensus MFE -14.36
Energy contribution -15.20
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.62
Structure conservation index 0.67
SVM decision value 1.70
SVM RNA-class probability 0.972961
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12267733 98 - 23771897
-UCUGCAUAGUUUUUCUAUAUCCAAAUGGCAAUUAAAUGCAGUCCAAUUAAAUGUACUGAGAGCUGCAAUCGACUAUUUUCGCAUUUAU-------UUGUCAUUUG
-.....((((.....))))...((((((((((.((((((((((.((......)).)))(((((..((....).)..)))))))))))).-------)))))))))) ( -23.10)
>DroSec_CAF1 2768 99 - 1
UUCUGCAUAGUUUUUCCAUUUCCAAAUGGCAAUUAAAUGCAGUCCAAUUAAAUGUACUGAGAGCUGCAAUCGACUAUUUUCGCAUUUAU-------UUGCCAUGUG
......................((.(((((((.((((((((((.((......)).)))(((((..((....).)..)))))))))))).-------))))))).)) ( -21.40)
>DroSim_CAF1 2717 84 - 1
UUUAGCAUAGUUUUUCUGCAUCCAAAUGGCAAUUAAAUGCAGUCCAAUUAAAUGUACUG---------------UAUUUUCGCAUUUAU-------UUGCCAUUGG
....(((.........)))..((((.((((((.((((((((((.((......)).)))(---------------......)))))))).-------)))))))))) ( -21.20)
>DroEre_CAF1 2810 97 - 1
U--UGCAUACUUUUUCUAUAUUCAAAUGGCAAUUAAAUGCAGUCCAAUUAAAUGCACUCACAACGGCAAUUGACUAUUUUCGCAUUUAU-------UUGCCAUUCG
.--.....................((((((((.(((((((((((.(((....(((.(.......)))))))))))......))))))).-------)))))))).. ( -20.20)
>DroYak_CAF1 2921 104 - 1
U--UGCAUAGUUUUUCUACAUUCAAAUGGCAAUUAAAUGCAGUCCAAUUAAAUGCACUCAGAACUGCAAUCGACUAAUUUCGCAUUUAUUUACGAUUUGCCAUUUG
.--...................((((((((((.(((((((............((((........))))...((......)))))))))........)))))))))) ( -20.60)
>consensus
UU_UGCAUAGUUUUUCUAUAUCCAAAUGGCAAUUAAAUGCAGUCCAAUUAAAUGUACUGAGAACUGCAAUCGACUAUUUUCGCAUUUAU_______UUGCCAUUUG
......................((((((((((.((((((((((.((......)).))).............((......)))))))))........)))))))))) (-14.36 = -15.20 +   0.84)

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 11:16:40 2006