Locus 4287

Sequence ID 3L_DroMel_CAF1
Location 12,555,648 – 12,555,824
Length 176
Max. P 0.992944
window6624 window6625 window6626

overview

Window 4

Location 12,555,648 – 12,555,759
Length 111
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 92.74
Mean single sequence MFE -26.28
Consensus MFE -24.02
Energy contribution -23.86
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.80
Structure conservation index 0.91
SVM decision value 2.36
SVM RNA-class probability 0.992944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12555648 111 + 23771897
AGCGCUUUUGGACUUUUCACUAAGCAGCAAAAACAGCUGCUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAA--------AAAACCAUAAUAAAUCAG
...(((..............((((((((.......)))))))).(((...((....(((.((((((....))))))))).))...))))))..--------.................. ( -24.30)
>DroSec_CAF1 43892 116 + 1
AGCGCUUUUGGACUUUUCACUAAGCAGCAAAAACGGCUGCUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAAA---AAAAAAAACCAUAAUAAAUCAG
...(((..............((((((((.......)))))))).(((...((....(((.((((((....))))))))).))...))))))...---...................... ( -24.20)
>DroSim_CAF1 45115 119 + 1
AGCGCUUUUGGACUUUUCACUAAGCAGCAAAAACAGCUGCUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAAAACAAAAAAAAACCAUAAUAAAUCAG
...(((..............((((((((.......)))))))).(((...((....(((.((((((....))))))))).))...))))))............................ ( -24.30)
>DroEre_CAF1 44594 110 + 1
AGCGCUUUCUGACUUUUAACUAAGCAGCAAAAACAGCUGCUUG-GGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUAGAAAGCCAGCAA--------AAAAGCAUAAUAAAUCAG
.(.((((((((...(((..(((((((((.......))))))))-)..)))......(((.((((((....)))))))))))))))))).((..--------....))............ ( -30.10)
>DroYak_CAF1 45027 111 + 1
AGCGCUUUCGGACUUUUCACUAAGCAGCAAAAACAGCUGCUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGAAGGCCAGCAA--------AAAAGCAUAAUAAAUCAG
...(((((............((((((((.......)))))))).(((...((((..(((.((((((....)))))))))..))))))).....--------.)))))............ ( -28.50)
>consensus
AGCGCUUUUGGACUUUUCACUAAGCAGCAAAAACAGCUGCUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAA________AAAACCAUAAUAAAUCAG
...(((..............((((((((.......)))))))).(((...((....(((.((((((....))))))))).))...))))))............................ (-24.02 = -23.86 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,555,687 – 12,555,799
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.80
Mean single sequence MFE -28.14
Consensus MFE -21.95
Energy contribution -22.35
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -2.28
Structure conservation index 0.78
SVM decision value 1.29
SVM RNA-class probability 0.940407
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12555687 112 + 23771897
CUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAA--------AAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGCCACUCCGAGGAA
((((..(....((((((((((((((((....))))))..))).(((((((....--------....((((..........))))........))))))).)))))))...)..))))... ( -27.49)
>DroSec_CAF1 43931 117 + 1
CUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAAA---AAAAAAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAGGGCACUCCGAGGAA
((((((((...((((((((((((((((....))))))..))))(((((((.....---.................(((((....)))))...))))))).)))))).)).)).))))... ( -29.41)
>DroSim_CAF1 45154 120 + 1
CUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAAAACAAAAAAAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCCGAGGAA
((((((((...((((((((((((((((....))))))..))).((((((((.....)..................(((((....)))))...))))))).))))))))).)).))))... ( -28.30)
>DroEre_CAF1 44633 111 + 1
CUUG-GGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUAGAAAGCCAGCAA--------AAAAGCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCGAAGGAA
((..-(((...(((((((((.((((((....))))))))).)))))).((((..--------....)).......(((((....)))))...)))))..))..........((....)). ( -25.40)
>DroYak_CAF1 45066 112 + 1
CUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGAAGGCCAGCAA--------AAAAGCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCCAAGGAA
((((((((........(((((((((((....))))))..)))))((((((((..--------....)).......(((((....)))))...)))))).........)).)).))))... ( -30.10)
>consensus
CUUGAGGCAAACUUUUUCCAUGUUUAUGACAGUAAAUUGGUGGCAGGCCAGCAA________AAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCCGAGGAA
((((.((....(((((((((.((((((....))))))))....(((((((.........................(((((....)))))...))))))).)))))))...)).))))... (-21.95 = -22.35 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,555,727 – 12,555,824
Length 97
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 91.35
Mean single sequence MFE -23.96
Consensus MFE -18.34
Energy contribution -18.98
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -2.29
Structure conservation index 0.77
SVM decision value 1.18
SVM RNA-class probability 0.926927
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12555727 97 + 23771897
UGGCAGGCCAGCAA--------AAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGCCACUCCGAGGAAUCAGGCGUUUUUGUCAACCUUCAAA
(((....)))....--------.................((.((.(((((((..((((((.......((.......))..))))))...))))))).)).))... ( -23.10)
>DroSec_CAF1 43971 102 + 1
UGGCAGGCCAGCAAA---AAAAAAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAGGGCACUCCGAGGAAUCAGGCGUUUUUGUCAACCUUCAAA
(((....))).....---.....................((.((.(((((((..((((((.....((.....))......))))))...))))))).)).))... ( -24.90)
>DroSim_CAF1 45194 105 + 1
UGGCAGGCCAGCAAAACAAAAAAAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCCGAGGAAUCAGGCGUUUUUGUCAACCUUCAAA
(((....))).............................((.((.(((((((..((((((......((....))......))))))...))))))).)).))... ( -24.60)
>DroEre_CAF1 44672 97 + 1
UAGAAAGCCAGCAA--------AAAAGCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCGAAGGAAUCAGGCGUUUUUGUCAACCUUCAAA
..(((.((((((..--------....)).......(((((....)))))...)))).(((.(((((.((..((....)).....)).))))).)))...)))... ( -23.00)
>DroYak_CAF1 45106 97 + 1
UGGAAGGCCAGCAA--------AAAAGCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCCAAGGAAUCAGUCGUUUUUGUCAACCUUUAAA
..(((((...((..--------....))..........(((((((((((.....((((.......))))..((....))))))))))))).......)))))... ( -24.20)
>consensus
UGGCAGGCCAGCAA________AAAACCAUAAUAAAUCAGAUGGCUGAUAAAUGGCCUGAGAAAAAGGCACUCCGAGGAAUCAGGCGUUUUUGUCAACCUUCAAA
(((....))).............................((.((.(((((((..((((((......((....))......))))))...))))))).)).))... (-18.34 = -18.98 +   0.64)

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 11:18:34 2006