Locus 8049

Sequence ID 3L_DroMel_CAF1
Location 21,222,297 – 21,222,457
Length 160
Max. P 0.778542
window13152 window13153 window13154

overview

Window 2

Location 21,222,297 – 21,222,417
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -46.60
Consensus MFE -41.54
Energy contribution -41.35
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -1.68
Structure conservation index 0.89
SVM decision value 0.26
SVM RNA-class probability 0.656852
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21222297 120 - 23771897
UGCUAGCCGUCUUGGUUUCCUCUGAGGCCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAAACCGGUGCGGCAUUGGAUUUGCUAUCGGCAGAGGAGGCCU
.(((.(((((.(((((((((...(((((..(((((.....)))))..)))))..((((.............)))).))))))))).)))))......(((((.....)))))...))).. ( -46.72)
>DroSim_CAF1 89338 120 - 1
UGCUAGCCGCCUUGGUUUCCUCUGAGGCCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAAACAGGCGCGGCAUUGGAUUUGCUAUCGGCAGAGGAGGCCU
.............(((((((((((((((..(((((.....)))))..)))))((((.((..((((((.(((.((.((....)).)).)))..)))))).))....)))))))))))))). ( -49.00)
>DroEre_CAF1 41721 120 - 1
UGCUAGCCGUCUUGGUUUCCUCUGAGGUCUCAGCUUCAGCAGCGGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAAACGGGAGCGGCGUUGGAUUUGCUAUCGGCAGAGGAGGCCU
.............(((((((((((.(((..(((.((((((.((.((.((((.(((...........))).)))).((....))...)).)))))))).)))..)))..))))))))))). ( -45.80)
>DroYak_CAF1 146876 120 - 1
UGCUAGCCGUCUUGGUUUCCUCUGAAGUCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAAACGGGAGCGGCGUUGGAUUUGCUAUCAGCAGAGGAGGCCU
.............(((((((((((..((..(((.((((((.(((((.((((.(((...........))).)))).((....))...))))))))))).)))..))...))))))))))). ( -44.90)
>consensus
UGCUAGCCGUCUUGGUUUCCUCUGAGGCCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAAACGGGAGCGGCAUUGGAUUUGCUAUCGGCAGAGGAGGCCU
.............(((((((((((((((....))))).((.(((((.((((.(((...........))).))))..(....)....)))))....(((.....))).)))))))))))). (-41.54 = -41.35 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,222,337 – 21,222,457
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -37.48
Consensus MFE -34.31
Energy contribution -34.38
Covariance contribution 0.06
Combinations/Pair 1.15
Mean z-score -1.79
Structure conservation index 0.92
SVM decision value 0.55
SVM RNA-class probability 0.778542
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21222337 120 + 23771897
UUCCAUGCCCAGUUUAGAUGAUGACAACGAGGCUGCAGCUGCUGAAGCUGAGGCCUCAGAGGAAACCAAGACGGCUAGCAAAGCAGGUCAAGAGAAAGCCAAGGCCAAGGCUGGAGAAAG
(((((.(((..((((.............((((((.(((((.....))))).)))))).(.(....)).))))((((.((...)).(((.........)))..))))..)))))))).... ( -40.70)
>DroSim_CAF1 89378 120 + 1
UUCCAUGCCCAGUUUAGAUGAUGACAACGAGGCUGCAGCUGCUGAAGCUGAGGCCUCAGAGGAAACCAAGGCGGCUAGCAAAGCAGGCCAAGAGAAAGCCAAGGCCAAGGUUGGAGAAAG
((((....((.(((........)))...((((((.(((((.....))))).))))))...)).((((..(((.(((.....))).(((.........)))...)))..)))))))).... ( -40.70)
>DroEre_CAF1 41761 120 + 1
UUCCAUGCCCAGUUUAGAUGAUGACAACGAGGCUGCCGCUGCUGAAGCUGAGACCUCAGAGGAAACCAAGACGGCUAGCAAAGCGGGCCAAGAGAAAGCCAAGGCCAAGACUGGAGAAAG
........(((((((............((..(((((((((.......((((....)))).(....)..)).)))).)))....))((((.............)))).)))))))...... ( -33.52)
>DroYak_CAF1 146916 120 + 1
UUCCAUGCCCAGUUUAGAUGAUGACAACGAGGCUGCAGCUGCUGAAGCUGAGACUUCAGAGGAAACCAAGACGGCUAGCAAAGCAGGCCAAGAGAAAGCCAAGGUCAAGGCUGGAGAAAG
(((((.(((((.......)).((((.....((((.(((((.....)))))....(((.(.(....)).....((((.((...)).))))....)))))))...)))).)))))))).... ( -35.00)
>consensus
UUCCAUGCCCAGUUUAGAUGAUGACAACGAGGCUGCAGCUGCUGAAGCUGAGACCUCAGAGGAAACCAAGACGGCUAGCAAAGCAGGCCAAGAGAAAGCCAAGGCCAAGGCUGGAGAAAG
(((((.(((..((((.............((((((.(((((.....))))).)))))).(.(....)).))))((((.((...)).(((.........)))..))))..)))))))).... (-34.31 = -34.38 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,222,337 – 21,222,457
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -35.22
Consensus MFE -31.91
Energy contribution -30.98
Covariance contribution -0.94
Combinations/Pair 1.18
Mean z-score -1.57
Structure conservation index 0.91
SVM decision value 0.08
SVM RNA-class probability 0.575092
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21222337 120 - 23771897
CUUUCUCCAGCCUUGGCCUUGGCUUUCUCUUGACCUGCUUUGCUAGCCGUCUUGGUUUCCUCUGAGGCCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAA
.....((((((((.(((....)).......((((..((...(..((((.....))))..)...(((((..(((((.....)))))..))))))).)))).........).)))).)))). ( -35.70)
>DroSim_CAF1 89378 120 - 1
CUUUCUCCAACCUUGGCCUUGGCUUUCUCUUGGCCUGCUUUGCUAGCCGCCUUGGUUUCCUCUGAGGCCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAA
.....((((.....((((..((.....))..))))(((.((((((((.((((..(......)..))))....)))..)))))..)))((((.(((...........))).)))).)))). ( -37.80)
>DroEre_CAF1 41761 120 - 1
CUUUCUCCAGUCUUGGCCUUGGCUUUCUCUUGGCCCGCUUUGCUAGCCGUCUUGGUUUCCUCUGAGGUCUCAGCUUCAGCAGCGGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAA
.....(((((((..((((..((.....))..)))).(((..(..((((.....))))..).(((((((....))))))).)))))).((((.(((...........))).)))).)))). ( -33.60)
>DroYak_CAF1 146916 120 - 1
CUUUCUCCAGCCUUGACCUUGGCUUUCUCUUGGCCUGCUUUGCUAGCCGUCUUGGUUUCCUCUGAAGUCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAA
.....((((((((.((...((((.....(..(((.(((...(((((((.....))))....(((((((....))))))).))).))))))..)..))))...))......)))).)))). ( -33.80)
>consensus
CUUUCUCCAGCCUUGGCCUUGGCUUUCUCUUGGCCUGCUUUGCUAGCCGUCUUGGUUUCCUCUGAGGCCUCAGCUUCAGCAGCUGCAGCCUCGUUGUCAUCAUCUAAACUGGGCAUGGAA
.....(((((((..(((...((((.......)))).(((.....))).)))..)))...(((((((((....))))))).)).....((((.(((...........))).)))).)))). (-31.91 = -30.98 +  -0.94)

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 13:04:53 2006