Locus 5167

Sequence ID 2R_DroMel_CAF1
Location 16,818,571 – 16,818,744
Length 173
Max. P 0.604778
window8259 window8260 window8261 window8262

overview

Window 9

Location 16,818,571 – 16,818,676
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 81.33
Mean single sequence MFE -34.12
Consensus MFE -22.61
Energy contribution -23.75
Covariance contribution 1.14
Combinations/Pair 1.21
Mean z-score -1.56
Structure conservation index 0.66
SVM decision value 0.14
SVM RNA-class probability 0.604778
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16818571 105 + 20766785
GGACUCAUUAACAGGGAGUUUGCAGAUGGUGUCCACCAUGUGGAAUUCCGGUGGCUCCUCUUUGUUGGCCUUCUGCUGGAUUUGUUCCAGCACCAACUCCGCUCG
(((....(((((((((((...((...(((..(((((...)))))...)))...))..))))))))))).....(((((((.....))))))).....)))..... ( -37.70)
>DroPse_CAF1 12937 105 + 1
GGACUCGCUCUUAGGCACUUUGUGUAUAGUGUCCACCAUAAGGAACUCCUCCUCCUGAUCCUCCAAUUUUUUCCGCUCGAACAGUUCGAGCACUUGCUUGGCCCG
((.(..((.....((((((........))))))...((..((((.....))))..)).................((((((.....))))))....))..)..)). ( -23.70)
>DroSec_CAF1 12669 105 + 1
GGACUCAUUAACAGGGAGCUUGCAGAUGGUGUCCACCAUGUGGAAUUCCCGUGGCUCAUCUUCGUUGGCCUUCUGCUGGAUCUGUUCCAGCACCAACUCCGCACG
(((........(((((((.((.((.(((((....))))).)).))))))).))..........(((((.....(((((((.....)))))))))))))))..... ( -37.40)
>DroSim_CAF1 12383 105 + 1
GGACUCAUUAACAGGGAGCUUGCAGAUGGUGUCCACCAUGUGGAAUUCCCGUGGCUCAUCUUUGUUGGCCUUCUGCUGGAUCUGUUCCAGCACCAACUCCGCACG
(((........(((((((.((.((.(((((....))))).)).))))))).))..........(((((.....(((((((.....)))))))))))))))..... ( -37.10)
>DroEre_CAF1 12633 105 + 1
CGACUCAUUAACAGGAAGCUUGCAGAUGGUGUCCACCAUGUGGAAUUCGGGCGGCUCCUCUUUGUUGGCCAUCUGCUGGAUCUGUUCCAGCACCAACUCCGCCCG
..............(((..((.((.(((((....))))).)).)))))((((((.........(((((.....(((((((.....)))))))))))).)))))). ( -37.70)
>DroYak_CAF1 12613 105 + 1
CGACUCAUUAACAGGAAGCUUGCAAAUGGCGUCCACCAUAUGGAAUUCGGACGGCUCUUCUUUGUUGGCCAUCUGCUGGAUCUGUUCCAGCACCAAUUCCGCCCG
.............(((.(((.......))).))).......((((((.((..((((..........))))...(((((((.....)))))))))))))))..... ( -31.10)
>consensus
GGACUCAUUAACAGGGAGCUUGCAGAUGGUGUCCACCAUGUGGAAUUCCGGCGGCUCAUCUUUGUUGGCCUUCUGCUGGAUCUGUUCCAGCACCAACUCCGCCCG
(((((((((..((((...))))..))))).)))).....(((((........((((..........))))....((((((.....))))))......)))))... (-22.61 = -23.75 +   1.14)

alignment

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secondary structure

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Window 0

Location 16,818,611 – 16,818,714
Length 103
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.42
Mean single sequence MFE -34.97
Consensus MFE -23.06
Energy contribution -23.32
Covariance contribution 0.26
Combinations/Pair 1.28
Mean z-score -1.51
Structure conservation index 0.66
SVM decision value 0.06
SVM RNA-class probability 0.565589
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16818611 103 + 20766785
UGGAAUUCCGGUGGCUCCUCUUUGUUGGCCUUCUGCUGGAUUUGUUCCAGCACCAACUCCGCUCGUGCUACGGCCAGACUACGCUUGUCUGCCUUGGACAGAU
......(((((((((........(((((.....(((((((.....)))))))))))).........)))))(((.((((.......))))))).))))..... ( -35.63)
>DroSec_CAF1 12709 103 + 1
UGGAAUUCCCGUGGCUCAUCUUCGUUGGCCUUCUGCUGGAUCUGUUCCAGCACCAACUCCGCACGUGCGACGGCCAGACUACGCUUGUCUGCCUUGGACAGAU
........(((.(((...........((((...(((((((.....))))))).......(((....)))..))))((((.......))))))).)))...... ( -34.60)
>DroSim_CAF1 12423 103 + 1
UGGAAUUCCCGUGGCUCAUCUUUGUUGGCCUUCUGCUGGAUCUGUUCCAGCACCAACUCCGCACGUGCGACGGCCAGACUACGCUUGUCUGCCUUGGACAGAU
........(((.(((...........((((...(((((((.....))))))).......(((....)))..))))((((.......))))))).)))...... ( -34.60)
>DroEre_CAF1 12673 103 + 1
UGGAAUUCGGGCGGCUCCUCUUUGUUGGCCAUCUGCUGGAUCUGUUCCAGCACCAACUCCGCCCGUGCGACGGCCAGACCACGCUUGUCCGCUUUGGACAGAU
.......(((((((.........(((((.....(((((((.....)))))))))))).))))))).(((..((.....)).)))((((((.....)))))).. ( -39.00)
>DroYak_CAF1 12653 103 + 1
UGGAAUUCGGACGGCUCUUCUUUGUUGGCCAUCUGCUGGAUCUGUUCCAGCACCAAUUCCGCCCGUGCGACAGCCAGACCACGCUUGUCUGCCUUGGACAGAU
.((((((.((..((((..........))))...(((((((.....)))))))))))))))(.(((.((((((((........)).)))).))..))).).... ( -34.10)
>DroAna_CAF1 14413 103 + 1
UGAACCUCCACUUGCUCCUGGUCGUCCUUCUUCUUUUGGAACAUCAGCAAUGCCAGUUCGGCCCGAGCUGUGGCUCUAUUUCGCUUGUCGGCCAGGGACAGAU
...........(((..(((((((((((..........)))(((..(((...(((.....)))..((((....))))......))))))))))))))..))).. ( -31.90)
>consensus
UGGAAUUCCGGUGGCUCCUCUUUGUUGGCCUUCUGCUGGAUCUGUUCCAGCACCAACUCCGCCCGUGCGACGGCCAGACUACGCUUGUCUGCCUUGGACAGAU
............((((.......(((((.....(((((((.....))))))))))))..(((....)))..)))).........((((((.....)))))).. (-23.06 = -23.32 +   0.26)

alignment

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secondary structure

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Window 1

Location 16,818,611 – 16,818,714
Length 103
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 81.42
Mean single sequence MFE -36.52
Consensus MFE -23.36
Energy contribution -24.92
Covariance contribution 1.56
Combinations/Pair 1.20
Mean z-score -1.67
Structure conservation index 0.64
SVM decision value 0.13
SVM RNA-class probability 0.596220
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16818611 103 - 20766785
AUCUGUCCAAGGCAGACAAGCGUAGUCUGGCCGUAGCACGAGCGGAGUUGGUGCUGGAACAAAUCCAGCAGAAGGCCAACAAAGAGGAGCCACCGGAAUUCCA
.(((.(((..(((((((.......)))).)))...((....)))))((((((((((((.....)))))).....))))))..)))(((.((...))...))). ( -34.30)
>DroSec_CAF1 12709 103 - 1
AUCUGUCCAAGGCAGACAAGCGUAGUCUGGCCGUCGCACGUGCGGAGUUGGUGCUGGAACAGAUCCAGCAGAAGGCCAACGAAGAUGAGCCACGGGAAUUCCA
.(((((.....)))))...........((((((((((....))...((((((((((((.....)))))).....))))))...)))).))))..((....)). ( -35.90)
>DroSim_CAF1 12423 103 - 1
AUCUGUCCAAGGCAGACAAGCGUAGUCUGGCCGUCGCACGUGCGGAGUUGGUGCUGGAACAGAUCCAGCAGAAGGCCAACAAAGAUGAGCCACGGGAAUUCCA
.(((((.....)))))...........((((((((((....))...((((((((((((.....)))))).....))))))...)))).))))..((....)). ( -35.90)
>DroEre_CAF1 12673 103 - 1
AUCUGUCCAAAGCGGACAAGCGUGGUCUGGCCGUCGCACGGGCGGAGUUGGUGCUGGAACAGAUCCAGCAGAUGGCCAACAAAGAGGAGCCGCCCGAAUUCCA
...(((((.....))))).((((((.....))).))).(((((((.((((((((((((.....)))))).....)))))).........)))))))....... ( -43.80)
>DroYak_CAF1 12653 103 - 1
AUCUGUCCAAGGCAGACAAGCGUGGUCUGGCUGUCGCACGGGCGGAAUUGGUGCUGGAACAGAUCCAGCAGAUGGCCAACAAAGAAGAGCCGUCCGAAUUCCA
....((((...((.((((.((........))))))))..))))((((((.((((((((.....)))))))(((((((.........).))))))).)))))). ( -40.20)
>DroAna_CAF1 14413 103 - 1
AUCUGUCCCUGGCCGACAAGCGAAAUAGAGCCACAGCUCGGGCCGAACUGGCAUUGCUGAUGUUCCAAAAGAAGAAGGACGACCAGGAGCAAGUGGAGGUUCA
...((..(((((.((...(((((....((((....))))..(((.....))).))))).....(((..........))))).)))))..))............ ( -29.00)
>consensus
AUCUGUCCAAGGCAGACAAGCGUAGUCUGGCCGUCGCACGGGCGGAGUUGGUGCUGGAACAGAUCCAGCAGAAGGCCAACAAAGAGGAGCCACCGGAAUUCCA
.....(((..(((((((.......))))((((.((((....))))......(((((((.....)))))))...))))...........)))...)))...... (-23.36 = -24.92 +   1.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,818,645 – 16,818,744
Length 99
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 78.67
Mean single sequence MFE -35.47
Consensus MFE -23.78
Energy contribution -24.62
Covariance contribution 0.84
Combinations/Pair 1.34
Mean z-score -1.23
Structure conservation index 0.67
SVM decision value 0.10
SVM RNA-class probability 0.582210
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16818645 99 + 20766785
GCUGGAUUUGUUCCAGCACCAACUCCGCUCGUGCUACGGCCAGACUACGCUUGUCUGCCUUGGACAGAUUC-ACAGUGUUGAACUCAACCUGG---GGCGGCC
((((((.....)))))).......((((((((.(((.(((.((((.......))))))).)))))......-.(((.((((....))))))))---))))).. ( -40.60)
>DroSec_CAF1 12743 99 + 1
GCUGGAUCUGUUCCAGCACCAACUCCGCACGUGCGACGGCCAGACUACGCUUGUCUGCCUUGGACAGAUUC-GCAGUGUUGGGUUCAACCUGG---GGCGGCU
((((((.....)))))).......((((..((.(((.(((.((((.......)))))))))).)).....(-.(((.((((....))))))).---))))).. ( -38.80)
>DroSim_CAF1 12457 99 + 1
GCUGGAUCUGUUCCAGCACCAACUCCGCACGUGCGACGGCCAGACUACGCUUGUCUGCCUUGGACAGAUUC-GCAGUGUUGGGUUCAACCUGG---GGCGGCU
((((((.....)))))).......((((..((.(((.(((.((((.......)))))))))).)).....(-.(((.((((....))))))).---))))).. ( -38.80)
>DroEre_CAF1 12707 99 + 1
GCUGGAUCUGUUCCAGCACCAACUCCGCCCGUGCGACGGCCAGACCACGCUUGUCCGCUUUGGACAGAUUC-ACAGUGUUAGGUUCAACCUGC---GGUGGCU
((((((.....)))))).(((...(((((((.....)))...((((((((((((((.....))))).....-..)))))..))))......))---))))).. ( -32.61)
>DroYak_CAF1 12687 99 + 1
GCUGGAUCUGUUCCAGCACCAAUUCCGCCCGUGCGACAGCCAGACCACGCUUGUCUGCCUUGGACAGAUUU-CCAGUGUUAGGUUCAACCUGC---GGUGUCU
((((((.....)))))).........((....))((((.((((((((((((.((((((....).)))))..-..)))))..))).....))).---).)))). ( -30.80)
>DroPer_CAF1 13012 98 + 1
GCUCGAACAGUUCGAGCACUUGCUUGGCCCGACUCUCGGCUAAGUUGCCCUUUUCUCGUUUUGUCAGCUUUUGUGGUGAUGGCU-----CUGGAUUGGCCGCC
((((((.....))))))....((((((((........)))))))).(((....(((.(..(..(((.(......).)))..)..-----).)))..))).... ( -31.20)
>consensus
GCUGGAUCUGUUCCAGCACCAACUCCGCCCGUGCGACGGCCAGACUACGCUUGUCUGCCUUGGACAGAUUC_GCAGUGUUGGGUUCAACCUGG___GGCGGCU
((((((.....)))))).......(((((.((.(((.(((.((((.......)))))))))).))........(((.(((......))))))....))))).. (-23.78 = -24.62 +   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 11:38:13 2006