Locus 2840

Sequence ID 2L_DroMel_CAF1
Location 8,139,331 – 8,139,506
Length 175
Max. P 0.983602
window4512 window4513 window4514 window4515

overview

Window 2

Location 8,139,331 – 8,139,448
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.53
Mean single sequence MFE -33.54
Consensus MFE -20.79
Energy contribution -21.87
Covariance contribution 1.08
Combinations/Pair 1.13
Mean z-score -2.66
Structure conservation index 0.62
SVM decision value 1.72
SVM RNA-class probability 0.973988
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8139331 117 - 22407834
--C-AAUCCUCCUCCAACAUCGACACUUGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGCGCCAUUUGGAACACAAGCGUCACCAGCAACACAAUCUGCAGGAUUCUUUAA
--.-(((((((((((((.........))))))))..(((((((...))))))).((((..(((((((((((...(((.....))))))....)))))))).....)))))))))...... ( -34.10)
>DroSec_CAF1 4737 117 - 1
--C-AAUCCUCCUCCAACAUCGGCACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGGCCAUUUGCAACACAAGCGACACCAGCAACACAAUCUGCAGGAUUCUUUAA
--.-(((((((((((......))....)))))))))(((((((...)))))))(((((..(((((((((.....((((.......))))..))))))))).....))))).......... ( -36.40)
>DroSim_CAF1 5730 117 - 1
--C-AAUCCUCCUCCAACAUCGGCACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGGCCAUUUGCAACACAAGCGACACCAGCAACACAAUCUGCAGGAUUCUUUAA
--.-(((((((((((......))....)))))))))(((((((...)))))))(((((..(((((((((.....((((.......))))..))))))))).....))))).......... ( -36.40)
>DroEre_CAF1 4925 117 - 1
--C-AAUCCUCCCCCAACAUCGGUACUAGGAGGAUUCUUUACCACAGGUGAAGUUCCACCUGCUGUUGGACCAUUUGCAACACAAGAGACAGCAGCAACGCAAUCUGUAGGAUUCUUAAA
--.-((((((((.((......)).....)))))))).....((((((((...(((....((((((((......((((.....)))).)))))))).)))...)))))).))......... ( -31.30)
>DroYak_CAF1 4705 105 - 1
--C-AAUCCUCCCCCCACAUCGACACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGA------------CAAGCGACUCCAGCAACACAACCUGUAGGAUUCUUAAA
--.-((((((((................)))))))).....((((((((...(((((....((((((...------------..))))))....)))))...)))))).))......... ( -33.69)
>DroAna_CAF1 4789 106 - 1
UCCAAGCCUUCCCCCAGCAGCAGUGCCCGGAAAUUUCUUCACCCCCGG---AGUUGUCCCAGCUGUUGCUCCAACUGCAACACCAGCGCCAGCAGCA---------GGAGGAUUUUUG--
..((((...(((.(((((((((((....(((.....((((......))---))...)))..)))))))))....((((.............))))..---------)).)))..))))-- ( -29.32)
>consensus
__C_AAUCCUCCCCCAACAUCGGCACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGGCCAUUUGCAACACAAGCGACACCAGCAACACAAUCUGCAGGAUUCUUUAA
....((((((((................)))))))).....((..(((((......)))))((((((((......................))))))))..........))......... (-20.79 = -21.87 +   1.08)

alignment

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secondary structure

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Window 3

Location 8,139,371 – 8,139,479
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -37.22
Consensus MFE -23.98
Energy contribution -24.18
Covariance contribution 0.20
Combinations/Pair 1.31
Mean z-score -2.50
Structure conservation index 0.64
SVM decision value 1.55
SVM RNA-class probability 0.963228
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8139371 108 + 22407834
UUCCAAAUGGCGCAACAACAGGUGCAACUUCACCUGUGGUAAAGAAUCCUCCAAGUGUCGAUGUUGGAGGAGGAUU-G--------CCU---GGUGGAACUGUUAAAGGUAUUGUUGGAA
.(((((...((((........))))...((((((...(((((....((((((((.........))))))))...))-)--------)).---))))))................))))). ( -34.40)
>DroSec_CAF1 4777 108 + 1
UUGCAAAUGGCCCAACAACAGGUGCAACUUCACCUGUGGUAAAGAAUCCUCCUAGUGCCGAUGUUGGAGGAGGAUU-G--------CCU---GGUGGUACUGUUAAAGGUAUUGUUGGAA
..((.....(((.....(((((((......))))))))))....(((((((((...((....))...)))))))))-)--------)(.---.(..(((((......)))))..)..).. ( -36.40)
>DroSim_CAF1 5770 108 + 1
UUGCAAAUGGCCCAACAACAGGUGCAACUUCACCUGUGGUAAAGAAUCCUCCUAGUGCCGAUGUUGGAGGAGGAUU-G--------CCU---GGUGGUACUGUUAAAGGUAUUGUUGGAA
..((.....(((.....(((((((......))))))))))....(((((((((...((....))...)))))))))-)--------)(.---.(..(((((......)))))..)..).. ( -36.40)
>DroEre_CAF1 4965 108 + 1
UUGCAAAUGGUCCAACAGCAGGUGGAACUUCACCUGUGGUAAAGAAUCCUCCUAGUACCGAUGUUGGGGGAGGAUU-G--------CCU---GGUGGAACUGUUAAAGGUAUUGUUGGAA
..........(((((((((((((((....)))))))).......(((((((((...((....))...)))))))))-(--------(((---..............))))..))))))). ( -36.84)
>DroYak_CAF1 4743 98 + 1
----------UCCAACAACAGGUGCAACUUCACCUGUGGUAAAGAAUCCUCCUAGUGUCGAUGUGGGGGGAGGAUU-G--------CCU---GGUGGAACUGUUAAAGGUAUUGUUGGAA
----------(((((((((....(((..((((((...(((((....((((((((.........))))))))...))-)--------)).---))))))..))).....))..))))))). ( -35.30)
>DroAna_CAF1 4818 117 + 1
UUGCAGUUGGAGCAACAGCUGGGACAACU---CCGGGGGUGAAGAAAUUUCCGGGCACUGCUGCUGGGGGAAGGCUUGGAGGAGGUCCUGCAGAGGGAGCGGCCAAAGGUGGAGUAGCAA
((.((((((......)))))).))..(((---((((..((......))..))((.(.((.((.(((.((((...((....))...)))).))).)).)).).))......)))))..... ( -44.00)
>consensus
UUGCAAAUGGCCCAACAACAGGUGCAACUUCACCUGUGGUAAAGAAUCCUCCUAGUGCCGAUGUUGGAGGAGGAUU_G________CCU___GGUGGAACUGUUAAAGGUAUUGUUGGAA
...........(((((((((((((......)))))))(((....(((((((((....((......)))))))))))..........((.......)).)))...........)))))).. (-23.98 = -24.18 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,139,371 – 8,139,479
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.81
Mean single sequence MFE -30.68
Consensus MFE -20.78
Energy contribution -21.47
Covariance contribution 0.70
Combinations/Pair 1.19
Mean z-score -3.22
Structure conservation index 0.68
SVM decision value 1.95
SVM RNA-class probability 0.983602
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8139371 108 - 22407834
UUCCAACAAUACCUUUAACAGUUCCACC---AGG--------C-AAUCCUCCUCCAACAUCGACACUUGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGCGCCAUUUGGAA
.....................(((((..---.((--------(-.....((((((((.........))))))))......((.(((((((......))))))).))...)))...))))) ( -31.10)
>DroSec_CAF1 4777 108 - 1
UUCCAACAAUACCUUUAACAGUACCACC---AGG--------C-AAUCCUCCUCCAACAUCGGCACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGGCCAUUUGCAA
.(((((((....................---(((--------.-(((((((((((......))....))))))))))))....(((((((......)))))))))))))).......... ( -32.10)
>DroSim_CAF1 5770 108 - 1
UUCCAACAAUACCUUUAACAGUACCACC---AGG--------C-AAUCCUCCUCCAACAUCGGCACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGGCCAUUUGCAA
.(((((((....................---(((--------.-(((((((((((......))....))))))))))))....(((((((......)))))))))))))).......... ( -32.10)
>DroEre_CAF1 4965 108 - 1
UUCCAACAAUACCUUUAACAGUUCCACC---AGG--------C-AAUCCUCCCCCAACAUCGGUACUAGGAGGAUUCUUUACCACAGGUGAAGUUCCACCUGCUGUUGGACCAUUUGCAA
.(((((((....................---(((--------.-((((((((.((......)).....))))))))))).....((((((......)))))).))))))).......... ( -29.90)
>DroYak_CAF1 4743 98 - 1
UUCCAACAAUACCUUUAACAGUUCCACC---AGG--------C-AAUCCUCCCCCCACAUCGACACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGA----------
.(((((((....................---(((--------.-((((((((................)))))))))))....(((((((......))))))))))))))---------- ( -29.09)
>DroAna_CAF1 4818 117 - 1
UUGCUACUCCACCUUUGGCCGCUCCCUCUGCAGGACCUCCUCCAAGCCUUCCCCCAGCAGCAGUGCCCGGAAAUUUCUUCACCCCCGG---AGUUGUCCCAGCUGUUGCUCCAACUGCAA
.(((............(((.((.......)).(((.....)))..))).......(((((((((....(((.....((((......))---))...)))..)))))))))......))). ( -29.80)
>consensus
UUCCAACAAUACCUUUAACAGUUCCACC___AGG________C_AAUCCUCCCCCAACAUCGGCACUAGGAGGAUUCUUUACCACAGGUGAAGUUGCACCUGUUGUUGGGCCAUUUGCAA
.(((((((....................................((((((((................))))))))........((((((......)))))).))))))).......... (-20.78 = -21.47 +   0.70)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,139,411 – 8,139,506
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.90
Mean single sequence MFE -19.96
Consensus MFE -12.70
Energy contribution -11.93
Covariance contribution -0.77
Combinations/Pair 1.43
Mean z-score -1.73
Structure conservation index 0.64
SVM decision value 0.62
SVM RNA-class probability 0.802597
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8139411 95 - 22407834
-CAG--------UUCCAUUUG---UUGACA-CACAAGCUGUUCCAACAAUACCUUUAACAGUUCCACC---AGG--------C-AAUCCUCCUCCAACAUCGACACUUGGAGGAUUCUUU
-...--------......(((---(((..(-((.....)))..))))))...................---(((--------.-((((((((................))))))))))). ( -17.29)
>DroSec_CAF1 4817 95 - 1
-CAG--------UUCCAUUUG---UUGACA-CACAAGCUGUUCCAACAAUACCUUUAACAGUACCACC---AGG--------C-AAUCCUCCUCCAACAUCGGCACUAGGAGGAUUCUUU
-...--------......(((---(((..(-((.....)))..))))))...................---(((--------.-(((((((((((......))....)))))))))))). ( -19.70)
>DroSim_CAF1 5810 95 - 1
-CAG--------UUCCAUUUG---UUGACA-CACAAGCUGUUCCAACAAUACCUUUAACAGUACCACC---AGG--------C-AAUCCUCCUCCAACAUCGGCACUAGGAGGAUUCUUU
-...--------......(((---(((..(-((.....)))..))))))...................---(((--------.-(((((((((((......))....)))))))))))). ( -19.70)
>DroEre_CAF1 5005 95 - 1
-CAG--------UUCCAUUUG---UUGACA-CACAAGCUGUUCCAACAAUACCUUUAACAGUUCCACC---AGG--------C-AAUCCUCCCCCAACAUCGGUACUAGGAGGAUUCUUU
-...--------......(((---(((..(-((.....)))..))))))...................---(((--------.-((((((((.((......)).....))))))))))). ( -17.70)
>DroYak_CAF1 4773 95 - 1
-CAG--------UUCCAUUUG---UUGACA-CACAAGCUGUUCCAACAAUACCUUUAACAGUUCCACC---AGG--------C-AAUCCUCCCCCCACAUCGACACUAGGAGGAUUCUUU
-...--------......(((---(((..(-((.....)))..))))))...................---(((--------.-((((((((................))))))))))). ( -16.29)
>DroAna_CAF1 4855 120 - 1
GCAGCAGGCUUCUUCAAUCCGGGAUUAACUCCGCCAGCGGUUGCUACUCCACCUUUGGCCGCUCCCUCUGCAGGACCUCCUCCAAGCCUUCCCCCAGCAGCAGUGCCCGGAAAUUUCUUC
((.....))........((((((.........(((((.(((.(.....).))).)))))......(.((((.(((.....)))..((.........)).)))).)))))))......... ( -29.10)
>consensus
_CAG________UUCCAUUUG___UUGACA_CACAAGCUGUUCCAACAAUACCUUUAACAGUUCCACC___AGG________C_AAUCCUCCCCCAACAUCGGCACUAGGAGGAUUCUUU
....................................((((((..............))))))......................((((((((................)))))))).... (-12.70 = -11.93 +  -0.77)

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 10:37:35 2006