Locus 2723

Sequence ID 3R_DroMel_CAF1
Location 7,320,223 – 7,320,411
Length 188
Max. P 0.920659
window4423 window4424 window4425 window4426 window4427

overview

Window 3

Location 7,320,223 – 7,320,338
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.18
Mean single sequence MFE -38.18
Consensus MFE -33.97
Energy contribution -34.85
Covariance contribution 0.88
Combinations/Pair 1.05
Mean z-score -2.18
Structure conservation index 0.89
SVM decision value 1.14
SVM RNA-class probability 0.920659
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7320223 115 + 27905053
GGUUAGUAUCAACAAUUGGAUAUCUGUGUUUGUCGGCACAGGGUUAAAUUGCCCAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCAUUUGCCGUAGUUGCAGUUGCAACU-----
(((..(((((.((.((((....(((((((......)))))))......((((((.(((.........))))))))).)))).)).)))))....)))..((((((....))))))----- ( -37.40)
>DroSim_CAF1 370 115 + 1
GGUUAGUAUCAACAAUUGGAUAUCUCUGUUUGUCGGCACUGGGUUAAAUUGCCUAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCAUUUGCCGUAGUUGCAGUUGCAACU-----
(((..(((((.((.((((....((((.((..(((..((.(((((......))))).))...))).)).)))).....)))).)).)))))....)))..((((((....))))))----- ( -34.50)
>DroEre_CAF1 386 115 + 1
GGUUAGUAUCAACAAUUGGAUAUCUGUGUUUGUCGGCACUGGGUUAAAUUGCCCAUUGAAAGGCCGCCGGGGGCAAACAAUCGUAGAUGCUUUUGCCGUAGUUGCAGUUGCAACU-----
(((.((((((.((.((((......(((.((((.((((..(((((......))))).......)))).)))).)))..)))).)).))))))...)))..((((((....))))))----- ( -38.90)
>DroYak_CAF1 386 120 + 1
GGUUAGUAUCAACAAUUGGAUAUCUGUGUUUGUCGGCACUGGCUUAAAUUGCCCAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCUUUUGCCGUAGUUGCAGUUGCAACUACCAA
(((.((((((.((.((((......(((.((((.((((.(((((.......))).......)))))).)))).)))..)))).)).))))))...)))((((((((....))))))))... ( -41.91)
>consensus
GGUUAGUAUCAACAAUUGGAUAUCUGUGUUUGUCGGCACUGGGUUAAAUUGCCCAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCAUUUGCCGUAGUUGCAGUUGCAACU_____
(((.((((((.((.((((......(((.((((.((((..(((((......))))).......)))).)))).)))..)))).)).))))))...)))..((((((....))))))..... (-33.97 = -34.85 +   0.88)

alignment

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secondary structure

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Window 4

Location 7,320,223 – 7,320,338
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.18
Mean single sequence MFE -31.13
Consensus MFE -27.41
Energy contribution -27.98
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.88
SVM decision value 0.72
SVM RNA-class probability 0.833728
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7320223 115 - 27905053
-----AGUUGCAACUGCAACUACGGCAAAUGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUGGGCAAUUUAACCCUGUGCCGACAAACACAGAUAUCCAAUUGUUGAUACUAACC
-----((((((....))))))..((((((((.(((...))))))))))).((((((((((......)))).........(((((........))))).........))))))........ ( -30.80)
>DroSim_CAF1 370 115 - 1
-----AGUUGCAACUGCAACUACGGCAAAUGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUAGGCAAUUUAACCCAGUGCCGACAAACAGAGAUAUCCAAUUGUUGAUACUAACC
-----((((((....)))))).((((((.((.((((....(((((((...(((((.((((......)))).(((......)))))))))))))))))))...)).))))))......... ( -30.90)
>DroEre_CAF1 386 115 - 1
-----AGUUGCAACUGCAACUACGGCAAAAGCAUCUACGAUUGUUUGCCCCCGGCGGCCUUUCAAUGGGCAAUUUAACCCAGUGCCGACAAACACAGAUAUCCAAUUGUUGAUACUAACC
-----((((((....)))))).(((((...........((..(..((((...))))..)..))..((((........)))).)))))........((.((((........)))))).... ( -27.80)
>DroYak_CAF1 386 120 - 1
UUGGUAGUUGCAACUGCAACUACGGCAAAAGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUGGGCAAUUUAAGCCAGUGCCGACAAACACAGAUAUCCAAUUGUUGAUACUAACC
...((((((((....))))))))(((((..(((........))))))))...(((.((((......)))).......)))((((.((((((..............)))))).)))).... ( -35.04)
>consensus
_____AGUUGCAACUGCAACUACGGCAAAAGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUGGGCAAUUUAACCCAGUGCCGACAAACACAGAUAUCCAAUUGUUGAUACUAACC
.....((((((....)))))).((((((.((.((((.....((((((...((((((((((......))))............)))))))))))).))))...)).))))))......... (-27.41 = -27.98 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,320,263 – 7,320,376
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.85
Mean single sequence MFE -40.00
Consensus MFE -32.47
Energy contribution -32.35
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.89
Structure conservation index 0.81
SVM decision value 0.31
SVM RNA-class probability 0.684689
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7320263 113 + 27905053
GGGUUAAAUUGCCCAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCAUUUGCCGUAGUUGCAGUUGCAACU-------ACUAAGGCCAUCGAGUGCUGCAGUGUCAGCUCACCGAU
((((......)))).......((((......((((((..(((...)))...))))))((((((((....))))))-------))...))))((((.(((..((.......)).))))))) ( -41.80)
>DroSim_CAF1 410 113 + 1
GGGUUAAAUUGCCUAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCAUUUGCCGUAGUUGCAGUUGCAACU-------ACCAAGGCCAUCGAGUGCUGCAGUGUCAGCUCACCGCU
(((((..(((((...((((..((((......((((((..(((...)))...))))))((((((((....))))))-------))...)))).)))).....)))))...)))))...... ( -38.60)
>DroEre_CAF1 426 113 + 1
GGGUUAAAUUGCCCAUUGAAAGGCCGCCGGGGGCAAACAAUCGUAGAUGCUUUUGCCGUAGUUGCAGUUGCAACU-------ACCAAGGCCAUCGAGUGCUGCAGUGUCAGCUCACCGAU
((((......)))).......((((......((((((..(((...)))...))))))((((((((....))))))-------))...))))((((.(((..((.......)).))))))) ( -41.40)
>DroYak_CAF1 426 120 + 1
GGCUUAAAUUGCCCAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCUUUUGCCGUAGUUGCAGUUGCAACUACCAACUACCAAGGCCAACGAGUGCUGCAGUGUCAGCUCACCGAU
((((...(((((.((((....((((....((((((((..(((...)))...))))))((((((((....))))))))...)).....))))....))))..)))))...))))....... ( -38.20)
>consensus
GGGUUAAAUUGCCCAUUGAAAGGCCGCCGAGGGCAAACAAUCGUAGAUGCAUUUGCCGUAGUUGCAGUUGCAACU_______ACCAAGGCCAUCGAGUGCUGCAGUGUCAGCUCACCGAU
((((......)))).......((((....(.((((((..(((...)))...)))))).)((((((....))))))............)))).....(.((((......)))).)...... (-32.47 = -32.35 +  -0.12)

alignment

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secondary structure

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Window 6

Location 7,320,263 – 7,320,376
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.85
Mean single sequence MFE -40.38
Consensus MFE -32.39
Energy contribution -32.70
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.80
SVM decision value 0.58
SVM RNA-class probability 0.788465
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7320263 113 - 27905053
AUCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUAGU-------AGUUGCAACUGCAACUACGGCAAAUGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUGGGCAAUUUAACCC
(((((.(.((((......)))).)))))).(((...((-------((((((....))))))))((((((((.(((...)))))))))))...))).((((......)))).......... ( -40.60)
>DroSim_CAF1 410 113 - 1
AGCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUGGU-------AGUUGCAACUGCAACUACGGCAAAUGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUAGGCAAUUUAACCC
.((((((......))))))...........(((...((-------((((((....))))))))((((((((.(((...)))))))))))...))).((((......)))).......... ( -40.20)
>DroEre_CAF1 426 113 - 1
AUCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUGGU-------AGUUGCAACUGCAACUACGGCAAAAGCAUCUACGAUUGUUUGCCCCCGGCGGCCUUUCAAUGGGCAAUUUAACCC
(((((.(.((((......)))).)))))).(((...((-------((((((....))))))))(((((..(((........))))))))...))).((((......)))).......... ( -39.40)
>DroYak_CAF1 426 120 - 1
AUCGGUGAGCUGACACUGCAGCACUCGUUGGCCUUGGUAGUUGGUAGUUGCAACUGCAACUACGGCAAAAGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUGGGCAAUUUAAGCC
...(((..((((......)))).((((((((....(((.((((((((((((....))))))))(((((..(((........))))))))..)))).)))..))))))))........))) ( -41.30)
>consensus
AUCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUGGU_______AGUUGCAACUGCAACUACGGCAAAAGCAUCUACGAUUGUUUGCCCUCGGCGGCCUUUCAAUGGGCAAUUUAACCC
(((((.(.((((......)))).)))))).(((............((((((....))))))..(((((..(((........))))))))...))).((((......)))).......... (-32.39 = -32.70 +   0.31)

alignment

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secondary structure

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Window 7

Location 7,320,303 – 7,320,411
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.16
Mean single sequence MFE -35.00
Consensus MFE -23.07
Energy contribution -23.57
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -2.10
Structure conservation index 0.66
SVM decision value 0.22
SVM RNA-class probability 0.637709
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7320303 108 - 27905053
UAUUAGCACACAC-----UUUUCCCUUGUUGCCUAGUGUAAUCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUAGU-------AGUUGCAACUGCAACUACGGCAAAUGCAUCUACGA
.....(((.....-----........((((((..((((...((((....)))))))))))))).......(((...((-------((((((....)))))))))))...)))........ ( -31.50)
>DroSim_CAF1 450 108 - 1
UAUUAGCACACAC-----UUUUCCUUUGUUGGCUAGUGUAAGCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUGGU-------AGUUGCAACUGCAACUACGGCAAAUGCAUCUACGA
.....((..((((-----(...((......))..)))))..((((((......)))))).))....(((((((...((-------((((((....))))))))))).....))))..... ( -35.10)
>DroEre_CAF1 466 113 - 1
UAUUAGUACACAUACUCGUAUUCCUGUGUUGCCUAGUGUAAUCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUGGU-------AGUUGCAACUGCAACUACGGCAAAAGCAUCUACGA
...............(((((.....(((((((..((((...((((....)))))))))))))))..(((((((...((-------((((((....))))))))))).....))))))))) ( -36.50)
>DroYak_CAF1 466 114 - 1
UAUUAGUGCACAU-----UAU-ACCGUGUUGCCUAGUGUAAUCGGUGAGCUGACACUGCAGCACUCGUUGGCCUUGGUAGUUGGUAGUUGCAACUGCAACUACGGCAAAAGCAUCUACGA
...((((((.((.-----..(-((((....(((.(((((...(((((......)))))..)))))....)))..)))))..))((((((((....)))))))).......))).)))... ( -36.90)
>consensus
UAUUAGCACACAC_____UAUUCCCGUGUUGCCUAGUGUAAUCGGUGAGCUGACACUGCAGCACUCGAUGGCCUUGGU_______AGUUGCAACUGCAACUACGGCAAAAGCAUCUACGA
.....((..................(((((((..(((((...(((....)))))))))))))))......(((............((((((....))))))..)))....))........ (-23.07 = -23.57 +   0.50)

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 10:43:17 2006