Locus 2357

Sequence ID 2R_DroMel_CAF1
Location 8,565,825 – 8,566,028
Length 203
Max. P 0.982646
window3891 window3892 window3893 window3894

overview

Window 1

Location 8,565,825 – 8,565,923
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 94.52
Mean single sequence MFE -22.33
Consensus MFE -22.34
Energy contribution -22.57
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -1.54
Structure conservation index 1.00
SVM decision value 0.51
SVM RNA-class probability 0.762319
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8565825 98 - 20766785
UUAUCUAACAUCCUGUUUUUAAGGAAUCCAAAAUGGUCUUAAAGUGGGCUUAGAGUAACGAAAGUGUUUCGACUGUCAGAAUGACGAAAGCAUAAAAG
...(((.((.((((.......)))).........((((...(((....))).(((..((....))..))))))))).)))(((.(....))))..... ( -17.90)
>DroSec_CAF1 41500 96 - 1
CUAUCUAACAUCCUGUUUUUAAGGAAUCCA-AAUGGUCUUA-AGUGGGCUCAGAGAUACGAAAGUGUUUCGACUGUCAGAAUGACGAAAGCAUAAAAG
...(((.(((((((.......)))).....-..((((((..-...)))).))(((((((....)))))))...))).)))(((.(....))))..... ( -23.60)
>DroSim_CAF1 44773 96 - 1
CUAUCUAGCAUCCUGUUUUUAAGGAAUCCA-AAUGGUCUUA-AGUGGACUUAGAGAUACGAAAGUGUUUCGACUGUCAGAAUGACGAAAGCAUAAAAG
...(((..(.((((.......)))).....-...((((.((-((....))))(((((((....))))))))))))..)))(((.(....))))..... ( -25.50)
>consensus
CUAUCUAACAUCCUGUUUUUAAGGAAUCCA_AAUGGUCUUA_AGUGGGCUUAGAGAUACGAAAGUGUUUCGACUGUCAGAAUGACGAAAGCAUAAAAG
...(((.(((((((.......)))).........(((((......)))))..(((((((....)))))))...))).)))(((.(....))))..... (-22.34 = -22.57 +   0.23)

alignment

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secondary structure

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Window 2

Location 8,565,901 – 8,565,995
Length 94
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 74.34
Mean single sequence MFE -24.34
Consensus MFE -16.22
Energy contribution -16.26
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -1.30
Structure conservation index 0.67
SVM decision value 0.01
SVM RNA-class probability 0.536644
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8565901 94 - 20766785
GCCAAUUGUCGAAUCUGACGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUAGUGUACAAUCGCCUUUA--------------------UUAUCUAACAUCCUGUUUUUAA
.......((((....))))(((((((((.((.....(((((((((........)))))))))...)).))))--------------------)))))................. ( -22.10)
>DroSec_CAF1 41574 94 - 1
GCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUGGUGUACAAAGCUCUUCA--------------------CUAUCUAACAUCCUGUUUUUAA
((((..(.....)..))))(((((((((.((.....((((((((..........))))))))..)).))).)--------------------)))))................. ( -24.40)
>DroSim_CAF1 44847 94 - 1
GCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUAGUGUACAAAGCUCUUUA--------------------CUAUCUAGCAUCCUGUUUUUAA
((((..(.....)..))))(((((((((.((.....(((((((((........)))))))))..)).).)))--------------------)))))................. ( -25.40)
>DroEre_CAF1 32634 100 - 1
GCCAAUUGUCGAAUCUGGCGAUGCUAAGUGCAUGUGUGUGCACUGAAAACAAAUUGCUGAGGCAACUCAUUAUA--------UACUGUAAAA------GGCGUCCUGUUUGUGU
((((..(.....)..))))((((((...((((.(((((((((.(........).)))((((....))))..)))--------)))))))...------)))))).......... ( -27.90)
>DroYak_CAF1 45075 114 - 1
GCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUUGUUAAGCCAACUCAUUAUAACGCCUUAUACCCCUAGAUUGCUCAGCAUCCUGAAUUAAU
((((.((((((....)))))))))).(((((((....))))))).....((...((((.(((...((...(((((....))))).....))...))).))))...))....... ( -21.90)
>consensus
GCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUAGUGUACAAAACUCUUUA____________________CUAUCUAGCAUCCUGUUUUUAA
((((.((((((....)))))))))).(((((((....)))))))...................................................................... (-16.22 = -16.26 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,565,923 – 8,566,028
Length 105
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 91.17
Mean single sequence MFE -24.54
Consensus MFE -19.32
Energy contribution -19.16
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.55
Structure conservation index 0.79
SVM decision value 1.92
SVM RNA-class probability 0.982646
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8565923 105 + 20766785
--UAAAGGCGAUUGUACACUAUUUGUUUUCAGUGCACACACAUGCACUUACCAUCGUCAGAUUCGACAAUUGGCAAAUUUAAAAGCAAUAAACGUACAGAGAGCAAA
--.....((..((((((.....(((((((.((((((......))))))..(((..(((......)))...)))........))))))).....))))))...))... ( -23.50)
>DroSec_CAF1 41596 105 + 1
--UGAAGAGCUUUGUACACCAUUUGUUUUCAGUGCACACACAUGCACUUACCAUCGCCAGAUUCGACAAUUGGCAAAUUUAAAAGCAAUAAACGUACAGAGAGCAAA
--....(..((((((((.....(((((((.((((((......)))))).......(((((.........))))).......))))))).....))))))))..)... ( -27.00)
>DroSim_CAF1 44869 105 + 1
--UAAAGAGCUUUGUACACUAUUUGUUUUCAGUGCACACACAUGCACUUACCAUCGCCAGAUUCGACAAUUGGCAAAUUUAAAAGCAAUAAACGUACAGAGAGCAAA
--....(..((((((((.....(((((((.((((((......)))))).......(((((.........))))).......))))))).....))))))))..)... ( -27.00)
>DroEre_CAF1 32660 107 + 1
UAUAAUGAGUUGCCUCAGCAAUUUGUUUUCAGUGCACACACAUGCACUUAGCAUCGCCAGAUUCGACAAUUGGCAAAUUUAAAAGCAAUAAACGUACAGAGAGCAAA
......(((((((....)))))))((((((.((((......((((.....)))).(((((.........)))))...................)))).))))))... ( -23.80)
>DroYak_CAF1 45115 107 + 1
UAUAAUGAGUUGGCUUAACAAUUUGUUUUCAGUGCACACACAUGCACUUACCAUCGCCAGAUUCGACAAUUGGCAAAUUUAAAAGCAAUAAACGUACAGAGAGCAAA
......((((((......))))))((((((((((((......)))))).......(((((.........)))))........................))))))... ( -21.40)
>consensus
__UAAAGAGCUUUGUACACAAUUUGUUUUCAGUGCACACACAUGCACUUACCAUCGCCAGAUUCGACAAUUGGCAAAUUUAAAAGCAAUAAACGUACAGAGAGCAAA
.....................(((((((((((((((......)))))).......(((((.........)))))........................))))))))) (-19.32 = -19.16 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,565,923 – 8,566,028
Length 105
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 91.17
Mean single sequence MFE -26.36
Consensus MFE -20.12
Energy contribution -20.16
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.61
Structure conservation index 0.76
SVM decision value 0.14
SVM RNA-class probability 0.603296
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8565923 105 - 20766785
UUUGCUCUCUGUACGUUUAUUGCUUUUAAAUUUGCCAAUUGUCGAAUCUGACGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUAGUGUACAAUCGCCUUUA--
...((....((((((((..(((.(((((...((((((.((((((....))))))))))))((((((....))))))))))).)))..))))))))...)).....-- ( -27.10)
>DroSec_CAF1 41596 105 - 1
UUUGCUCUCUGUACGUUUAUUGCUUUUAAAUUUGCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUGGUGUACAAAGCUCUUCA--
...(((...((((((((..(((.(((((...((((((.((((((....))))))))))))((((((....))))))))))).)))..)))))))).)))......-- ( -28.20)
>DroSim_CAF1 44869 105 - 1
UUUGCUCUCUGUACGUUUAUUGCUUUUAAAUUUGCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUAGUGUACAAAGCUCUUUA--
...(((...((((((((..(((.(((((...((((((.((((((....))))))))))))((((((....))))))))))).)))..)))))))).)))......-- ( -28.30)
>DroEre_CAF1 32660 107 - 1
UUUGCUCUCUGUACGUUUAUUGCUUUUAAAUUUGCCAAUUGUCGAAUCUGGCGAUGCUAAGUGCAUGUGUGUGCACUGAAAACAAAUUGCUGAGGCAACUCAUUAUA
((((.((..((((((..(((.((.((((...((((((..(.....)..))))))...)))).)))))..))))))..))...))))....((((....))))..... ( -24.90)
>DroYak_CAF1 45115 107 - 1
UUUGCUCUCUGUACGUUUAUUGCUUUUAAAUUUGCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUUGUUAAGCCAACUCAUUAUA
..(((.....)))........((((...(((((((((.((((((....)))))))))..(((((((....))))))).....))))))...))))............ ( -23.30)
>consensus
UUUGCUCUCUGUACGUUUAUUGCUUUUAAAUUUGCCAAUUGUCGAAUCUGGCGAUGGUAAGUGCAUGUGUGUGCACUGAAAACAAAUAGUGUACAAAACUCUUUA__
((((.((..((((((..(((.((......((((((((.((((((....)))))))))))))))))))..))))))..))...))))..................... (-20.12 = -20.16 +   0.04)

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 10:27:55 2006