Locus 7446

Sequence ID 3R_DroMel_CAF1
Location 19,836,118 – 19,836,250
Length 132
Max. P 0.985149
window12038 window12039 window12040

overview

Window 8

Location 19,836,118 – 19,836,231
Length 113
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 86.06
Mean single sequence MFE -23.62
Consensus MFE -21.50
Energy contribution -21.00
Covariance contribution -0.50
Combinations/Pair 1.15
Mean z-score -2.34
Structure conservation index 0.91
SVM decision value 2.00
SVM RNA-class probability 0.985149
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19836118 113 + 27905053
CAUAGUUGAUACCACGAGUGUUAUUGCCAUGAAAAAUUAAUGAGCCAAACACUCCGAUUAAAACACUCAUAAAACAUUUAUGAGUACUUAAC-CGGCAGAACACAUAUUCA-----GUA
.................(((((.(((((........((((((((.......)))..)))))...((((((((.....)))))))).......-.)))))))))).......-----... ( -22.10)
>DroSec_CAF1 14371 118 + 1
CGUAGUUGAUACCACGAGUGUUAUUGCCAUGAAAAAUUAAUGAGCCGAACACUCCGAUUAAAACACUCAUAAAACAUUUAUGAGUACUUAAC-CGGCAGAACGUACAUAUAUAUAUGUA
(((..(((.......(((((((...(((((.........))).))..)))))))((.((((...((((((((.....))))))))..)))).-)).))).)))((((((....)))))) ( -25.20)
>DroEre_CAF1 14468 114 + 1
CGUAGUUAAUACCACGAGUGUUAUUGCCAUGCAAAAUGAAUGAGCCGAACACUCCGAUUUAAACACUUAUAAAACAUUUAUGAGUACUUAAC-CAGCAGAACAUAUACAUGCCUA----
....(((((......(((((((...(((((.(.....).))).))..)))))))..........((((((((.....))))))))..)))))-..(((...........)))...---- ( -20.30)
>DroYak_CAF1 14434 119 + 1
CGCAGUUGAUACUGCGAGUGUUAUUGCCAUGAAAAAUUAAUGAGCCGAACACUCCGAUUAAAGCACUCAUAAAACAUUUAUGAGUACUCAACCCAGCAGAACACAUACAUACAUAUUCA
.(((((....)))))(((((((...(((((.........))).))..))))))).......((.((((((((.....)))))))).))............................... ( -26.90)
>consensus
CGUAGUUGAUACCACGAGUGUUAUUGCCAUGAAAAAUUAAUGAGCCGAACACUCCGAUUAAAACACUCAUAAAACAUUUAUGAGUACUUAAC_CAGCAGAACACAUACAUACAUA_GUA
.((.(((((......(((((((...(((((.........))).))..)))))))..........((((((((.....))))))))..)))))...))...................... (-21.50 = -21.00 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,836,118 – 19,836,231
Length 113
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 86.06
Mean single sequence MFE -31.10
Consensus MFE -26.12
Energy contribution -24.62
Covariance contribution -1.50
Combinations/Pair 1.22
Mean z-score -2.44
Structure conservation index 0.84
SVM decision value 1.78
SVM RNA-class probability 0.977126
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19836118 113 - 27905053
UAC-----UGAAUAUGUGUUCUGCCG-GUUAAGUACUCAUAAAUGUUUUAUGAGUGUUUUAAUCGGAGUGUUUGGCUCAUUAAUUUUUCAUGGCAAUAACACUCGUGGUAUCAACUAUG
...-----.......(((((.(((((-(((((((((((((((.....))))))))).))))))).((((.....)))).............))))..))))).((((((....)))))) ( -28.60)
>DroSec_CAF1 14371 118 - 1
UACAUAUAUAUAUGUACGUUCUGCCG-GUUAAGUACUCAUAAAUGUUUUAUGAGUGUUUUAAUCGGAGUGUUCGGCUCAUUAAUUUUUCAUGGCAAUAACACUCGUGGUAUCAACUACG
((((((....))))))........((-(((((((((((((((.....))))))))).))))))))(((((((..((.(((.........)))))...)))))))(((((....))))). ( -31.90)
>DroEre_CAF1 14468 114 - 1
----UAGGCAUGUAUAUGUUCUGCUG-GUUAAGUACUCAUAAAUGUUUUAUAAGUGUUUAAAUCGGAGUGUUCGGCUCAUUCAUUUUGCAUGGCAAUAACACUCGUGGUAUUAACUACG
----..(.((((((.(((....((((-(.....(((((.((((..((.....))..)))).....))))).))))).....)))..)))))).).........((((((....)))))) ( -25.00)
>DroYak_CAF1 14434 119 - 1
UGAAUAUGUAUGUAUGUGUUCUGCUGGGUUGAGUACUCAUAAAUGUUUUAUGAGUGCUUUAAUCGGAGUGUUCGGCUCAUUAAUUUUUCAUGGCAAUAACACUCGCAGUAUCAACUGCG
.((((((((....)))))))).....((((((((((((((((.....)))))))))).)))))).(((((((..((.(((.........)))))...)))))))(((((....))))). ( -38.90)
>consensus
UAC_UAUGUAUAUAUAUGUUCUGCCG_GUUAAGUACUCAUAAAUGUUUUAUGAGUGUUUUAAUCGGAGUGUUCGGCUCAUUAAUUUUUCAUGGCAAUAACACUCGUGGUAUCAACUACG
........................((....((((((((((((.....))))))))))))....))(((((((..((.(((.(.....).)))))...)))))))(((((....))))). (-26.12 = -24.62 +  -1.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,836,158 – 19,836,250
Length 92
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 78.14
Mean single sequence MFE -25.30
Consensus MFE -14.90
Energy contribution -14.14
Covariance contribution -0.75
Combinations/Pair 1.21
Mean z-score -2.05
Structure conservation index 0.59
SVM decision value 0.65
SVM RNA-class probability 0.811350
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19836158 92 - 27905053
GAGGAUUGUAAGGAAUAU------GUAC-----UGAAUAUGUGUUCUGCCG-GUUAAGUACUCAUAAAUGUUUUAUGAGUGUUUUAAUCGGAGUGUUUGGCUCA
(((........(((((((------(((.-----....)))))))))).(((-(((((((((((((((.....))))))))).))))))))).........))). ( -26.00)
>DroSec_CAF1 14411 97 - 1
GAGGACUGUAAGGAAUAU------AUACAUAUAUAUAUGUACGUUCUGCCG-GUUAAGUACUCAUAAAUGUUUUAUGAGUGUUUUAAUCGGAGUGUUCGGCUCA
(((.(((....(((((..------.((((((....)))))).))))).(((-(((((((((((((((.....))))))))).)))))))))))).)))...... ( -27.60)
>DroEre_CAF1 14508 98 - 1
AAGGACGUAAUGGAAUC-GUCGAAA----UAGGCAUGUAUAUGUUCUGCUG-GUUAAGUACUCAUAAAUGUUUUAUAAGUGUUUAAAUCGGAGUGUUCGGCUCA
.((((((((.....((.-(((....----..)))))...))))))))((((-(.....(((((.((((..((.....))..)))).....))))).)))))... ( -17.80)
>DroYak_CAF1 14474 103 - 1
AAGGACUGCAAGGAAUC-GUCGAAAUGAAUAUGUAUGUAUGUGUUCUGCUGGGUUGAGUACUCAUAAAUGUUUUAUGAGUGCUUUAAUCGGAGUGUUCGGCUCA
.................-((((((..((((((((....))))))))..((((...((((((((((((.....))))))))))))...))))....))))))... ( -29.80)
>consensus
AAGGACUGUAAGGAAUA_______AUAC_UAUGUAUAUAUAUGUUCUGCCG_GUUAAGUACUCAUAAAUGUUUUAUGAGUGUUUUAAUCGGAGUGUUCGGCUCA
..((((.....(((((..........................))))).(((....((((((((((((.....))))))))))))....)))...))))...... (-14.90 = -14.14 +  -0.75)

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 12:46:15 2006