Locus 984

Sequence ID 3R_DroMel_CAF1
Location 3,165,130 – 3,165,289
Length 159
Max. P 0.959908
window1588 window1589 window1590

overview

Window 8

Location 3,165,130 – 3,165,250
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -43.18
Consensus MFE -36.70
Energy contribution -37.95
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.85
SVM decision value 1.06
SVM RNA-class probability 0.909007
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3165130 120 + 27905053
GCACAGCCUCGGCAAGGAAUGAGGUAGUGCUGGGUGGUCGGGGUCGAUUGGGUCUGCUGUGCAAAUUUAAAUUUGGUAAUGGUCCUGGCACUUUUUGCCACGGACUGUAAAGCAAAUAAG
((((((((((((((..(.......)..)))))))......((..(.....)..)))))))))........(((((.(.((((((((((((.....))))).)))))))..).)))))... ( -40.90)
>DroSec_CAF1 13193 120 + 1
GCACAGCCUCGGCAAGGAAUGAGGUAGUGCUGGGGGGUCGGGGUCGAUUGGGUCUGCUGUGCAAAUUUAAAUUUGGUAAUGGUCCUGGCACUUUUUGCCAGGGACUGUUAAGCAAAUAAG
((((((((((((((..(.......)..)))))))((..(.((.....)).)..)))))))))........(((((.((((((((((((((.....))))).)))))))))..)))))... ( -45.90)
>DroSim_CAF1 15432 120 + 1
GCACAGCCUCGGAAAGGAAUGAGGUAGUGCUGGGUGGUCGGGGUCGAUUGGGUCUGCUGUGCAAAUUUAAAUUUGGUAAUGGUCCUGGCACUUUUUGCCAGGGACUGUUAAGCAAAUAAG
((((.((((((........)))))).))))((.(..(.((((.((....)).)))))..).)).......(((((.((((((((((((((.....))))).)))))))))..)))))... ( -44.40)
>DroEre_CAF1 4891 120 + 1
GCACAGCCUCGGUAAGGAAUGAGGUAGUGCUGAGUGGUCGGGGUCGAUUGGGUCUGCUGUGCAAAUUUAAAUUCGGUAAUGGUCCUGCCACUUUUUGCCAGAGACUGCUAGGCAAAUAAG
((((.((((((........)))))).)))).((((((.((((..((((...)))(((((..............)))))..)..))))))))))((((((((......)).)))))).... ( -41.54)
>consensus
GCACAGCCUCGGCAAGGAAUGAGGUAGUGCUGGGUGGUCGGGGUCGAUUGGGUCUGCUGUGCAAAUUUAAAUUUGGUAAUGGUCCUGGCACUUUUUGCCAGGGACUGUUAAGCAAAUAAG
((((.((((((........)))))).))))((.(..(.((((.((....)).)))))..).)).......(((((.((((((((((((((.....))))).)))))))))..)))))... (-36.70 = -37.95 +   1.25)

alignment

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secondary structure

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Window 9

Location 3,165,130 – 3,165,250
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -29.00
Consensus MFE -26.70
Energy contribution -26.57
Covariance contribution -0.13
Combinations/Pair 1.07
Mean z-score -2.33
Structure conservation index 0.92
SVM decision value 1.51
SVM RNA-class probability 0.959908
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3165130 120 - 27905053
CUUAUUUGCUUUACAGUCCGUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCCCGACCACCCAGCACUACCUCAUUCCUUGCCGAGGCUGUGC
....((((((.....((((.(((((.....)))))))))......(((((....)))))...)))))).....(((....))).......((((..((((..........))))..)))) ( -29.70)
>DroSec_CAF1 13193 120 - 1
CUUAUUUGCUUAACAGUCCCUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCCCGACCCCCCAGCACUACCUCAUUCCUUGCCGAGGCUGUGC
....((((((.....(..(((((((.....)))))))..).....(((((....)))))...)))))).....(((....))).......((((..((((..........))))..)))) ( -29.80)
>DroSim_CAF1 15432 120 - 1
CUUAUUUGCUUAACAGUCCCUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCCCGACCACCCAGCACUACCUCAUUCCUUUCCGAGGCUGUGC
....((((((.....(..(((((((.....)))))))..).....(((((....)))))...)))))).....(((....))).......((((..((((..........))))..)))) ( -29.80)
>DroEre_CAF1 4891 120 - 1
CUUAUUUGCCUAGCAGUCUCUGGCAAAAAGUGGCAGGACCAUUACCGAAUUUAAAUUUGCACAGCAGACCCAAUCGACCCCGACCACUCAGCACUACCUCAUUCCUUACCGAGGCUGUGC
....((((((.((......)))))))).(((((..((........(((.......(((((...))))).....)))...))..)))))..((((..((((..........))))..)))) ( -26.70)
>consensus
CUUAUUUGCUUAACAGUCCCUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCCCGACCACCCAGCACUACCUCAUUCCUUGCCGAGGCUGUGC
....(((((......((((.(((((.....)))))))))......(((((....)))))....))))).....(((....))).......((((..((((..........))))..)))) (-26.70 = -26.57 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,165,170 – 3,165,289
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.19
Mean single sequence MFE -26.03
Consensus MFE -21.90
Energy contribution -22.65
Covariance contribution 0.75
Combinations/Pair 1.10
Mean z-score -2.09
Structure conservation index 0.84
SVM decision value 1.03
SVM RNA-class probability 0.902918
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3165170 119 - 27905053
AGGCAUAUUCCCAAGCCUUAGAAU-CAAAGAAGUAAAGCACUUAUUUGCUUUACAGUCCGUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCC
.(((..........)))(((((..-.......((((((((......)))))))).((((.(((((.....)))))))))..........))))).(((((...)))))............ ( -28.00)
>DroSec_CAF1 13233 119 - 1
AGGCAUAUUACCAAGCCUUAGAAU-CCAAAAAGUUAAGCACUUAUUUGCUUAACAGUCCCUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCC
((((..........))))......-.......((((((((......)))))))).((((((((((.....)))))))..................(((((...))))).......))).. ( -29.50)
>DroSim_CAF1 15472 119 - 1
AGGCAUAUUACCAAGCCUUAGAAU-CCAAAAAGUAAAGCACUUAUUUGCUUAACAGUCCCUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCC
((((..........))))......-.......((.(((((......))))).)).((((((((((.....)))))))..................(((((...))))).......))).. ( -25.60)
>DroEre_CAF1 4931 117 - 1
AGGCAU--UC-CGAACCUUAGAAUUCCAGGAAGUAAAGCACUUAUUUGCCUAGCAGUCUCUGGCAAAAAGUGGCAGGACCAUUACCGAAUUUAAAUUUGCACAGCAGACCCAAUCGACCC
(((((.--..-....(((.........)))((((.....))))...)))))....((((((((((((.(((((.....)))))............))))).))).))))........... ( -21.02)
>consensus
AGGCAUAUUACCAAGCCUUAGAAU_CCAAAAAGUAAAGCACUUAUUUGCUUAACAGUCCCUGGCAAAAAGUGCCAGGACCAUUACCAAAUUUAAAUUUGCACAGCAGACCCAAUCGACCC
.(((..........)))(((((..........((((((((......)))))))).((((.(((((.....)))))))))..........))))).(((((...)))))............ (-21.90 = -22.65 +   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 09:57:33 2006