Locus 7616

Sequence ID 3R_DroMel_CAF1
Location 20,418,950 – 20,419,097
Length 147
Max. P 0.964577
window12289 window12290 window12291

overview

Window 9

Location 20,418,950 – 20,419,057
Length 107
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 80.41
Mean single sequence MFE -17.07
Consensus MFE -14.97
Energy contribution -14.46
Covariance contribution -0.50
Combinations/Pair 1.20
Mean z-score -1.36
Structure conservation index 0.88
SVM decision value 0.24
SVM RNA-class probability 0.650245
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20418950 107 + 27905053
AAAUCAGAUUAUUUUCCCCCCCCUGGCUUUUAUCAGGGUUAAAUCAGCGUAAUUGUUUGGCCAUCUCCUUAUCAUUAUCAGACUGAAUCUAAUCAAAAGCCAAACAA
....................((((((......))))))..............(((((((((..(((...((....))..))).(((......)))...))))))))) ( -18.30)
>DroSec_CAF1 2378 104 + 1
AAAUCAGAUUACUU---CCCCCCUGACUUUUAUCAGGGUUAAAUCAGCGUAAUUGUUUGGCCAUCUUCUUAUCGUUAUCAGCCUAGAUCUAAUCAAAAGCCAAACAA
......((((....---...((((((......))))))...)))).......(((((((((.........(((............)))..........))))))))) ( -19.21)
>DroSim_CAF1 1947 104 + 1
AAAUCAGAUUAUUU---CCCCCCUGGCUUUUAUCAGGGUUAAAUCAGCGUAAUUGUUUGGCCAUCUUCUUAUCAUUAUCAGACUAGAUCUAAUCAAAAGCCAAACAA
......((((....---...((((((......))))))...)))).......(((((((((.....(((..((.......))..)))...........))))))))) ( -18.49)
>DroYak_CAF1 1962 82 + 1
-----------GUU-----CACUUGGCUUUUAUCAGGGAUUAAUCAGCGUAAUUGUUUGGUCUUCU---------UAUCAGACUUUACCUAAUCAAAAACCAAACAA
-----------...-----...((((.((((((.((((((((.......)))))(((((((.....---------.)))))))....))).)).)))).)))).... ( -12.30)
>consensus
AAAUCAGAUUAUUU___CCCCCCUGGCUUUUAUCAGGGUUAAAUCAGCGUAAUUGUUUGGCCAUCUUCUUAUCAUUAUCAGACUAGAUCUAAUCAAAAGCCAAACAA
....................((((((......))))))..............(((((((((.....................................))))))))) (-14.97 = -14.46 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,418,950 – 20,419,057
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 80.41
Mean single sequence MFE -25.23
Consensus MFE -19.73
Energy contribution -19.98
Covariance contribution 0.25
Combinations/Pair 1.09
Mean z-score -2.17
Structure conservation index 0.78
SVM decision value 1.57
SVM RNA-class probability 0.964577
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20418950 107 - 27905053
UUGUUUGGCUUUUGAUUAGAUUCAGUCUGAUAAUGAUAAGGAGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAAGCCAGGGGGGGGAAAAUAAUCUGAUUU
((((((((((.((.(((((((...)))))))...........)).)))))))))).........(((..(((((........)))))..)))............... ( -25.00)
>DroSec_CAF1 2378 104 - 1
UUGUUUGGCUUUUGAUUAGAUCUAGGCUGAUAACGAUAAGAAGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAAGUCAGGGGGG---AAGUAAUCUGAUUU
(((((((((((((..(((.(((......))).....)))..))).)))))))))).........(((..(((((((....)))))))..)---))............ ( -28.50)
>DroSim_CAF1 1947 104 - 1
UUGUUUGGCUUUUGAUUAGAUCUAGUCUGAUAAUGAUAAGAAGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAAGCCAGGGGGG---AAAUAAUCUGAUUU
((((((((((.((.(((((((...)))))))...........)).)))))))))).........(((..(((((........)))))..)---))............ ( -26.20)
>DroYak_CAF1 1962 82 - 1
UUGUUUGGUUUUUGAUUAGGUAAAGUCUGAUA---------AGAAGACCAAACAAUUACGCUGAUUAAUCCCUGAUAAAAGCCAAGUG-----AAC-----------
(((((((((((((.((((((.....)))))).---------.)))))))))))))(((((((.((((.....))))...)))...)))-----)..----------- ( -21.20)
>consensus
UUGUUUGGCUUUUGAUUAGAUCUAGUCUGAUAAUGAUAAGAAGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAAGCCAGGGGGG___AAAUAAUCUGAUUU
((((((((((.((.((((((.....))))))...........)).))))))))))..............(((((........))))).................... (-19.73 = -19.98 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,418,977 – 20,419,097
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.50
Mean single sequence MFE -23.60
Consensus MFE -18.40
Energy contribution -18.20
Covariance contribution -0.20
Combinations/Pair 1.15
Mean z-score -1.38
Structure conservation index 0.78
SVM decision value -0.00
SVM RNA-class probability 0.532003
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20418977 120 - 27905053
CUAGCAAAGUUCUCAUUGCCUUCUCAACAAAUAUAGCAAAUUGUUUGGCUUUUGAUUAGAUUCAGUCUGAUAAUGAUAAGGAGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAA
...((((.(....).)))).........((((.((((.((((((((((((.((.(((((((...)))))))...........)).))))))))))))..))))))))............. ( -24.30)
>DroSec_CAF1 2402 120 - 1
CCAGCAAAGUUCCCAUUGCCUUCUCAACAAAUAUAGCAAAUUGUUUGGCUUUUGAUUAGAUCUAGGCUGAUAACGAUAAGAAGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAA
.((((...........(((................)))(((((((((((((((..(((.(((......))).....)))..))).))))))))))))..))))................. ( -24.09)
>DroSim_CAF1 1971 120 - 1
CCAGCAAAGUUCUCAUUGCCUUCUCAACAAAUAUAGGAAAUUGUUUGGCUUUUGAUUAGAUCUAGUCUGAUAAUGAUAAGAAGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAA
.((((.............(((.............))).((((((((((((.((.(((((((...)))))))...........)).))))))))))))..))))................. ( -25.32)
>DroEre_CAF1 1919 109 - 1
CGAGCA-AGUUCUAUAUGCAGUCUCAGCAAAUGUUGGAAAUUGUUUGACUUUUGAUUAGGUCUAGUCUGAUA---------AGAAGGCCAAACAAUUACGCUGAUUUAUCCAUGA-AAAA
..(((.-..............((.((((....))))))(((((((((.(((((.((((((.....)))))).---------)))))..)))))))))..))).............-.... ( -23.30)
>DroYak_CAF1 1973 98 - 1
CUAGUA-AGUUCUAUAUGCAAUCUCA------------AAUUGUUUGGUUUUUGAUUAGGUAAAGUCUGAUA---------AGAAGACCAAACAAUUACGCUGAUUAAUCCCUGAUAAAA
.((((.-.((.......)).......------------(((((((((((((((.((((((.....)))))).---------.)))))))))))))))..))))................. ( -21.00)
>consensus
CCAGCAAAGUUCUCAUUGCCUUCUCAACAAAUAUAGCAAAUUGUUUGGCUUUUGAUUAGAUCUAGUCUGAUAA_GAUAAG_AGAUGGCCAAACAAUUACGCUGAUUUAACCCUGAUAAAA
.((((...((.......))...................((((((((((((.((.((((((.....))))))...........)).))))))))))))..))))................. (-18.40 = -18.20 +  -0.20)

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 12:50:17 2006