Locus 5809

Sequence ID 3L_DroMel_CAF1
Location 15,719,396 – 15,719,567
Length 171
Max. P 0.884088
window9230 window9231

overview

Window 0

Location 15,719,396 – 15,719,499
Length 103
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 65.59
Mean single sequence MFE -24.00
Consensus MFE -9.80
Energy contribution -10.05
Covariance contribution 0.25
Combinations/Pair 1.27
Mean z-score -1.86
Structure conservation index 0.41
SVM decision value 0.87
SVM RNA-class probability 0.869791
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15719396 103 - 23771897
ACCUCUCACCUUCGUCCUU-------UCCCUCUUUCUACAAUCUCCUG--CCACCCUCGAA-AAACCCCUUUUUUUGACGGGCUGUCAGUGACAGAGGCGAGUCAGUAGUCAG
...................-------.....((..((((...(((..(--((.((((((((-(((.....)))))))).)))(((((...))))).))))))...))))..)) ( -24.60)
>DroPse_CAF1 49872 99 - 1
AGCCCCUAGCCCUGUCCAAGUCGCUGUCCCUGUCCCAG----CUCCAUCUCCAUCUCC-----AUCUCUUUCUUUUGACAGCCUGUCACUGACAGGGC-----ACACACUCAG
........((((((((...(..((((.........)))----)..)............-----............((((.....))))..))))))))-----.......... ( -23.90)
>DroSec_CAF1 34805 104 - 1
ACCUCUCACCUUCAUCCUCC------UCCCUCUUCCUACACACUCCUG--CCACACCCGAA-AACCCCCUUUUUUUGACGGGCUGUCAGUGACAGAGGCGAGUCAGUAGUCAG
....................------.....((..((((..((((..(--((...((((((-((........))))..))))(((((...))))).)))))))..))))..)) ( -20.50)
>DroSim_CAF1 35897 95 - 1
ACCUCUCACCUUCAUCCUCU------CCCCUCUUCCUA------------CCACCCCCGAAAAACCCCCUUUUUUUGACGGGCUGUCAGUGACAGAGGCGAGUCAGUAGUCAG
..................((------(.(((((((((.------------.(((((.(((((((......)))))))..))).))..)).)).))))).)))........... ( -20.80)
>DroYak_CAF1 71942 101 - 1
AGCUCUCACCUCCGCCCUAC--GC--CCCCCCUUCCUG----CUCCUG--CCGCCCCCGAA-AACC-CCCGUUUUUGACAGGCUGUCAGUGGCAGAGGCGAGUCAGUAGUGAG
....(((((..(.(..((.(--((--(........(((----(..(((--(.(((..((((-(((.-...)))))))...))).).)))..)))).)))))).).)..))))) ( -30.80)
>DroPer_CAF1 49736 99 - 1
AGCCCCUAGCCCUGUCCAAGUCGCUGUCCCUGUCCCUG----UCCCAGCUCCAUCUCC-----AUCUCUUUCUUUUGACAGCCUGUCACUGACAGGGC-----ACACACUCAG
........((((((((...(..((((...(.......)----...))))..)......-----............((((.....))))..))))))))-----.......... ( -23.40)
>consensus
ACCUCUCACCUCCGUCCUAC______UCCCUCUUCCUA____CUCCUG__CCACCCCCGAA_AACCCCCUUUUUUUGACAGGCUGUCAGUGACAGAGGCGAGUCAGUAGUCAG
....(((.((((.(((...................................(......)................((((.....))))..))).)))).)))........... ( -9.80 = -10.05 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,719,466 – 15,719,567
Length 101
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 65.46
Mean single sequence MFE -33.42
Consensus MFE -13.92
Energy contribution -15.73
Covariance contribution 1.81
Combinations/Pair 1.50
Mean z-score -1.87
Structure conservation index 0.42
SVM decision value 0.93
SVM RNA-class probability 0.884088
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15719466 101 + 23771897
UGUAGAAAGAGGGA-------AAGGACGAAGGUGAGAGGUCCAAGAGGGGGAUUGAAUAUCCUCCAGUUGUCGUGAACGGCAAUGUGCCGCUAUUUUCUUUUAUCCUG
..........((((-------.((((.((((((.((.((..(....(((((((.....))))))).(((((((....))))))))..)).)))))))))))).)))). ( -35.00)
>DroSec_CAF1 34875 102 + 1
UGUAGGAAGAGGGA------GGAGGAUGAAGGUGAGAGGUCCACAGAGGGGAUUGAAUGUCCUCCAGUUGUCGUGAACGACAAUGUGCCGCUAUCUUCUUGUAUUCUG
....((((...(.(------((((((((..(((............(.((((((.....))))))).(((((((....)))))))..)))..))))))))).).)))). ( -34.40)
>DroSim_CAF1 35960 100 + 1
--UAGGAAGAGGGG------AGAGGAUGAAGGUGAGAGGUCCACAAAGGGGAUUGAAUGUCCUCCAGUUGUCGUGAACGGCAAUGCGCCGCUAUCUUCUUGUAUCCUG
--(((((....(.(------((((((((..((((.............((((((.....)))).)).(((((((....))))))).))))..))))))))).).))))) ( -37.20)
>DroEre_CAF1 26138 77 + 1
------------------------------GGCAGGAGCAGGAGC-AGGCGAUUGAAUGUCCUCCAGUUGUCGUGAACGGUAAUGUGCCGCUAUCUGCUCUUAUCCUG
------------------------------((.((((((((((((-.((((((((.........))))))))......(((.....)))))).)))))))))..)).. ( -28.70)
>DroYak_CAF1 72009 101 + 1
--CAGGAAGGGGGG--GC--GUAGGGCGGAGGUGAGAGCUACACG-AAGGGAUUGAAUGUCCUCCUGUUGUCGUGAACGGUAAUGUGCCGCUUUCUUCUCUUAUCCUG
--((((((((((((--(.--..(((((((.(((....))).(((.-..(((((.....)))))...(((..((....))..))))))))))))))))))))).))))) ( -37.20)
>DroPer_CAF1 49797 105 + 1
--CAGGGACAGGGACAGCGACUUGGACAGGGCUAGGGGCUAGGGG-CUGGAAGUAGAUGUCCUCCACUUUUUGUUAACUUUAAUGUUGCUCAUUGUGCCCCAUUGCAU
--(..(..((((........))))..)..)((..(((((...(((-(.((((((.((.....)).))))))....(((......))))))).....)))))...)).. ( -28.00)
>consensus
__UAGGAAGAGGGA_______GAGGACGAAGGUGAGAGCUCCACG_AGGGGAUUGAAUGUCCUCCAGUUGUCGUGAACGGCAAUGUGCCGCUAUCUUCUCUUAUCCUG
..............................(((((((((........((((((.....))))))..(((((((....)))))))............))))))).)).. (-13.92 = -15.73 +   1.81)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:30 2006