Locus 4095

Sequence ID 2R_DroMel_CAF1
Location 13,486,507 – 13,486,636
Length 129
Max. P 0.685391
window6595 window6596

overview

Window 5

Location 13,486,507 – 13,486,600
Length 93
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 78.28
Mean single sequence MFE -23.77
Consensus MFE -8.25
Energy contribution -8.78
Covariance contribution 0.53
Combinations/Pair 1.32
Mean z-score -2.63
Structure conservation index 0.35
SVM decision value 0.19
SVM RNA-class probability 0.624420
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13486507 93 - 20766785
UGCAUGUUUUGCUGCG---AAAAAAAAGCACAUAGAGCUUGCAAUAUUCAUAUGGUAAACAUGCAGCAGUGGAAUGCACAGAGAAAAA-UAUUGCAA
((((((((((((((((---((....((((.......))))......)))..(((.....)))))))).(((.....))).....))))-)).)))). ( -21.90)
>DroSec_CAF1 35055 91 - 1
UGCACGUUUUUCUGCG---AAA--AAAGCAUAGAGAGCUUGCAAUAUUCAUAUGGCAAACAUACUGCAGUGGAAUGCACAGCGAAAAA-UAUUGCAA
((((.((((((((((.---...--...)))......(((((((...(((((...(((.......))).))))).)))).)))))))))-)..)))). ( -22.60)
>DroSim_CAF1 35269 91 - 1
UGCAUGUUUUGCUGCG---AAA--AAAGCACAGAGAGCUUGCAAUAUUCAUAUGGCAAACAUCCUGCAGUGGAAUGCACAGCGAAAAA-UAUUGCAA
((((..((((((((..---...--.((((.......))))(((...(((((...(((.......))).))))).))).))))))))..-...)))). ( -22.70)
>DroEre_CAF1 35402 91 - 1
UGCAUGUUUGGCCGGG---AAA--AAAGCACAGGGAGCGUGCAAUAUUCAUAUGGCAAACAUGCUGCAGUGGAGUGCACAGGGAAAAA-UAAUUCAA
.(((((((((.(((.(---((.--...((((.(....)))))....)))...))))))))))))((((......))))..........-........ ( -25.50)
>DroYak_CAF1 36770 92 - 1
UGCAUGUUUUGCCGGGGUAAAA--AGAGCACAGGCAACGUGCAAUAUUCAUAUGGCAAACAUGCAGCAGUGAAAUGCACAGUGAAAAA-U--UGGAA
(((((((((.((((........--...((((.(....)))))..........)))))))))))))(((......))).((((.....)-)--))... ( -28.50)
>DroAna_CAF1 36798 82 - 1
UGCAUGUUUUUCCGGC---GAA--A--GCGC--------UGCAAUACUCAUAGAGCAAACAAAUGGGGGAGGAAUGCACAGAGAAUAAACUCUAUAA
(((((.(((..(((((---...--.--))((--------(.............))).......)))..)))..))))).((((......)))).... ( -21.42)
>consensus
UGCAUGUUUUGCCGCG___AAA__AAAGCACAGAGAGCUUGCAAUAUUCAUAUGGCAAACAUGCUGCAGUGGAAUGCACAGAGAAAAA_UAUUGCAA
((((..((((((((.............(((.........)))........((((.....))))...))))))))))))................... ( -8.25 =  -8.78 +   0.53)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,486,538 – 13,486,636
Length 98
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 82.76
Mean single sequence MFE -26.18
Consensus MFE -18.83
Energy contribution -18.75
Covariance contribution -0.08
Combinations/Pair 1.19
Mean z-score -1.88
Structure conservation index 0.72
SVM decision value 0.32
SVM RNA-class probability 0.685391
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13486538 98 - 20766785
UGGAGCCAAUUAUUAUUGUGACAGGACAUGGCCUGUUGCAUGUUUUGCUGCG---AAAAAAAAGCACAUAGAGCUUGCAAUAUUCAUAUGGUAAACAUGCA
....((...(((((((.((((((((......))))(((((.((((((.(((.---........)))..)))))).)))))...)))))))))))....)). ( -22.60)
>DroSec_CAF1 35086 96 - 1
UGGAGCCAAUUAUUAUUGUGACAGGACAUGGCCUGUUGCACGUUUUUCUGCG---AAA--AAAGCAUAGAGAGCUUGCAAUAUUCAUAUGGCAAACAUACU
....((((...........((((((......))))))(((.((((((.(((.---...--...)))..)))))).)))..........))))......... ( -24.20)
>DroSim_CAF1 35300 96 - 1
UGGAGCCAAUUAUUAUUGUGACAGGACAUGGCCUGUUGCAUGUUUUGCUGCG---AAA--AAAGCACAGAGAGCUUGCAAUAUUCAUAUGGCAAACAUCCU
.(((((((.....((((((((((((......))))))((...(((((.(((.---...--...)))))))).))..))))))......)))).....))). ( -25.50)
>DroEre_CAF1 35433 93 - 1
UGAAGCCAAUU---AUUGUGACAGGACAUGGCCUGUUGCAUGUUUGGCCGGG---AAA--AAAGCACAGGGAGCGUGCAAUAUUCAUAUGGCAAACAUGCU
...........---.....((((((......))))))(((((((((.(((.(---((.--...((((.(....)))))....)))...)))))))))))). ( -30.30)
>DroYak_CAF1 36799 96 - 1
UGAAGCCAAUU---AUUGUGACAGGACAUGGCCUGUUGCAUGUUUUGCCGGGGUAAAA--AGAGCACAGGCAACGUGCAAUAUUCAUAUGGCAAACAUGCA
...........---.....((((((......))))))((((((((.((((........--...((((.(....)))))..........)))))))))))). ( -30.30)
>DroAna_CAF1 36830 83 - 1
UGGAGCCAAUU---AUUGCGACAGGACAUGGCCUGUUGCAUGUUUUUCCGGC---GAA--A--GCGC--------UGCAAUACUCAUAGAGCAAACAAAUG
((.(((.....---..(((((((((......)))))))))..........((---...--.--))))--------).))...................... ( -24.20)
>consensus
UGGAGCCAAUU___AUUGUGACAGGACAUGGCCUGUUGCAUGUUUUGCCGCG___AAA__AAAGCACAGAGAGCUUGCAAUAUUCAUAUGGCAAACAUGCU
....((((........(((((((((......))))))))).......................(((.........)))..........))))......... (-18.83 = -18.75 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:40 2006