Locus 1699

Sequence ID 3L_DroMel_CAF1
Location 4,957,081 – 4,957,208
Length 127
Max. P 0.938382
window2621 window2622 window2623

overview

Window 1

Location 4,957,081 – 4,957,188
Length 107
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 82.84
Mean single sequence MFE -31.63
Consensus MFE -21.99
Energy contribution -23.27
Covariance contribution 1.28
Combinations/Pair 1.20
Mean z-score -1.76
Structure conservation index 0.70
SVM decision value 0.13
SVM RNA-class probability 0.600220
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4957081 107 - 23771897
AGAAACGCUUGGGCAGCGGAACAGUUGAUAGCUCAAUUGG---UGCUGACCGAAAAUCGUCGAGAAUCGGA--GGGGGUGGAGAAAUGAGAGAAAUCAGCCUCGUUAGCAGC
.....((((.....))))...(((((((....))))))).---(((((((.......(..((.....))..--)(((((.((....(....)...)).)))))))))))).. ( -28.00)
>DroSec_CAF1 177879 109 - 1
AGAAACGCUUGGGCAGCGAAACAGUUGAUAGCUCAAUUGGCGGCGCUGCCCGAAAAUCGUUGAGAAUCG-A--GGGGGUGGAGAAAUGAGAGAAAGCAGCCUCGUUAGCAGC
........((((((((((...(((((((....)))))))....)))))))))).....((((..((.((-(--((..((................))..)))))))..)))) ( -38.39)
>DroSim_CAF1 195341 106 - 1
AGAAACGCUUGGGCAGCGAAACAGUUGAUAGCUCAAUUGG---CGCUGCCCGAAAAUCGUUGAGAAUCA-A--GGGGGUGGAGAAAUGAGAGAAAGCAGCCUCGUUAGCAGC
........((((((((((...(((((((....))))))).---)))))))))).....((((..(((..-.--((((.((................)).)))))))..)))) ( -35.59)
>DroEre_CAF1 178894 108 - 1
AGGAACGCUUGGGCAGCGGAACAGUUGAUAACUCAAUUGG---CUCUGCCCGAAAAUCGUUGAGAAUCG-AGAGGGGGUGGAGAAAAGAGAGAAAGCAGCCUCGUUAGCAGG
......(((.((((.((....(((((((....))))))).---(((..(((.....(((........))-)....)))..)))............)).))))....)))... ( -32.90)
>DroYak_CAF1 183943 106 - 1
AGGAACGCUUGGGCAGCGGAACAGUUGAUAGCUCAAUUGG---CGCUGCACGAAAAUCGCUGAGAAUCG-A--GGGGGUGGAGAAAUGAGAGAAAGCAGCCUCGUUAGCAGG
........(((.((((((...(((((((....))))))).---)))))).))).....(((((....((-(--((..((................))..))))))))))... ( -30.89)
>DroAna_CAF1 186095 103 - 1
CGAAACGAAUGGCUAAUGGAACAGUUGAUAGCUCAAUUCG---AAAUGC--GGGGGUGGGUGAAAGUG--C--GGAGCGAAAGCGAAGAGAGAGUGCUGCCUUGUUAGCAGG
...........(((((..(..((((...(..(((..((((---...(((--....)))..))))....--.--...((....))...)))..)..))))..)..)))))... ( -24.00)
>consensus
AGAAACGCUUGGGCAGCGGAACAGUUGAUAGCUCAAUUGG___CGCUGCCCGAAAAUCGUUGAGAAUCG_A__GGGGGUGGAGAAAUGAGAGAAAGCAGCCUCGUUAGCAGC
......((((((((((((...(((((((....)))))))....))))))))))....................((((.((................)).))))....))... (-21.99 = -23.27 +   1.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,957,113 – 4,957,208
Length 95
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 75.71
Mean single sequence MFE -20.02
Consensus MFE -10.85
Energy contribution -12.47
Covariance contribution 1.61
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.54
SVM decision value 0.57
SVM RNA-class probability 0.783930
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4957113 95 + 23771897
CACCCCC--UCCGAUUCUCGACGAUUUUCGGUCAGCA---CCAAUUGAGCUAUCAACUGUUCCGCUGCCCAAGCGUUUCUCUCCUCGCUGU--CGCUCUCUC
.......--.........((((.......((.((((.---.((.((((....)))).))....)))).)).((((..........))))))--))....... ( -18.80)
>DroSec_CAF1 177911 97 + 1
CACCCCC--U-CGAUUCUCAACGAUUUUCGGGCAGCGCCGCCAAUUGAGCUAUCAACUGUUUCGCUGCCCAAGCGUUUCUCUCCGCUCUGU--CGCUCUCUC
.......--.-..........((((....((((((((....((.((((....)))).))...)))))))).((((........))))..))--))....... ( -26.10)
>DroSim_CAF1 195373 94 + 1
CACCCCC--U-UGAUUCUCAACGAUUUUCGGGCAGCG---CCAAUUGAGCUAUCAACUGUUUCGCUGCCCAAGCGUUUCUCUCCGCUCUGU--CGCUCUCUC
.......--.-..........((((....((((((((---.((.((((....)))).))...)))))))).((((........))))..))--))....... ( -26.10)
>DroEre_CAF1 178926 95 + 1
CACCCCCUCU-CGAUUCUCAACGAUUUUCGGGCAGAG---CCAAUUGAGUUAUCAACUGUUCCGCUGCCCAAGCGUUCCUCUCCGC-UUGC--CGCUCUCUC
.........(-((........))).....((((((..---.((.((((....)))).)).....))))))(((((........)))-))..--......... ( -20.50)
>DroYak_CAF1 183975 96 + 1
CACCCCC--U-CGAUUCUCAGCGAUUUUCGUGCAGCG---CCAAUUGAGCUAUCAACUGUUCCGCUGCCCAAGCGUUCCUCUCUGCCUUGCUUUGCUCUCUG
.......--.-........(((((.......((((((---.((.((((....)))).))...)))))).((((.((........))))))..)))))..... ( -19.60)
>DroAna_CAF1 186127 74 + 1
UCGCUCC--G--CACUUUCACCCACCCCC--GCAUUU---CGAAUUGAGCUAUCAACUGUUCCAUUAGCCAUUCGUUUCGCUC-------------------
.......--.--.................--((....---(((((.(.((((.............))))))))))....))..------------------- (  -9.02)
>consensus
CACCCCC__U_CGAUUCUCAACGAUUUUCGGGCAGCG___CCAAUUGAGCUAUCAACUGUUCCGCUGCCCAAGCGUUUCUCUCCGC_CUGU__CGCUCUCUC
.............................((((((((....((.((((....)))).))...))))))))................................ (-10.85 = -12.47 +   1.61)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,957,113 – 4,957,208
Length 95
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 75.71
Mean single sequence MFE -27.80
Consensus MFE -16.92
Energy contribution -18.12
Covariance contribution 1.20
Combinations/Pair 1.18
Mean z-score -1.91
Structure conservation index 0.61
SVM decision value 1.27
SVM RNA-class probability 0.938382
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4957113 95 - 23771897
GAGAGAGCG--ACAGCGAGGAGAGAAACGCUUGGGCAGCGGAACAGUUGAUAGCUCAAUUGG---UGCUGACCGAAAAUCGUCGAGAAUCGGA--GGGGGUG
..((...((--((.(((..........)))((((.(((((...(((((((....))))))).---))))).)))).....))))....))...--....... ( -26.20)
>DroSec_CAF1 177911 97 - 1
GAGAGAGCG--ACAGAGCGGAGAGAAACGCUUGGGCAGCGAAACAGUUGAUAGCUCAAUUGGCGGCGCUGCCCGAAAAUCGUUGAGAAUCG-A--GGGGGUG
..((...((--((.(((((........)))))((((((((...(((((((....)))))))....)))))))).......))))....)).-.--....... ( -37.30)
>DroSim_CAF1 195373 94 - 1
GAGAGAGCG--ACAGAGCGGAGAGAAACGCUUGGGCAGCGAAACAGUUGAUAGCUCAAUUGG---CGCUGCCCGAAAAUCGUUGAGAAUCA-A--GGGGGUG
..((...((--((.(((((........)))))((((((((...(((((((....))))))).---)))))))).......))))....)).-.--....... ( -37.30)
>DroEre_CAF1 178926 95 - 1
GAGAGAGCG--GCAA-GCGGAGAGGAACGCUUGGGCAGCGGAACAGUUGAUAACUCAAUUGG---CUCUGCCCGAAAAUCGUUGAGAAUCG-AGAGGGGGUG
...(((((.--.(((-(((........))))))..........(((((((....))))))))---))))((((.....(((........))-)....)))). ( -30.60)
>DroYak_CAF1 183975 96 - 1
CAGAGAGCAAAGCAAGGCAGAGAGGAACGCUUGGGCAGCGGAACAGUUGAUAGCUCAAUUGG---CGCUGCACGAAAAUCGCUGAGAAUCG-A--GGGGGUG
..((...(..(((.((((..........))))..((((((...(((((((....))))))).---)))))).........)))..)..)).-.--....... ( -24.70)
>DroAna_CAF1 186127 74 - 1
-------------------GAGCGAAACGAAUGGCUAAUGGAACAGUUGAUAGCUCAAUUCG---AAAUGC--GGGGGUGGGUGAAAGUG--C--GGAGCGA
-------------------..............(((.......((.((....(((((.((((---.....)--)))..)))))..)).))--.--..))).. ( -10.70)
>consensus
GAGAGAGCG__ACAG_GCGGAGAGAAACGCUUGGGCAGCGGAACAGUUGAUAGCUCAAUUGG___CGCUGCCCGAAAAUCGUUGAGAAUCG_A__GGGGGUG
..............................((((((((((...(((((((....)))))))....))))))))))........................... (-16.92 = -18.12 +   1.20)

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 10:13:59 2006