Locus 524

Sequence ID 3L_DroMel_CAF1
Location 1,550,787 – 1,550,978
Length 191
Max. P 0.980556
window784 window785 window786

overview

Window 4

Location 1,550,787 – 1,550,901
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.42
Mean single sequence MFE -54.12
Consensus MFE -43.86
Energy contribution -44.25
Covariance contribution 0.39
Combinations/Pair 1.12
Mean z-score -2.91
Structure conservation index 0.81
SVM decision value 1.25
SVM RNA-class probability 0.935810
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1550787 114 + 23771897
CGGUGGUGAAUCCUCCAAACGGAGGUAUCCUGCCGCCUCU---GGGAACGGGC---GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUAGGCAUCA
.(((((.((..(((((....))))).....((((((((..---(....)))))---)))))).))))).((((.(((....)))))))(((.((((((........)))))).))).... ( -54.20)
>DroPse_CAF1 10316 111 + 1
AG---------CAGCCAAGUGGUGGAAUACUGCCGCCUCUUCCGGCAGUCGGCAAUGGGAUCUCCACCAGCCAGCGGCCCUAUGUGGCGCCGAGGCUGCGCAACAAUGGCCUUGGCAUCA
..---------..((((.((((.((...(((((((.......))))))).(((..(((........)))))).....)))))).))))(((((((((..........))))))))).... ( -47.20)
>DroSec_CAF1 8463 114 + 1
CGGUGGUGUCUCCUCCCAACGGAGGUAUCCUGCCGCCUCU---GGGAACGGGC---GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCA
.((..(.(...(((((....)))))...))..))(((.(.---((((...(((---(((......))).)))....))))...).)))((((((((((........)))))))))).... ( -58.10)
>DroSim_CAF1 8581 114 + 1
CGGUGGUGUCUCCUCCCAACGGAGGUAUCCUGCCGCCUCU---GGGAACGGGC---GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCA
.((..(.(...(((((....)))))...))..))(((.(.---((((...(((---(((......))).)))....))))...).)))((((((((((........)))))))))).... ( -58.10)
>DroYak_CAF1 9146 114 + 1
CGGUGGUGACUCCUCCGAACGGAGGUAUCCUGCCGCCUCU---GGGAACGGGC---GGAAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGGAACAACGGCCUGGGCAUCA
.(((((.((.(((((((..(((((((........))))))---)....)))).---))).)).))))).((((.(((....)))))))((((((((((........)))))))))).... ( -59.90)
>DroPer_CAF1 10002 111 + 1
AG---------CAGCCAAGUGGUGGAAUACUGCCGCCUCUUCCGGCAGUCGGCAAUGGGAUCUCCACCAGCCAGCGGCCCUAUGUGGCGCCGAGGCUGCGCAACAAUGGCCUUGGCAUCA
..---------..((((.((((.((...(((((((.......))))))).(((..(((........)))))).....)))))).))))(((((((((..........))))))))).... ( -47.20)
>consensus
CGGUGGUG_CUCCUCCAAACGGAGGUAUCCUGCCGCCUCU___GGGAACGGGC___GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCA
.(((((.....(((((....)))))....)))))(((.(....(((....(((...((........)).)))....)))....).)))((((((((((........)))))))))).... (-43.86 = -44.25 +   0.39)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,550,827 – 1,550,940
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.54
Mean single sequence MFE -48.64
Consensus MFE -35.21
Energy contribution -36.68
Covariance contribution 1.47
Combinations/Pair 1.12
Mean z-score -1.35
Structure conservation index 0.72
SVM decision value 0.41
SVM RNA-class probability 0.726364
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1550827 113 + 23771897
---GGGAACGGGC---GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUAGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAU-UCAGAUUCCCG
---((((((((((---(((......)))..((.(.((.....((.(((((((((((((........))))))..((....)).)))))))))..)).).)))))))..-.....))))). ( -48.31)
>DroPse_CAF1 10347 102 + 1
UCCGGCAGUCGGCAAUGGGAUCUCCACCAGCCAGCGGCCCUAUGUGGCGCCGAGGCUGCGCAACAAUGGCCUUGGCAUCAGUCGGGGAC---------------CGGUGUCACCUUU---
....(((((((((..(((........))))))..((((((.....)).)))).))))))...(((.((((((((((....))))))).)---------------)).))).......--- ( -41.80)
>DroSec_CAF1 8503 113 + 1
---GGGAACGGGC---GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAU-UCAGAUUCCCG
---((((((((((---(((......))).((..(((.((((...((..((((((((((........))))))))))..))..)))))))...)).......)))))..-.....))))). ( -54.41)
>DroSim_CAF1 8621 113 + 1
---GGGAACGGGC---GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAU-UCAGAUUCCCG
---((((((((((---(((......))).((..(((.((((...((..((((((((((........))))))))))..))..)))))))...)).......)))))..-.....))))). ( -54.41)
>DroYak_CAF1 9186 113 + 1
---GGGAACGGGC---GGAAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGGAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGUCCGAU-UCAGAUUCCCG
---((((((((((---((.....))....((..(((.((((...((..((((((((((........))))))))))..))..)))))))...)).......)))))..-.....))))). ( -51.11)
>DroPer_CAF1 10033 102 + 1
UCCGGCAGUCGGCAAUGGGAUCUCCACCAGCCAGCGGCCCUAUGUGGCGCCGAGGCUGCGCAACAAUGGCCUUGGCAUCAGUCGGGGAC---------------CGGUGUCACCUUU---
....(((((((((..(((........))))))..((((((.....)).)))).))))))...(((.((((((((((....))))))).)---------------)).))).......--- ( -41.80)
>consensus
___GGGAACGGGC___GGUAUCUCCACCAGCCAGCGUCCCUAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAU_UCAGAUUCCCG
...(((((..(((...((........)).)))..((.((((...((..((((((((((........))))))))))..))..)))).((((........)))).))........))))). (-35.21 = -36.68 +   1.47)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,550,861 – 1,550,978
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 95.24
Mean single sequence MFE -51.60
Consensus MFE -48.55
Energy contribution -48.92
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -2.45
Structure conservation index 0.94
SVM decision value 1.86
SVM RNA-class probability 0.980556
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1550861 117 + 23771897
UAUGUGGCGCCCAGGCUGCGAAACAACGGCCUAGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAUUCAGAUUCCCGGGCAACCUGGCCUCGUGGGUAACAACAAUCCACAGCAG
..((.(((((((((((((........))))))..((....)).)))))))))((...(((((((((...........)))))...))))....((((((.......)))))).)).. ( -49.00)
>DroSec_CAF1 8537 114 + 1
UAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAUUCAGAUUCCCGGGCAACCUGGCCUCGUGGGUAA---CAAUCCACAGCAG
..((((((((((((((((........)))))))))).....((((((.....)).......(((((...........)))))..)))))))..((((((..---..)))))).))). ( -52.30)
>DroSim_CAF1 8655 114 + 1
UAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAUUCAGAUUCCCGGGCAACCUGGCCUCGUGGGUAA---CAAUCCACAGCAG
..((((((((((((((((........)))))))))).....((((((.....)).......(((((...........)))))..)))))))..((((((..---..)))))).))). ( -52.30)
>DroYak_CAF1 9220 114 + 1
UAUGUGGCGCCCAGGCUGCGGAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGUCCGAUUCAGAUUCCCGGGCAACCUGGCCUCGUGGGAAA---CAACCCCCCACAG
...(.(((((((((((((........)))))))))).....((((..((((.(.....)(((..(......)...)))))))..))))))).)(((((...---......))))).. ( -52.80)
>consensus
UAUGUGGCGCCCAGGCUGCGAAACAACGGCCUGGGCAUCAGCAGGGCGCCCAGCACUCCGGGCCCGAUUCAGAUUCCCGGGCAACCUGGCCUCGUGGGUAA___CAAUCCACAGCAG
..((((((((((((((((........)))))))))).....((((..((((.(.....)(((..(......)...)))))))..)))))))..((((((.......)))))).))). (-48.55 = -48.92 +   0.38)

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 09:44:14 2006