Locus 5839

Sequence ID X_DroMel_CAF1
Location 15,101,711 – 15,101,886
Length 175
Max. P 0.733616
window9472 window9473 window9474

overview

Window 2

Location 15,101,711 – 15,101,812
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.18
Mean single sequence MFE -36.35
Consensus MFE -11.44
Energy contribution -12.11
Covariance contribution 0.67
Combinations/Pair 1.19
Mean z-score -3.14
Structure conservation index 0.31
SVM decision value 0.43
SVM RNA-class probability 0.733616
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15101711 101 + 22224390
GGAAUACGGCCGUCUUUGU--------CUGCAU-UAAUGCAUAUGCAUGA--GACUUAAGCGACGGCCACGCCUCGAAGUUGGU--------AGUGGGUACCGACUACCCACUACCAAAU
((.....(((((((...((--------((((((-........))))...)--)))......)))))))...))......(((((--------((((((((.....))))))))))))).. ( -42.30)
>DroSec_CAF1 14527 102 + 1
GGAAUACGGCCGUCUUUGU--------CUGCAU-UAAUGCAUAUGCAUGAGAGACUUAAGCG-UGGCCACGCCUCGCAGUUGGU--------AGUGGGUACCGACUACCCACUACCAAAU
((.......))((((((..--------.(((((-........)))))..))))))....(((-.(((...))).)))..(((((--------((((((((.....))))))))))))).. ( -41.10)
>DroSim_CAF1 18819 95 + 1
GGAAUACGGCCGUCUUUGU--------CUGCAU-UAAUGCAUAUGCAUGAGAGACUUAAGCG-UGGCCACGCCUCGCAG---------------UGGGUACCGACUACCCACUACCAAAU
((.........((((((..--------.(((((-........)))))..))))))....(((-.(((...))).)))((---------------((((((.....)))))))).)).... ( -32.50)
>DroEre_CAF1 22274 100 + 1
GGAAUACGGCCGUCUUUGU--------CUGCAU-UAAUGCAUAUGCAUGA--GACUUAAGCG-CGGCCACGCCUCGAAGUUGGU--------AGUUGGAAGCGACUACCCACUACCAAAU
((.....(((((((((.((--------((((((-........))))...)--)))..))).)-))))).........(((.(((--------(((((....)))))))).))).)).... ( -37.20)
>DroYak_CAF1 19641 116 + 1
GGAAUACGGCCUUCUUUGUCUGCUUGUCUGCAU-UAAUGCAUAUGCAUGA--GACUUAAGCG-CGGCCACGCCUCGAAGUUGGUAGUUUGGUAGUUGGAAACGACUACCCACUACCAAAU
((.....((((..(((.((((((......))..-..((((....)))).)--)))..)))..-.))))...))......((((((((..((((((((....)))))))).)))))))).. ( -43.90)
>DroPer_CAF1 55746 86 + 1
-GCAUCCCAC--UCUUCUU--------CUGUGUGUUAUGCAUAUGCAUGA--GUCUUAAGCA-GGGCCACACCUCGAGGUGG-------------------C-GCCACCCAAUACCAAAU
-((....(((--.(.....--------..).)))((((((....))))))--.......)).-(((((((........))))-------------------)-.)).............. ( -21.10)
>consensus
GGAAUACGGCCGUCUUUGU________CUGCAU_UAAUGCAUAUGCAUGA__GACUUAAGCG_CGGCCACGCCUCGAAGUUGGU________AGUGGGUACCGACUACCCACUACCAAAU
((.....((((.................(((((...)))))...((.(((.....))).))...)))).........(((((...................)))))........)).... (-11.44 = -12.11 +   0.67)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,101,742 – 15,101,852
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.30
Mean single sequence MFE -37.75
Consensus MFE -15.73
Energy contribution -16.29
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.55
Structure conservation index 0.42
SVM decision value -0.05
SVM RNA-class probability 0.508954
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15101742 110 - 22224390
GCAAGCCCAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCACU--------ACCAACUUCGAGGCGUGGCCGUCGCUUAAGUC--UCAUGCAUAU
(((.((....))((((((((........))))))))((....(((((((((((((.....))))))))--------)))))..))(((((..(((....)))...)))--)).))).... ( -45.80)
>DroSec_CAF1 14558 110 - 1
-GUGGUGGGUGCGACGUUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCACU--------ACCAACUGCGAGGCGUGGCCA-CGCUUAAGUCUCUCAUGCAUAU
-((((((((...(((...((((((((.....)))).......(((((((((((((.....))))))))--------))))).))))((((((....)-)))))..))).))))).))).. ( -40.20)
>DroSim_CAF1 18850 103 - 1
-CAAACCCAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCA---------------CUGCGAGGCGUGGCCA-CGCUUAAGUCUCUCAUGCAUAU
-((((......(((((((((........)))))))))....))))((((((((((.....))))))---------------))))(((((..(((..-.)))...))))).......... ( -36.50)
>DroEre_CAF1 22305 101 - 1
--------GGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGCUUCCAACU--------ACCAACUUCGAGGCGUGGCCG-CGCUUAAGUC--UCAUGCAUAU
--------..((((((((((........))))))))((....(((((((((((........))).)))--------)))))..))(((((..(((..-.)))...)))--))..)).... ( -33.40)
>DroYak_CAF1 19680 115 - 1
GCAAA--CAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGUUUCCAACUACCAAACUACCAACUUCGAGGCGUGGCCG-CGCUUAAGUC--UCAUGCAUAU
(((..--.((((((((((((........))))))))((....((((((((.((((((........))))))..))))))))..)).((((((....)-)))))..)))--)..))).... ( -40.80)
>DroPer_CAF1 55775 95 - 1
CCAAG--CAAGCGAAGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAUUGGGUGGC-G-------------------CCACCUCGAGGUGUGGCCC-UGCUUAAGAC--UCAUGCAUAU
....(--(((((...))))))....((((((((.((((....))))....((((.((-(-------------------((.......))))).))))-.)))))))).--.......... ( -29.80)
>consensus
_CAAG__CAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCACU________ACCAACUUCGAGGCGUGGCCG_CGCUUAAGUC__UCAUGCAUAU
.........(((.((((((.(.((((.....))))((((.((((......)))).))))..........................))))))).)))...((.............)).... (-15.73 = -16.29 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,101,780 – 15,101,886
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 64.01
Mean single sequence MFE -30.58
Consensus MFE -9.29
Energy contribution -9.32
Covariance contribution 0.03
Combinations/Pair 1.11
Mean z-score -1.80
Structure conservation index 0.30
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15101780 106 - 22224390
---AAAACAGAC---GGGGGGUGAGUGCGAGGUUGGGUUGGCAAGCCCAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCACU--------ACCA
---......(((---(.((((((..((((((..((((((....))))))(....).)))))).))))))...)))).......((((((((((((.....))))))))--------)))) ( -42.70)
>DroSec_CAF1 14597 86 - 1
---AAAACGGAU---GGGGUG--------------------GUGGUGGGUGCGACGUUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCACU--------ACCA
---.........---....((--------------------((((((((((((((...(((..((((((((((.......)))))).)))).)))))).)))))))))--------)))) ( -29.80)
>DroSim_CAF1 18888 80 - 1
---AAAGCGGAU---GGGGGG--------------------CAAACCCAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCA--------------
---....(((((---.(((..--------------------....)))...(((((((((........)))))))))...)))))....((((((.....))))))-------------- ( -24.30)
>DroEre_CAF1 22342 89 - 1
---CAAGUGGGG---GAGGGG----UGCAG----GGCGG---------GGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGCUUCCAACU--------ACCA
---..(((..((---(((((.----(((..----.((.(---------((.(((((((((........)))))))))....))).)).....))).)).))))).)))--------.... ( -27.10)
>DroYak_CAF1 19717 108 - 1
-GACAGGGGGUGUA-GAGGGG----UAGAG----GGAUUGGCAAA--CAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGUUUCCAACUACCAAACUACCA
-.............-....((----(((..----...........--....(((((((((........)))))))))....((((((((((((........))).)))))))))))))). ( -32.30)
>DroPer_CAF1 55812 90 - 1
AGACAGUGGCAGUGGCAGUGG----CAGGG----GCAGUGCCAAG--CAAGCGAAGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAUUGGGUGGC-G-------------------CC
.......(((..(((((.((.----(...)----.)).))))).(--(((((...))))))..((((...(((..(((....)))..))).))))..-)-------------------)) ( -27.30)
>consensus
___AAAGCGGAG___GAGGGG____U___G____GG__U__CAAG__CAGGCGACGCUUGCAACAUUUUAAGUGUCGAUAAUUUGGUAGUGGGUAGUCGGUACCCACU________ACCA
...................................................(((((((((........)))))))))........................................... ( -9.29 =  -9.32 +   0.03)

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 11:57:35 2006