Locus 2416

Sequence ID X_DroMel_CAF1
Location 6,463,129 – 6,463,263
Length 134
Max. P 0.946112
window3926 window3927 window3928 window3929

overview

Window 6

Location 6,463,129 – 6,463,228
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.80
Mean single sequence MFE -29.98
Consensus MFE -18.43
Energy contribution -18.83
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.61
SVM decision value 0.94
SVM RNA-class probability 0.886941
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6463129 99 + 22224390
CAGUUGCUCCAUCCGGUUGCAGUUGCAUGUUGCAUAC---------------------UGCAUAUGGCAGAUUGCACAUUGCACAUUACACGUUGCACGUUGCACAUAUGUUUGUAUGUU
((..(((.((....))..)))..))......((((((---------------------.(((((((((((..((((...((.......))...))))..)))).)))))))..)))))). ( -28.20)
>DroSec_CAF1 17506 120 + 1
CAGUUGCUCCAUCCGGUUGCAGUUGCAUGUUGCAUACUGCAUAUUGCAUACUGCAUACUGCAUAUGGCAGAUUGCACAUUGCACAUUACACGCUGCACGUUGCACAUAUGUUUGUACGUU
.............((..((((((((((...(((.....)))...)))).))))))(((.(((((((((((..((((....((.........))))))..)))).)))))))..))))).. ( -34.50)
>DroSim_CAF1 17988 113 + 1
CAGUUGCUCCAUCCGGUUGCAGUUGCAUGUUGCAUACUGCA-------UACUGCAUACUGCAUAUGGCAGAUUGCACAUUGCACAUUACACGCUGCACGUUGCACAUAUGUUUGUAUGUU
.............(((((((((((((.....))).))))))-------.))))(((((.(((((((((((..((((....((.........))))))..)))).)))))))..))))).. ( -35.30)
>DroEre_CAF1 16758 95 + 1
CAGUUGCUCCAUCCGGUUGCAGUUGCAUGUUGCAUACU--------------GCAUACUGCAUAUGGCAGAUUGCACAUUGCACAU-------UGCACGUUGCACAUAUGU----GUGUU
(((((...((((.(((((((((((((.....))).)))--------------))).))))...))))..)))))......((((((-------(((.....)))...))))----))... ( -28.40)
>DroYak_CAF1 17546 81 + 1
CAGUUGCUCCAUCCGGUUGCAGUUGCAUGUUGCAUAC---------------------UGCAAAUGGCAGAUUGCAC-------AU-------UACACGUUGCACAUAUGU----GUGUU
..((.((.....(((.((((((((((.....))).))---------------------))))).)))......))))-------..-------(((((((.......))))----))).. ( -23.50)
>consensus
CAGUUGCUCCAUCCGGUUGCAGUUGCAUGUUGCAUACU______________GCAUACUGCAUAUGGCAGAUUGCACAUUGCACAUUACACG_UGCACGUUGCACAUAUGUUUGUAUGUU
...((((.((....))..)))).(((.....))).........................(((((((((((..((((.................))))..)))).)))))))......... (-18.43 = -18.83 +   0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,463,129 – 6,463,228
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.80
Mean single sequence MFE -29.58
Consensus MFE -18.49
Energy contribution -19.28
Covariance contribution 0.79
Combinations/Pair 1.04
Mean z-score -2.29
Structure conservation index 0.63
SVM decision value 1.36
SVM RNA-class probability 0.946112
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6463129 99 - 22224390
AACAUACAAACAUAUGUGCAACGUGCAACGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCA---------------------GUAUGCAACAUGCAACUGCAACCGGAUGGAGCAACUG
..........((((((.(((...((((...(((.....)))...))))...)))))))))((---------------------((.(((....(((....))).((....)).))))))) ( -26.40)
>DroSec_CAF1 17506 120 - 1
AACGUACAAACAUAUGUGCAACGUGCAGCGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGCAGUAUGCAAUAUGCAGUAUGCAACAUGCAACUGCAACCGGAUGGAGCAACUG
..(((((...((((((.(((...((((...(((.....)))...))))...)))))))))..)))))((((.(((....((((((.(((.....))))))))).((....)).))))))) ( -38.30)
>DroSim_CAF1 17988 113 - 1
AACAUACAAACAUAUGUGCAACGUGCAGCGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGCAGUA-------UGCAGUAUGCAACAUGCAACUGCAACCGGAUGGAGCAACUG
..(((((...((((((.(((...((((...(((.....)))...))))...)))))))))..)))))((((.-------((((((.(((.....))))))))).((....))....)))) ( -34.70)
>DroEre_CAF1 16758 95 - 1
AACAC----ACAUAUGUGCAACGUGCA-------AUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGC--------------AGUAUGCAACAUGCAACUGCAACCGGAUGGAGCAACUG
....(----((((.((..((.......-------.))..))))))).....(((..(((.(.((.(((--------------(((.(((.....))))))))))).).)))..))).... ( -27.20)
>DroYak_CAF1 17546 81 - 1
AACAC----ACAUAUGUGCAACGUGUA-------AU-------GUGCAAUCUGCCAUUUGCA---------------------GUAUGCAACAUGCAACUGCAACCGGAUGGAGCAACUG
..(((----(.(((((.....))))).-------.)-------)))...((((((..(((((---------------------((.(((.....))))))))))..)).))))....... ( -21.30)
>consensus
AACAUACAAACAUAUGUGCAACGUGCA_CGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGC______________AGUAUGCAACAUGCAACUGCAACCGGAUGGAGCAACUG
..........((((((.(((...((((...(((.....)))...))))...))))))))).......................((.(((....(((....))).((....)).))))).. (-18.49 = -19.28 +   0.79)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,463,166 – 6,463,263
Length 97
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 78.44
Mean single sequence MFE -25.46
Consensus MFE -16.73
Energy contribution -17.37
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -1.83
Structure conservation index 0.66
SVM decision value 0.70
SVM RNA-class probability 0.825694
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6463166 97 + 22224390
------------------UGCAUAUGGCAGAUUGCACAUUGCACAUUACACGUUGCACGUUGCACAUAUGUUUGUAUGUUGCAAGGCUCAAGUGUUUAUAUGUGACUGCUUUUUU
------------------.......(((((...((.....))((((.((((.(((..(.((((((((((....))))).))))).)..)))))))....))))..)))))..... ( -26.10)
>DroSec_CAF1 17546 115 + 1
AUAUUGCAUACUGCAUACUGCAUAUGGCAGAUUGCACAUUGCACAUUACACGCUGCACGUUGCACAUAUGUUUGUACGUUGCAAGGCUCAAGUGUUUAUAUGUGACUGCUUUUCU
.....(((...((((..((((.....))))..)))).....(((((.((((..((..(.(((((...((((....))))))))).)..)).))))....)))))..)))...... ( -28.60)
>DroSim_CAF1 18028 108 + 1
A-------UACUGCAUACUGCAUAUGGCAGAUUGCACAUUGCACAUUACACGCUGCACGUUGCACAUAUGUUUGUAUGUUGCAAGGCUCAAGUGUUUAUAUGCGACUGCUUUUUU
.-------...((((..((((.....))))..))))..(((((.((.((((..((..(.((((((((((....))))).))))).)..)).))))..)).))))).......... ( -29.40)
>DroEre_CAF1 16796 92 + 1
------------GCAUACUGCAUAUGGCAGAUUGCACAUUGCACAU-------UGCACGUUGCACAUAUGU----GUGUUGCAAGGCUCAAGUGUUUAUAUGUGACUGCUUUUUU
------------(((..((((.....))))....(((((.((((.(-------((..(.((((((((....----))).))))).)..)))))))....)))))..)))...... ( -26.20)
>DroYak_CAF1 17583 77 + 1
------------------UGCAAAUGGCAGAUUGCAC-------AU-------UACACGUUGCACAUAUGU----GUGUUGCAAGGCUCAAGUGUUUAUAUGUUUCU--UUUUUU
------------------.(((..((((...(((((.-------..-------(((((((.......))))----))).))))).)).))..)))............--...... ( -17.00)
>consensus
____________GCAUACUGCAUAUGGCAGAUUGCACAUUGCACAUUACACG_UGCACGUUGCACAUAUGUUUGUAUGUUGCAAGGCUCAAGUGUUUAUAUGUGACUGCUUUUUU
...................(((((((((((..((((.................))))..)))).)))))))......((((((((((......))))...))))))......... (-16.73 = -17.37 +   0.64)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,463,166 – 6,463,263
Length 97
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 78.44
Mean single sequence MFE -23.12
Consensus MFE -12.37
Energy contribution -13.16
Covariance contribution 0.79
Combinations/Pair 1.06
Mean z-score -2.16
Structure conservation index 0.54
SVM decision value 0.96
SVM RNA-class probability 0.889872
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6463166 97 - 22224390
AAAAAAGCAGUCACAUAUAAACACUUGAGCCUUGCAACAUACAAACAUAUGUGCAACGUGCAACGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCA------------------
......((((.(((((....(((((((.((.(((((.((((......))))))))).)).))).)))).)))))).(((.((.....))))).))).------------------ ( -24.70)
>DroSec_CAF1 17546 115 - 1
AGAAAAGCAGUCACAUAUAAACACUUGAGCCUUGCAACGUACAAACAUAUGUGCAACGUGCAGCGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGCAGUAUGCAAUAU
......((((.(((((....(((((((.((.(((((.((((......))))))))).)).))).)))).))))))....((((..((((.....))))..))))...)))..... ( -30.00)
>DroSim_CAF1 18028 108 - 1
AAAAAAGCAGUCGCAUAUAAACACUUGAGCCUUGCAACAUACAAACAUAUGUGCAACGUGCAGCGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGCAGUA-------U
......(((...((((((..(((((((.((.(((((.((((......))))))))).)).))).)))).))))))..)))(((..((((.....))))..)))....-------. ( -30.10)
>DroEre_CAF1 16796 92 - 1
AAAAAAGCAGUCACAUAUAAACACUUGAGCCUUGCAACAC----ACAUAUGUGCAACGUGCA-------AUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGC------------
......((((.(((((....(((.(((.((.(((((.((.----.....))))))).)).))-------))))...))))))...((((.....))))..)))------------ ( -19.80)
>DroYak_CAF1 17583 77 - 1
AAAAAA--AGAAACAUAUAAACACUUGAGCCUUGCAACAC----ACAUAUGUGCAACGUGUA-------AU-------GUGCAAUCUGCCAUUUGCA------------------
......--............(((.(((.((.(((((.((.----.....))))))).)).))-------))-------))((((........)))).------------------ ( -11.00)
>consensus
AAAAAAGCAGUCACAUAUAAACACUUGAGCCUUGCAACAUACAAACAUAUGUGCAACGUGCA_CGUGUAAUGUGCAAUGUGCAAUCUGCCAUAUGCAGUAUGC____________
.............................................((((((.(((...((((...(((.....)))...))))...))))))))).................... (-12.37 = -13.16 +   0.79)

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 10:33:57 2006