Locus 6095

Sequence ID 2R_DroMel_CAF1
Location 19,171,041 – 19,171,225
Length 184
Max. P 0.999895
window9763 window9764 window9765 window9766

overview

Window 3

Location 19,171,041 – 19,171,145
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.95
Mean single sequence MFE -34.31
Consensus MFE -28.18
Energy contribution -29.25
Covariance contribution 1.06
Combinations/Pair 1.07
Mean z-score -2.79
Structure conservation index 0.82
SVM decision value 2.49
SVM RNA-class probability 0.994599
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19171041 104 - 20766785
AGUGUGACCUUGCUCUUAAAGUAAGGUCCAAAUUAUUUUGCGAGCUAAGGUCACGCUUAUUUUGAGCU----------------AAGUUCCUCCCACAUUUUUCUCCGUGCAGCAUUCGA
(((((((((((((((.((((((((........)))))))).)))).)))))))))))......(((..----------------((((.........))))..))).............. ( -29.20)
>DroSec_CAF1 54848 104 - 1
AGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAGUUUGCCAGCUAAGGUCACGCCUAUCUUGAGCU----------------AAGUUGCUCCUACAUUUUUCUCCGUGCAGCAUCCGA
.(((((((((((((..((((.(((........))).))))..))).))))))))))............----------------..(((((..................)))))...... ( -29.37)
>DroEre_CAF1 62423 120 - 1
AGUGUGACCUUGCUCUUAAAGUAGGGUCCAAAUUAUUUCGCGAGCUAAGGUCACGCUUAGCUUGAGCUAAGGCACUCGCCUUUUAAGUUGCUUGUACAUUUUUCUCCGUGCAGCAUUCGA
(((((((((((((((...((((((........))))))...)))).))))))))))).(((((((...(((((....))))))))))))(((.((((..........)))))))...... ( -40.80)
>DroYak_CAF1 61917 120 - 1
AGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAUUUUGCGUGCUAUGGUCACGCUUAGCUUGAGCUGAGGCAUUUGCCUUCAAAGUUGCUCCUACUUUUUUCUCCGUGCAGCAUCCGA
.((((((((..((.(.((((((((........)))))))).).))...))))))))(((((....)))))(((....)))......(((((..................)))))...... ( -37.87)
>consensus
AGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAUUUUGCGAGCUAAGGUCACGCUUAGCUUGAGCU________________AAGUUGCUCCUACAUUUUUCUCCGUGCAGCAUCCGA
.((((((((((((((.((((((((........)))))))).)))).))))))))))..............................(((((..................)))))...... (-28.18 = -29.25 +   1.06)

alignment

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secondary structure

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Window 4

Location 19,171,077 – 19,171,185
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.25
Mean single sequence MFE -32.13
Consensus MFE -21.65
Energy contribution -24.15
Covariance contribution 2.50
Combinations/Pair 1.12
Mean z-score -1.61
Structure conservation index 0.67
SVM decision value 0.10
SVM RNA-class probability 0.585719
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19171077 108 + 20766785
------------AGCUCAAAAUAAGCGUGACCUUAGCUCGCAAAAUAAUUUGGACCUUACUUUAAGAGCAAGGUCACACUGCAUAUAGAUUAAAGUGCCUGUGCAAAGGAUUGGAGUUUG
------------(((((......((.((((((((.((((..(((.(((........))).)))..)))))))))))).))(((((..............))))).........))))).. ( -27.74)
>DroSec_CAF1 54884 95 + 1
------------AGCUCAAGAUAGGCGUGACCUUAGCUGGCAAACUAAUUUGGACCUUACUUUGAGAGCAAGGUCACACUGCACCUAGAUUAAAGGGCCUG-------------AGUUUG
------------((((((.....(((((((((((.(((..((((.(((........))).))))..)))))))))))......(((.......))))))))-------------)))).. ( -30.40)
>DroEre_CAF1 62463 120 + 1
GGCGAGUGCCUUAGCUCAAGCUAAGCGUGACCUUAGCUCGCGAAAUAAUUUGGACCCUACUUUAAGAGCAAGGUCACACUGCAGCUAGCCUAAAGGGCCUAUGCAAGGGAUUGGAGUUUG
..(.(((.((((.((...((((.((.((((((((.((((..(((.((..........)).)))..)))))))))))).))..)))).(((.....)))....)))))).))).)...... ( -38.50)
>DroYak_CAF1 61957 120 + 1
GGCAAAUGCCUCAGCUCAAGCUAAGCGUGACCAUAGCACGCAAAAUAAUUUGGACCUUACUUUGAGAGCAAGGUCACACUGCAGCCAGCUUAAAGGACCUAAGCAAAGGAUUGGAGUUUG
(((....)))..(((((..(((.((.((((((...((.(.((((.(((........))).)))).).))..)))))).))..)))..(((((.......))))).........))))).. ( -31.90)
>consensus
____________AGCUCAAGAUAAGCGUGACCUUAGCUCGCAAAAUAAUUUGGACCUUACUUUAAGAGCAAGGUCACACUGCAGCUAGAUUAAAGGGCCUAUGCAAAGGAUUGGAGUUUG
............(((((.((((.((.((((((((.((((.((((.(((........))).)))).)))))))))))).))..))))...........(((......)))....))))).. (-21.65 = -24.15 +   2.50)

alignment

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secondary structure

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Window 5

Location 19,171,077 – 19,171,185
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.25
Mean single sequence MFE -37.10
Consensus MFE -29.35
Energy contribution -30.23
Covariance contribution 0.87
Combinations/Pair 1.19
Mean z-score -3.59
Structure conservation index 0.79
SVM decision value 4.42
SVM RNA-class probability 0.999895
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19171077 108 - 20766785
CAAACUCCAAUCCUUUGCACAGGCACUUUAAUCUAUAUGCAGUGUGACCUUGCUCUUAAAGUAAGGUCCAAAUUAUUUUGCGAGCUAAGGUCACGCUUAUUUUGAGCU------------
................((.((((((..(......)..)))(((((((((((((((.((((((((........)))))))).)))).)))))))))))....))).)).------------ ( -32.70)
>DroSec_CAF1 54884 95 - 1
CAAACU-------------CAGGCCCUUUAAUCUAGGUGCAGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAGUUUGCCAGCUAAGGUCACGCCUAUCUUGAGCU------------
....((-------------((((((((.......))).)).(((((((((((((..((((.(((........))).))))..))).)))))))))).....)))))..------------ ( -32.80)
>DroEre_CAF1 62463 120 - 1
CAAACUCCAAUCCCUUGCAUAGGCCCUUUAGGCUAGCUGCAGUGUGACCUUGCUCUUAAAGUAGGGUCCAAAUUAUUUCGCGAGCUAAGGUCACGCUUAGCUUGAGCUAAGGCACUCGCC
............((((((...((((.....))))(((((.(((((((((((((((...((((((........))))))...)))).))))))))))))))))...)).))))........ ( -41.40)
>DroYak_CAF1 61957 120 - 1
CAAACUCCAAUCCUUUGCUUAGGUCCUUUAAGCUGGCUGCAGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAUUUUGCGUGCUAUGGUCACGCUUAGCUUGAGCUGAGGCAUUUGCC
.......(((.((((.((((((((....((((((((((..((..((((((((((.....)))))))))((((....)))).)..))..))))).))))))))))))).))))...))).. ( -41.50)
>consensus
CAAACUCCAAUCCUUUGCACAGGCCCUUUAAGCUAGCUGCAGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAUUUUGCGAGCUAAGGUCACGCUUAGCUUGAGCU____________
..............................(((((((((.(((((((((((((((.((((((((........)))))))).)))).))))))))))))))))..))))............ (-29.35 = -30.23 +   0.87)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,171,105 – 19,171,225
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.30
Mean single sequence MFE -27.00
Consensus MFE -16.58
Energy contribution -16.77
Covariance contribution 0.19
Combinations/Pair 1.18
Mean z-score -2.12
Structure conservation index 0.61
SVM decision value 1.02
SVM RNA-class probability 0.902264
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19171105 120 - 20766785
AGUUGAAUUUGAAAUGAUUAAAGGCUAACUUUUGCCAUGCCAAACUCCAAUCCUUUGCACAGGCACUUUAAUCUAUAUGCAGUGUGACCUUGCUCUUAAAGUAAGGUCCAAAUUAUUUUG
.....((((((....((((((((((........))).((((......(((....)))....)))).)))))))............(((((((((.....)))))))))))))))...... ( -28.80)
>DroSec_CAF1 54912 100 - 1
CUUUGCAUUUUAAAUGAUUAAAUGAU-------UUCAUGCCAAACU-------------CAGGCCCUUUAAUCUAGGUGCAGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAGUUUG
..((((((((.....(((((((((..-------..)))(((.....-------------..)))...)))))).))))))))((.(((((((((.....))))))))))).......... ( -26.70)
>DroEre_CAF1 62503 118 - 1
CUUUGAAUUUUAAAUGAUUC-AG-CUUUUUUUAUCCAUGCCAAACUCCAAUCCCUUGCAUAGGCCCUUUAGGCUAGCUGCAGUGUGACCUUGCUCUUAAAGUAGGGUCCAAAUUAUUUCG
...........(((((((((-((-((..........((((................)))).((((.....)))))))))...((.(((((((((.....))))))))))))))))))).. ( -26.19)
>DroYak_CAF1 61997 119 - 1
CUUUGAAUUUUAAAUGCUUAAAG-CUUUUUUCGUCCAAGCCAAACUCCAAUCCUUUGCUUAGGUCCUUUAAGCUGGCUGCAGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAUUUUG
..............(((....((-(((.....(.((((((.(((.........))))))).)).)....)))))....))).((.(((((((((.....))))))))))).......... ( -26.30)
>consensus
CUUUGAAUUUUAAAUGAUUAAAG_CUUUUUUU_UCCAUGCCAAACUCCAAUCCUUUGCACAGGCCCUUUAAGCUAGCUGCAGUGUGACCUUGCUCUCAAAGUAAGGUCCAAAUUAUUUUG
...............((((((((...............(((....................))).)))))))).........((.(((((((((.....))))))))))).......... (-16.58 = -16.77 +   0.19)

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 12:02:43 2006