Locus 896

Sequence ID 2R_DroMel_CAF1
Location 4,043,340 – 4,043,539
Length 199
Max. P 0.999821
window1565 window1566 window1567

overview

Window 5

Location 4,043,340 – 4,043,459
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.47
Mean single sequence MFE -45.48
Consensus MFE -40.30
Energy contribution -40.02
Covariance contribution -0.28
Combinations/Pair 1.09
Mean z-score -2.50
Structure conservation index 0.89
SVM decision value 3.54
SVM RNA-class probability 0.999368
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4043340 119 - 20766785
CAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUGGGCCAGUGUCAAAGACGGCGCUCGGCGCUUAUAUAUGACUUACUGAUGCUCCGCCUUU
...((((((((.((-.((((..(((((.((((((((..(....((....))....)..)))))(((((((((......)))))).))).....))).)).)))..)))).)))))))))) ( -48.50)
>DroSec_CAF1 26013 116 - 1
CAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUUGGCCAGUGUCAAAGACGGCGCUCGG---UUAUAUAUGACUUACUGAUGCUCCGCCUUU
...((((((((((.-.(((....)))...)))).(((((((((((....)..(((......(((((((((((......)))))).))---))).......))))))).)))))))))))) ( -46.42)
>DroSim_CAF1 28175 116 - 1
CAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUGGGCCAGUGUCAAAGACGGCGCUCGG---UUAUAUAUGACUUACUGAUGCUCCGCCUUU
...((((((((.((-.((((..(((((.((((((((..(....((....))....)..)))))(((((((((......)))))).))---)..))).)).)))..)))).)))))))))) ( -45.90)
>DroEre_CAF1 25142 116 - 1
CAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACGUUGGCAACAAGAGGAACGGGAGCCAGUGUCAAAGACGGCGCUCGG---UUAUAUAUGACUUACUGAUGCUCCGCCUUU
...((((((((((.-.(((....)))...)))).((((((..(((....)))(((.......((((((((((......)))))).))---))........))).....)))))))))))) ( -43.06)
>DroYak_CAF1 29082 117 - 1
AAAGAGGGCGGCAGGGGUCAAAGGGCAAGUGCCGGGGGCACAGUGGCAACAAAAGGAACGUAGGCCAGUGUCAAAGACGGCGCUCGG---UUAUAUAUGACUUGCUGAUGUUCCGCCUUU
...((((((((((...(((....)))...)))).(((((((((((....)..(((..(..((((((((((((......)))))).))---)).))..)..))))))).)))))))))))) ( -43.50)
>consensus
CAAGAGGGCGGCAG_GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUGGGCCAGUGUCAAAGACGGCGCUCGG___UUAUAUAUGACUUACUGAUGCUCCGCCUUU
...((((((((((...(((....)))...)))).(((((((((((....)..............((((((((......)))))).))................)))).)))))))))))) (-40.30 = -40.02 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,043,380 – 4,043,499
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.63
Mean single sequence MFE -50.50
Consensus MFE -45.44
Energy contribution -46.20
Covariance contribution 0.76
Combinations/Pair 1.08
Mean z-score -2.69
Structure conservation index 0.90
SVM decision value 4.16
SVM RNA-class probability 0.999821
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4043380 119 - 20766785
GCUGAUUUAUGGCACGGGCCCUGAGUUCGCCUCUCGUGGCCAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUGGGCCAGUGUCAAAGACGG
.(((.(((.((((((.(((((.(.((((((((((....(((.....)))((((.-.(((....)))...))))))))))....((....))....))))).))))).)))))).)))))) ( -52.90)
>DroSec_CAF1 26050 119 - 1
GCUGAUUUAUGGCACAGGCCCUGAGUUCGCCUCUCGUGGCCAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUUGGCCAGUGUCAAAGACGG
.(((.(((.((((((.((((..(.((((((((((....(((.....)))((((.-.(((....)))...))))))))))....((....))....)))))..)))).)))))).)))))) ( -48.80)
>DroSim_CAF1 28212 119 - 1
GCUGAUUUAUGGCACAGGCCCUGAGUUCGCCUCUCGUGGCCAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUGGGCCAGUGUCAAAGACGG
.(((.(((.((((((.(((((.(.((((((((((....(((.....)))((((.-.(((....)))...))))))))))....((....))....))))).))))).)))))).)))))) ( -52.20)
>DroEre_CAF1 25179 118 - 1
GCUGAUUUAUGGCACAGGCCCUG-GUUCGCCCCUCGUGGCCAAGAGGGCGGCAG-GGUCAAAGGGCAAAUGCCGGGGGCACGUUGGCAACAAGAGGAACGGGAGCCAGUGUCAAAGACGG
.(((.(((.((((((.(((.((.-((((((((((....(((.....)))((((.-.(((....)))...))))))))))...(((....)))...)))).)).))).)))))).)))))) ( -53.20)
>DroYak_CAF1 29119 120 - 1
GCUGAUUUAUGGCACAGGCUCUGGGCUUGCCUCUCGUGGAAAAGAGGGCGGCAGGGGUCAAAGGGCAAGUGCCGGGGGCACAGUGGCAACAAAAGGAACGUAGGCCAGUGUCAAAGACGG
.(((.(((.((((((.((((((..(((.(((.(((........))))))))).))))))....(((..(((((...)))))..((....))............))).)))))).)))))) ( -45.40)
>consensus
GCUGAUUUAUGGCACAGGCCCUGAGUUCGCCUCUCGUGGCCAAGAGGGCGGCAG_GGUCAAAGGGCAAAUGCCGGGGGCACAGUGGCAACAAAAGGAACCUGGGCCAGUGUCAAAGACGG
.(((.(((.((((((.(((((...((((((((((....(((.....)))((((...(((....)))...))))))))))....((....))....))))..))))).)))))).)))))) (-45.44 = -46.20 +   0.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,043,420 – 4,043,539
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.06
Mean single sequence MFE -38.39
Consensus MFE -35.96
Energy contribution -35.88
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -2.18
Structure conservation index 0.94
SVM decision value 3.49
SVM RNA-class probability 0.999290
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4043420 119 + 20766785
UGCCCCCGGCAUUUGCCCUUUGACC-CUGCCGCCCUCUUGGCCACGAGAGGCGAACUCAGGGCCCGUGCCAUAAAUCAGCUUUGUUGCAUUUAAGUCGGUGCAAACAAGCUCACAACAAU
.......(((((..(((((..((..-....((((.(((((....)))))))))...)))))))..))))).......(((((..(((((((......)))))))..)))))......... ( -39.10)
>DroSec_CAF1 26090 119 + 1
UGCCCCCGGCAUUUGCCCUUUGACC-CUGCCGCCCUCUUGGCCACGAGAGGCGAACUCAGGGCCUGUGCCAUAAAUCAGCUUUGUUGCAUUUAAGUCGGUGCAAACAAGCUCACAACAAU
.......(((((..(((((..((..-....((((.(((((....)))))))))...)))))))..))))).......(((((..(((((((......)))))))..)))))......... ( -40.00)
>DroSim_CAF1 28252 119 + 1
UGCCCCCGGCAUUUGCCCUUUGACC-CUGCCGCCCUCUUGGCCACGAGAGGCGAACUCAGGGCCUGUGCCAUAAAUCAGCUUUGUUGCAUUUAAGUCGGUGCAAACAAGCUCACAACAAU
.......(((((..(((((..((..-....((((.(((((....)))))))))...)))))))..))))).......(((((..(((((((......)))))))..)))))......... ( -40.00)
>DroEre_CAF1 25219 118 + 1
UGCCCCCGGCAUUUGCCCUUUGACC-CUGCCGCCCUCUUGGCCACGAGGGGCGAAC-CAGGGCCUGUGCCAUAAAUCAGCUUUGUUGCAUUUAAGUCGGUGCAAACAAGCUCACAACAAU
.......(((((..(((((......-....(((((.((((....)))))))))...-.)))))..))))).......(((((..(((((((......)))))))..)))))......... ( -41.04)
>DroYak_CAF1 29159 120 + 1
UGCCCCCGGCACUUGCCCUUUGACCCCUGCCGCCCUCUUUUCCACGAGAGGCAAGCCCAGAGCCUGUGCCAUAAAUCAGCUUUGUUGCAUUUAAGUCAGUGCAAACAAGCUCACAACAAU
.......(((((..((..((((..(..((((...(((........))).)))).)..))))))..))))).......(((((..(((((((......)))))))..)))))......... ( -31.80)
>consensus
UGCCCCCGGCAUUUGCCCUUUGACC_CUGCCGCCCUCUUGGCCACGAGAGGCGAACUCAGGGCCUGUGCCAUAAAUCAGCUUUGUUGCAUUUAAGUCGGUGCAAACAAGCUCACAACAAU
.......(((((..(((((..(........)(((.(((((....))))))))......)))))..))))).......(((((..(((((((......)))))))..)))))......... (-35.96 = -35.88 +  -0.08)

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 09:50:26 2006