Locus 7332

Sequence ID 2L_DroMel_CAF1
Location 20,476,971 – 20,477,165
Length 194
Max. P 0.995660
window11759 window11760 window11761

overview

Window 9

Location 20,476,971 – 20,477,091
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.41
Mean single sequence MFE -44.74
Consensus MFE -34.17
Energy contribution -36.13
Covariance contribution 1.96
Combinations/Pair 1.03
Mean z-score -3.21
Structure conservation index 0.76
SVM decision value 2.60
SVM RNA-class probability 0.995660
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20476971 120 + 22407834
GCUGCUCUGUUUAUAUUUGCUGCUCCCUGCGCGGCGCGGCGGUUGGUGGGGGGAGUCUUGAAAGUCGUAAAAGUAAACAGAGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAG
((((((((((((((.(((((..(((((..(.((((......)))))..))))).(.((....)).)))))).)))))))))))).))(((((((((((....))).))))))))...... ( -53.20)
>DroSec_CAF1 29981 116 + 1
GCUGCUCUGUUUAUAUUUGCUGCUCCCUGCGCGUUGAAGGGGU----UGGGGGAGUCUUGAAAAACGUAAAAGUAAACAGAGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAG
((((((((((((((.(((((.(((((((((.(.......).))----..))))))).((....)).))))).)))))))))))).))(((((((((((....))).))))))))...... ( -47.70)
>DroSim_CAF1 33758 116 + 1
GCUGCUCUGUUUAUAUUUGCUGCUCCCUGCGCGUUGAAGGGUU----GGGGGGAGUCUUGAAAGUCGUAAAAGUAAACAGAGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAG
((((((((((((((.(((((..(((((.((.(......).)).----)))))..(.((....)).)))))).)))))))))))).))(((((((((((....))).))))))))...... ( -48.80)
>DroEre_CAF1 32101 99 + 1
GCUGCUCCGUUUAUG-----CGCUCCCUGCGCGGCG-----------G-GGAAAGUCUUGAAAGUCGUAAAAGUAAACAGAGCAUGUGGUGUACUCCAU----GGCAGUGUGCCGUAAAG
(((((((.((((((.-----.(((((((((...)))-----------)-)))..(.((....)).)))....)))))).))))).))((..(((((...----.).))))..))...... ( -33.10)
>DroYak_CAF1 29190 105 + 1
GCUGCUCUGUUUAUAUUUGCCGCUCCCUGCGCGGCG-----------GGGGAAAGUCUUGAAAGUCGUAAAAGUAAACAGAGCAUGUGGUGUACUCCAU----GGCAGUGUGCCGUAAAG
((((((((((((((.(((((.(((((((((...)))-----------)))............))).))))).)))))))))))).))((..(((((...----.).))))..))...... ( -40.90)
>consensus
GCUGCUCUGUUUAUAUUUGCUGCUCCCUGCGCGGCG__G_G_U____GGGGGGAGUCUUGAAAGUCGUAAAAGUAAACAGAGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAG
((((((((((((((.(((((.(((((((.(.................).)))))))...(.....)))))).)))))))))))).))((((((((((......)).))))))))...... (-34.17 = -36.13 +   1.96)

alignment

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secondary structure

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Window 0

Location 20,476,971 – 20,477,091
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.41
Mean single sequence MFE -30.20
Consensus MFE -23.84
Energy contribution -23.60
Covariance contribution -0.24
Combinations/Pair 1.12
Mean z-score -1.91
Structure conservation index 0.79
SVM decision value 0.78
SVM RNA-class probability 0.849396
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20476971 120 - 22407834
CUUUACGGCGCACUGCCAUCCAUGGAGUACACCACAUGCUCUGUUUACUUUUACGACUUUCAAGACUCCCCCCACCAACCGCCGCGCCGCGCAGGGAGCAGCAAAUAUAAACAGAGCAGC
......((.(.(((.(((....)))))).).))...(((((((((((..(((.((.....)..(.(((((.........(((......)))..)))))).).)))..))))))))))).. ( -31.10)
>DroSec_CAF1 29981 116 - 1
CUUUACGGCGCACUGCCAUCCAUGGAGUACACCACAUGCUCUGUUUACUUUUACGUUUUUCAAGACUCCCCCA----ACCCCUUCAACGCGCAGGGAGCAGCAAAUAUAAACAGAGCAGC
......((.(.(((.(((....)))))).).))...(((((((((((..(((.(((((....)))).......----..((((.(.....).))))....).)))..))))))))))).. ( -29.50)
>DroSim_CAF1 33758 116 - 1
CUUUACGGCGCACUGCCAUCCAUGGAGUACACCACAUGCUCUGUUUACUUUUACGACUUUCAAGACUCCCCCC----AACCCUUCAACGCGCAGGGAGCAGCAAAUAUAAACAGAGCAGC
......((.(.(((.(((....)))))).).))...(((((((((((..(((.((.....)..(.(((((...----................)))))).).)))..))))))))))).. ( -29.21)
>DroEre_CAF1 32101 99 - 1
CUUUACGGCACACUGCC----AUGGAGUACACCACAUGCUCUGUUUACUUUUACGACUUUCAAGACUUUCC-C-----------CGCCGCGCAGGGAGCG-----CAUAAACGGAGCAGC
(((((.(((.....)))----.))))).........(((((((((((.......(.....)..(.(.((((-(-----------.((...)).))))).)-----).))))))))))).. ( -28.20)
>DroYak_CAF1 29190 105 - 1
CUUUACGGCACACUGCC----AUGGAGUACACCACAUGCUCUGUUUACUUUUACGACUUUCAAGACUUUCCCC-----------CGCCGCGCAGGGAGCGGCAAAUAUAAACAGAGCAGC
(((((.(((.....)))----.))))).........(((((((((((..(((..(.....)............-----------.(((((.......))))))))..))))))))))).. ( -33.00)
>consensus
CUUUACGGCGCACUGCCAUCCAUGGAGUACACCACAUGCUCUGUUUACUUUUACGACUUUCAAGACUCCCCCC____A_C_C__CGCCGCGCAGGGAGCAGCAAAUAUAAACAGAGCAGC
......((.(.(((.((......))))).).))...(((((((((((.......(.....)..(.(((((.......................))))))........))))))))))).. (-23.84 = -23.60 +  -0.24)

alignment

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secondary structure

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Window 1

Location 20,477,051 – 20,477,165
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.06
Mean single sequence MFE -41.10
Consensus MFE -31.00
Energy contribution -31.12
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.595132
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20477051 114 + 22407834
AGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAGCGCUUAAUUUUUUGU-----UGCCCUUCGCUGGCUCCAAUUUGAAGGAAGGUGAGAAAUAUGGCGCUCUGGCUGCCC-UG
.(((...(((((((((((....))).))))))))((..((((((..((((((..(-----(..((((((.((....))...))))))..))..))))))..))))))...)))))..-.. ( -41.80)
>DroSec_CAF1 30057 113 + 1
AGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAGCGCUUAAUUUUUUGU-----UGCCCUUCGCCGGCUCCAAUUUGG-GGAAGGUGAGAAAUAUGGCGCUCUGGCUGCCC-UG
..((((..(....)..))))...((((((((((((((..(((..(((....))).-----)))..((((((..((((.....))-))..))))))...))))))))....)))))).-.. ( -42.00)
>DroSim_CAF1 33834 113 + 1
AGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAGCGCUUAAUUUUUUGU-----UGCCCUUCGCCGGCUCCAAUUUGG-GGAAGGUGAGAAAUAUGGCGCUCUGGCUGCCC-UG
..((((..(....)..))))...((((((((((((((..(((..(((....))).-----)))..((((((..((((.....))-))..))))))...))))))))....)))))).-.. ( -42.00)
>DroEre_CAF1 32164 110 + 1
AGCAUGUGGUGUACUCCAU----GGCAGUGUGCCGUAAAGCGCUUAAUUUUUUGU-----UGCCCUUCGCUGGCUCCAAUUUGG-GGAAGGUGAGAAAAAUGGCGCACUGGCUGCCACCG
.(((.((((......))))----(.(((((((((((...(((..(((....))).-----)))..((((((..((((.....))-))..))))))....))))))))))).))))..... ( -39.70)
>DroYak_CAF1 29259 109 + 1
AGCAUGUGGUGUACUCCAU----GGCAGUGUGCCGUAAAGCGCUUAAUUUUUUGUUGCCU------UCGCUGGCUCCAAUUUGG-GGAAGGUGAGAAAUAUGGCGCUCUGGCUGCCGCCG
.((..((((......))))----((((((((((((((..(((..(((....))).))).(------(((((..((((.....))-))..))))))...))))))))....)))))))).. ( -40.00)
>consensus
AGCAUGUGGUGUACUCCAUGGAUGGCAGUGCGCCGUAAAGCGCUUAAUUUUUUGU_____UGCCCUUCGCUGGCUCCAAUUUGG_GGAAGGUGAGAAAUAUGGCGCUCUGGCUGCCC_UG
.(((...((((((((((......)).))))))))((..((((((..(((((...............(((((..((((.....)).))..))))))))))..))))))...)))))..... (-31.00 = -31.12 +   0.12)

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 12:33:54 2006