Locus 4483

Sequence ID 3L_DroMel_CAF1
Location 12,973,279 – 12,973,508
Length 229
Max. P 0.906086
window6995 window6996 window6997

overview

Window 5

Location 12,973,279 – 12,973,390
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.35
Mean single sequence MFE -35.42
Consensus MFE -33.90
Energy contribution -33.66
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -1.14
Structure conservation index 0.96
SVM decision value 0.38
SVM RNA-class probability 0.713923
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12973279 111 + 23771897
AAACCGAAGGAUAGUCGGACAUACCGCCGGCGGUUUUGCUCUGAAGUGCGCUUUAAUAGUUGGCUGUCUGCAGCUGG---------CGCAGCUGGGAAAUCGGAAAAGCGAAAAAGCGAA
...((((.(((((((((..((.((((....))))..))..)(((((....)))))......)))))))).((((((.---------..)))))).....))))....((......))... ( -35.40)
>DroSec_CAF1 90663 103 + 1
AAACCGAAGGAUAGUCGGACAUACCGCCGGCGGUUUUGCUCUGAAGUGCGCUUUAAUAGUUGGCUGUCUGCAGCUGG---------CGCAGCUGGGAAAUCGGAAAAG--------CGAA
...((((.(((((((((..((.((((....))))..))..)(((((....)))))......)))))))).((((((.---------..)))))).....)))).....--------.... ( -33.30)
>DroSim_CAF1 100356 103 + 1
AAACCGAAGGAUAGUCGGACAUACCGCCGGCGGUUUUGCUCUGAAGUGCGCUUUAAUAGUUGGCUGUCUGCAGCUGG---------CGCAGCUGGGAAAUCGGAAAAG--------CGAA
...((((.(((((((((..((.((((....))))..))..)(((((....)))))......)))))))).((((((.---------..)))))).....)))).....--------.... ( -33.30)
>DroEre_CAF1 96034 112 + 1
AAACCGAAGGAUAGUCAGACAUACCGCCGGCGGUUUUGCUCUGAAGUGCGCUUUAAUAGUUGGCUGUCUGCAGCUGCCGCAGCUGCCGCAGCUGGGAAAUCGGAAAAG--------CGAA
...((((.(((((((((((((.((((....))))..)).))(((((....))))).....))))))))).(((((((.((....)).))))))).....)))).....--------.... ( -41.70)
>DroYak_CAF1 94598 103 + 1
AAACCGAAGGAUAGUCAGACAUACCGCCGGCGGUUUUGCUCUGAAGUGCGCUUUAAUAGUUGGCUGUCUGCAGCUGC---------CGCAGCUGGGAAAUCGGAAAAG--------CGCA
...((((.(((((((((((((.((((....))))..)).))(((((....))))).....))))))))).((((((.---------..)))))).....)))).....--------.... ( -33.40)
>consensus
AAACCGAAGGAUAGUCGGACAUACCGCCGGCGGUUUUGCUCUGAAGUGCGCUUUAAUAGUUGGCUGUCUGCAGCUGG_________CGCAGCUGGGAAAUCGGAAAAG________CGAA
...((((.(((((((((((((.((((....))))..)).))(((((....))))).....))))))))).((((((............)))))).....))))................. (-33.90 = -33.66 +  -0.24)

alignment

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secondary structure

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Window 6

Location 12,973,356 – 12,973,469
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.02
Mean single sequence MFE -33.31
Consensus MFE -27.20
Energy contribution -27.44
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.30
Structure conservation index 0.82
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12973356 113 + 23771897
------CGCAGCUGGGAAAUCGGAAAAGCGAAAAAGCGAAA-AGCAACAGCACCGUGGCUGCGGCAUUUGAAUGUGGCGUGUCGGCAGGCCAGAGUGCUGUUUAAUAAAAUGGUGGGGAA
------(((..((((....))))....))).....((....-.))((((((((..(((((((.((((....)))).))((....)).)))))..)))))))).................. ( -33.40)
>DroSec_CAF1 90740 105 + 1
------CGCAGCUGGGAAAUCGGAAAAG--------CGAAA-AGCAACAGCACCGUGGCUGCGGCAUUUGAAUGUGGCGUGUCGGCAGGCCAGAGUGCUGUUUAAUAAAAUGGUGGGGCA
------.((.(((..............(--------(....-.))((((((((..(((((((.((((....)))).))((....)).)))))..)))))))).........)))...)). ( -32.70)
>DroSim_CAF1 100433 105 + 1
------CGCAGCUGGGAAAUCGGAAAAG--------CGAAA-AGCAACAGCACCGUGGCUGCGGCAUUUGAAUGUGGCGUGUCGGCAGGCCAGAGUGCUGUUUAAUAAAAUGGUGGGGCA
------.((.(((..............(--------(....-.))((((((((..(((((((.((((....)))).))((....)).)))))..)))))))).........)))...)). ( -32.70)
>DroEre_CAF1 96114 108 + 1
AGCUGCCGCAGCUGGGAAAUCGGAAAAG--------CGAAAAUGCAACAGCACCGU----GCGGCAUUUGAAUGUGGCGUGUCGGCAGACCAGAGUGCUGUUUAAUAAAAUGGUGGGGCA
.(((.((((..((((....))))....(--------(......))(((((((((..----((.((((....)))).))(.(((....)))).).))))))))..........))))))). ( -32.50)
>DroYak_CAF1 94675 106 + 1
------CGCAGCUGGGAAAUCGGAAAAG--------CGCAAAUGCAACAGCACCGUGGCUGCGGCAUUUGAAUGUGGCGUGUCGGCAGGCCAAAGUGCUGUUUAAUAAAAUGGUGGGGCA
------.((.((((........(((.((--------(((((((((..((((......))))..)))))).....((((.((....)).))))..))))).))).......))))...)). ( -35.26)
>consensus
______CGCAGCUGGGAAAUCGGAAAAG________CGAAA_AGCAACAGCACCGUGGCUGCGGCAUUUGAAUGUGGCGUGUCGGCAGGCCAGAGUGCUGUUUAAUAAAAUGGUGGGGCA
.......((..((((....))))...........................((((((....(((((((((.....((((.((....)).)))))))))))))........))))))..)). (-27.20 = -27.44 +   0.24)

alignment

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secondary structure

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Window 7

Location 12,973,390 – 12,973,508
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.47
Mean single sequence MFE -31.48
Consensus MFE -28.52
Energy contribution -29.32
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.91
SVM decision value 1.05
SVM RNA-class probability 0.906086
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12973390 118 - 23771897
CAGUUCGUGUUGCAGAUCCAAUGUGCCAUGACUUCUGUG-UUCCCCACCAUUUUAUUAAACAGCACUCUGGCCUGCCGACACGCCACAUUCAAAUGCCGCAGCCACGGUGCUGUUGCU-U
(((.(((((..(((.......)))..)))))...)))..-..................(((((((((.((((.(((.(.((.............))).))))))).)))))))))...-. ( -31.92)
>DroSec_CAF1 90766 118 - 1
CAGUUCGUGUUGCAGAUCCAAUGUGCCAUGACUUCUGUU-UGCCCCACCAUUUUAUUAAACAGCACUCUGGCCUGCCGACACGCCACAUUCAAAUGCCGCAGCCACGGUGCUGUUGCU-U
(((.(((((..(((.......)))..)))))...)))..-..................(((((((((.((((.(((.(.((.............))).))))))).)))))))))...-. ( -31.92)
>DroSim_CAF1 100459 118 - 1
CAGUUCGUGUUGCAGAUCCAAUGUGCCAUGACUUCUGUU-UGCCCCACCAUUUUAUUAAACAGCACUCUGGCCUGCCGACACGCCACAUUCAAAUGCCGCAGCCACGGUGCUGUUGCU-U
(((.(((((..(((.......)))..)))))...)))..-..................(((((((((.((((.(((.(.((.............))).))))))).)))))))))...-. ( -31.92)
>DroEre_CAF1 96146 116 - 1
CAGUUCGUGUUGCAGCUCCAAUGUGCCAUGACUUCUGUUUUGCCCCACCAUUUUAUUAAACAGCACUCUGGUCUGCCGACACGCCACAUUCAAAUGCCGC----ACGGUGCUGUUGCAUU
..((.((((((((((..(((..((((((.(((....))).))........(((....)))..))))..))).))).)))))))..)).....(((((.((----(......))).))))) ( -27.60)
>DroYak_CAF1 94701 119 - 1
CAGUUCGUGUUGCAGCUCCAAUGUGCCAUGACUUCUGUU-UGCCCCACCAUUUUAUUAAACAGCACUUUGGCCUGCCGACACGCCACAUUCAAAUGCCGCAGCCACGGUGCUGUUGCAUU
..((.((((((((((..((((.((((.........((((-((..............)))))))))).)))).))).)))))))..)).....(((((.(((((......))))).))))) ( -34.04)
>consensus
CAGUUCGUGUUGCAGAUCCAAUGUGCCAUGACUUCUGUU_UGCCCCACCAUUUUAUUAAACAGCACUCUGGCCUGCCGACACGCCACAUUCAAAUGCCGCAGCCACGGUGCUGUUGCU_U
(((.(((((..(((.......)))..)))))...))).....................(((((((((.((((.(((.(.((.............))).))))))).)))))))))..... (-28.52 = -29.32 +   0.80)

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 11:24:32 2006