Locus 1079

Sequence ID 3R_DroMel_CAF1
Location 3,302,411 – 3,302,611
Length 200
Max. P 0.916202
window1746 window1747 window1748

overview

Window 6

Location 3,302,411 – 3,302,531
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.33
Mean single sequence MFE -24.71
Consensus MFE -20.46
Energy contribution -20.10
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -1.86
Structure conservation index 0.83
SVM decision value 1.11
SVM RNA-class probability 0.916202
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3302411 120 + 27905053
AAAGUGAACCAAAUAAUUCGCCACUAAUUUGAUUCUAAAUGUUAAAUGCACUAAUACGAAUUAGGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUU
...(((((........)))))..................((((....((.(((((....)))))))..))))..(((((((......(((.((....)).)))......))))))).... ( -23.00)
>DroSec_CAF1 6583 120 + 1
AAAGUGAAUCAAAUAAUUCGCCACUAAUUUGAUUCUAAAUGUUAAAUGCACUAAUACGAAUUAAGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUU
.....(((((((((............)))))))))....((((....((..((((....)))).))..))))..(((((((......(((.((....)).)))......))))))).... ( -22.50)
>DroSim_CAF1 4931 120 + 1
AAAGUGAAUCAAAUAAUUCGCCACUAAUUUGAUUCUAAAUGUUAAAUGCACUAAUACGAAUUAAGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUU
.....(((((((((............)))))))))....((((....((..((((....)))).))..))))..(((((((......(((.((....)).)))......))))))).... ( -22.50)
>DroEre_CAF1 3617 120 + 1
AAAGUGAACUAGAUAAUUCGCCACUAAUUUGAUUCUAAAUGUUAAAUGCACUAAAACGAAUUAAGCGGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGGCACAAUU
((((((((.....(((((((......(((((((.......))))))).........)))))))(((..(((.....))).)))))))))))......((((((.....))))))...... ( -26.16)
>DroYak_CAF1 9327 120 + 1
ACAGCGAACUAAAUAAUUCGCCACUAAUUUGAUUCUAAAUGUUAAAUGCACUAAUACGAAUUAAGCGGGACAAACUGUCAGGUUUCAUUUGGCAAAAGCCAGAGCUAAUCUGGCACAAUU
...(((((........)))))..((..((((((((....(((((.......))))).))))))))..))......(((((((((...((((((....))))))...)))))))))..... ( -29.40)
>consensus
AAAGUGAACCAAAUAAUUCGCCACUAAUUUGAUUCUAAAUGUUAAAUGCACUAAUACGAAUUAAGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUU
...(((((........)))))..((..((((((((....(((.....))).......))))))))..)).....(((((((.((...(((.((....)).)))...)).))))))).... (-20.46 = -20.10 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,302,451 – 3,302,571
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.99
Mean single sequence MFE -29.56
Consensus MFE -21.26
Energy contribution -23.26
Covariance contribution 2.00
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.72
SVM decision value 0.72
SVM RNA-class probability 0.833546
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3302451 120 + 27905053
GUUAAAUGCACUAAUACGAAUUAGGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUUUUGCUGGUUUAUUUGUAUUUUUAGCGCCAUCAACUAGCAG
(((....((.(((((((((((.(((((((.(((((((((((......(((.((....)).)))......)))))))...)))))))))))))))))))...))).))....)))...... ( -32.90)
>DroSec_CAF1 6623 95 + 1
GUUAAAUGCACUAAUACGAAUUAAGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUUUCGCUGGUUUAUUUG-------------------------
................(((((.(((((((.....(((((((......(((.((....)).)))......))))))).......))))))))))))------------------------- ( -22.50)
>DroSim_CAF1 4971 120 + 1
GUUAAAUGCACUAAUACGAAUUAAGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUUUCGCUGGUUUAUUUGUAUAUUUAGCGCCAUCAACCAGCAG
(((....((.(((((((((((.(((((((.....(((((((......(((.((....)).)))......))))))).......)))))))))))))))...))).))....)))...... ( -30.50)
>DroEre_CAF1 3657 117 + 1
GUUAAAUGCACUAAAACGAAUUAAGCGGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGGCACAAUUUCGCAGGUUUAUUUGUAUUUUGAGCGCCAUCAACC---AG
((((((((((....((..((((..(((..((((((((........))))))).....((((((.....))))))....)..))).))))..)))))))))..)))..........---.. ( -26.20)
>DroYak_CAF1 9367 117 + 1
GUUAAAUGCACUAAUACGAAUUAAGCGGGACAAACUGUCAGGUUUCAUUUGGCAAAAGCCAGAGCUAAUCUGGCACAAUUUCGCUGGUUUAUUUGUAUUUUUAGCGCCAUCAACC---AG
(((....((.(((((((((((..((((..(.....(((((((((...((((((....))))))...)))))))))...)..)))).....))))))))...))).))....))).---.. ( -35.70)
>consensus
GUUAAAUGCACUAAUACGAAUUAAGCCGGACAAAGUGUCAGUUUUCAUUUUGCAAAAGCCAGAGCUAAUCUGACACAAUUUCGCUGGUUUAUUUGUAUUUUUAGCGCCAUCAACC___AG
.......((...(((((((((.(((((((.....(((((((.((...(((.((....)).)))...)).))))))).......))))))))))))))))....))............... (-21.26 = -23.26 +   2.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,302,491 – 3,302,611
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -30.39
Consensus MFE -27.13
Energy contribution -26.75
Covariance contribution -0.37
Combinations/Pair 1.10
Mean z-score -1.53
Structure conservation index 0.89
SVM decision value 0.25
SVM RNA-class probability 0.651403
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3302491 120 - 27905053
GCAUUCGGUUUAAUGCCGCGUGCCUAAGUAAAGUAAAAUGCUGCUAGUUGAUGGCGCUAAAAAUACAAAUAAACCAGCAAAAUUGUGUCAGAUUAGCUCUGGCUUUUGCAAAAUGAAAAC
((((.((((.....)))).)))).........((((((.((((((((((..((((((...........................)))))))))))))...)))))))))........... ( -28.93)
>DroSim_CAF1 5011 120 - 1
GCAUUCGGUUUAAUGCCGCGUGCCUAAGUAAAGUAAAAUGCUGCUGGUUGAUGGCGCUAAAUAUACAAAUAAACCAGCGAAAUUGUGUCAGAUUAGCUCUGGCUUUUGCAAAAUGAAAAC
((((.((((.....)))).))))....((((((...(((..((((((((..((............))....))))))))..)))..((((((.....))))))))))))........... ( -30.70)
>DroEre_CAF1 3697 117 - 1
GCAUUCGGUUUAAUGCGGCGUGCCUAAGUAAAGUAAAAUGCU---GGUUGAUGGCGCUCAAAAUACAAAUAAACCUGCGAAAUUGUGCCAGAUUAGCUCUGGCUUUUGCAAAAUGAAAAC
...(((((((((((...(.(((((.......(((.....)))---.......))))).)...)).....))))))(((((((....((((((.....)))))))))))))....)))... ( -29.34)
>DroYak_CAF1 9407 117 - 1
GCAUUCGGUUUAAUGCCGCGUGCCUAAGUAAAGUAGAAUGCU---GGUUGAUGGCGCUAAAAAUACAAAUAAACCAGCGAAAUUGUGCCAGAUUAGCUCUGGCUUUUGCCAAAUGAAACC
((((.((((.....)))).)))).........((((((((((---((((..((............))....)))))))).......((((((.....))))))))))))........... ( -32.60)
>consensus
GCAUUCGGUUUAAUGCCGCGUGCCUAAGUAAAGUAAAAUGCU___GGUUGAUGGCGCUAAAAAUACAAAUAAACCAGCGAAAUUGUGCCAGAUUAGCUCUGGCUUUUGCAAAAUGAAAAC
((((.((((.....)))).)))).........((((((.(((...((((((((((((...........................))))))..))))))..)))))))))........... (-27.13 = -26.75 +  -0.37)

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 10:00:04 2006