Locus 119

Sequence ID 3R_DroMel_CAF1
Location 672,388 – 672,506
Length 118
Max. P 0.875216
window193 window194 window195

overview

Window 3

Location 672,388 – 672,492
Length 104
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 83.49
Mean single sequence MFE -31.55
Consensus MFE -23.70
Energy contribution -23.98
Covariance contribution 0.28
Combinations/Pair 1.30
Mean z-score -2.07
Structure conservation index 0.75
SVM decision value 0.40
SVM RNA-class probability 0.720527
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 672388 104 + 27905053
GACCGAUGCUUGCCGCUAUCUCAAAGGGCUGAUCUCCUGGCGUCGCCUGGGGACCAGCUUAAUUUGAUUUUAUUGAUAACAAAUUAUGACUCGCGGCACUGCAG-
......(((.((((((....(((((.(((((.(((((.(((...))).))))).)))))...))))).....(((....)))..........))))))..))).- ( -36.60)
>DroPse_CAF1 93021 104 + 1
-UCCGUUGUCUACCGCUAUCUCAAAGGGUUCAUCUCCAGGCGUCGCCUAGAGACGAAUUUAAUUUAAUUUUAUUGAUUACAAAUGAUGUCUCGAGACAAGACAAC
-...(((((((.........(((..((((((.((((.((((...)))).)))).))))))....(((((.....)))))....)))((((....))))))))))) ( -26.20)
>DroSec_CAF1 91753 104 + 1
GACCGAUGCAUGCCGCUAUCUCAAAGGGCUGAUCUCCUGGCGUCGCCUGGGGACCAACUUAAUUUGAUUUUAUUGAUAACAAAUUAUGCCUCGCGGCACUGCAG-
......((((((((((.........((((((.(((((.(((...))).))))).))...(((((((.((........))))))))).)))).)))))).)))).- ( -32.60)
>DroSim_CAF1 89464 104 + 1
GACCGAUGCAUGCCGCUAUCUCAAAGGGCUGAUCUCCUGGCGUCGCCUGGGGACCAACUUAAUUUGAUUUUAUUGAUAACAAAUUAUGCCUCGCGGCACUGCAG-
......((((((((((.........((((((.(((((.(((...))).))))).))...(((((((.((........))))))))).)))).)))))).)))).- ( -32.60)
>DroAna_CAF1 91858 103 + 1
--UCGAUGUCUGCCGCUAUCACAAAGAGCUCAUCGCCGGGCGUCACCUGGAGACGAGCUUAAUUUCAUUUUAUUGAUUACAAAUUAUGUCUCGCGGCCGGGCAAG
--....((((((((((....(((..((((((.((.(((((.....))))).)).))))))....(((......)))..........)))...)))).)))))).. ( -35.10)
>DroPer_CAF1 94064 104 + 1
-UCCGUUGUCUACCGCUAUCUCAAAGGGUUCAUCUCCAGGCGUCGCCUAGAGACGAAUUUAAUUUAAUUUUAUUGAUUACAAAUGAUGUCUCGAGACAAGACAAC
-...(((((((.........(((..((((((.((((.((((...)))).)))).))))))....(((((.....)))))....)))((((....))))))))))) ( -26.20)
>consensus
_ACCGAUGCCUGCCGCUAUCUCAAAGGGCUCAUCUCCUGGCGUCGCCUGGAGACCAACUUAAUUUGAUUUUAUUGAUAACAAAUUAUGUCUCGCGGCACGGCAA_
......((((((((((.........((((((.(((((.(((...))).))))).))))))............(((....)))..........)))))).)))).. (-23.70 = -23.98 +   0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 672,388 – 672,492
Length 104
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 83.49
Mean single sequence MFE -35.45
Consensus MFE -26.30
Energy contribution -25.22
Covariance contribution -1.08
Combinations/Pair 1.32
Mean z-score -2.98
Structure conservation index 0.74
SVM decision value 0.89
SVM RNA-class probability 0.875216
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 672388 104 - 27905053
-CUGCAGUGCCGCGAGUCAUAAUUUGUUAUCAAUAAAAUCAAAUUAAGCUGGUCCCCAGGCGACGCCAGGAGAUCAGCCCUUUGAGAUAGCGGCAAGCAUCGGUC
-.(((..((((((..(((.(((((((.............))))))).(((((((.((.(((...))).)).))))))).......))).)))))).)))...... ( -36.52)
>DroPse_CAF1 93021 104 - 1
GUUGUCUUGUCUCGAGACAUCAUUUGUAAUCAAUAAAAUUAAAUUAAAUUCGUCUCUAGGCGACGCCUGGAGAUGAACCCUUUGAGAUAGCGGUAGACAACGGA-
(((((((((((((((((((.....))).....................(((((((((((((...)))))))))))))...))))))))).....)))))))...- ( -36.90)
>DroSec_CAF1 91753 104 - 1
-CUGCAGUGCCGCGAGGCAUAAUUUGUUAUCAAUAAAAUCAAAUUAAGUUGGUCCCCAGGCGACGCCAGGAGAUCAGCCCUUUGAGAUAGCGGCAUGCAUCGGUC
-.((((.((((((((((((.....)))).)).......(((((....(((((((.((.(((...))).)).)))))))..)))))....))))))))))...... ( -35.40)
>DroSim_CAF1 89464 104 - 1
-CUGCAGUGCCGCGAGGCAUAAUUUGUUAUCAAUAAAAUCAAAUUAAGUUGGUCCCCAGGCGACGCCAGGAGAUCAGCCCUUUGAGAUAGCGGCAUGCAUCGGUC
-.((((.((((((((((((.....)))).)).......(((((....(((((((.((.(((...))).)).)))))))..)))))....))))))))))...... ( -35.40)
>DroAna_CAF1 91858 103 - 1
CUUGCCCGGCCGCGAGACAUAAUUUGUAAUCAAUAAAAUGAAAUUAAGCUCGUCUCCAGGUGACGCCCGGCGAUGAGCUCUUUGUGAUAGCGGCAGACAUCGA--
........(((((....(((((.......(((......))).....((((((((.((.((.....)).)).))))))))..)))))...))))).........-- ( -31.60)
>DroPer_CAF1 94064 104 - 1
GUUGUCUUGUCUCGAGACAUCAUUUGUAAUCAAUAAAAUUAAAUUAAAUUCGUCUCUAGGCGACGCCUGGAGAUGAACCCUUUGAGAUAGCGGUAGACAACGGA-
(((((((((((((((((((.....))).....................(((((((((((((...)))))))))))))...))))))))).....)))))))...- ( -36.90)
>consensus
_CUGCAGUGCCGCGAGACAUAAUUUGUAAUCAAUAAAAUCAAAUUAAGUUCGUCCCCAGGCGACGCCAGGAGAUCAGCCCUUUGAGAUAGCGGCAGACAUCGGU_
..((((.((((((((..((.....))...)).......(((((....(((((((.((.(((...))).)).)))))))..)))))....))))))))))...... (-26.30 = -25.22 +  -1.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 672,413 – 672,506
Length 93
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.02
Mean single sequence MFE -31.21
Consensus MFE -19.52
Energy contribution -18.83
Covariance contribution -0.69
Combinations/Pair 1.33
Mean z-score -2.26
Structure conservation index 0.63
SVM decision value 0.13
SVM RNA-class probability 0.599031
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 672413 93 - 27905053
UUG--------------AUGCCGCUUCG----CUGCAGUGCCGCGAGUCAUAAUUUGUUAUCAAUAAAAUCAAAUUAAGCUGGUCCCCAGGCGACGCCAGGAGAUCAGCCC
.((--------------((..(((..((----(....)))..))).))))(((((((.............))))))).(((((((.((.(((...))).)).))))))).. ( -28.72)
>DroSec_CAF1 91778 93 - 1
CUG--------------AUGCCGCUUCG----CUGCAGUGCCGCGAGGCAUAAUUUGUUAUCAAUAAAAUCAAAUUAAGUUGGUCCCCAGGCGACGCCAGGAGAUCAGCCC
...--------------.....((((((----(.((...)).))))))).(((((((.............))))))).(((((((.((.(((...))).)).))))))).. ( -30.52)
>DroSim_CAF1 89489 93 - 1
CUA--------------AUGCCGCUUCG----CUGCAGUGCCGCGAGGCAUAAUUUGUUAUCAAUAAAAUCAAAUUAAGUUGGUCCCCAGGCGACGCCAGGAGAUCAGCCC
...--------------.....((((((----(.((...)).))))))).(((((((.............))))))).(((((((.((.(((...))).)).))))))).. ( -30.52)
>DroEre_CAF1 88422 92 - 1
UUG--------------AUGCCGCUUCG----CCGCAGUGCCGCGAGACAUAAUUUGUUAUCAAUAAAAU-AAAUUAAGCCGGUCCCAAGGCGACGCCAGGAGAUCGGCCC
...--------------.....(..(((----(.((...)).))))..).(((((((((........)))-)))))).(((((((((..(((...))).)).))))))).. ( -27.80)
>DroYak_CAF1 100557 92 - 1
UUG--------------AUGCAGCUUCG----CUGCAGUGCCGCAAGACAUAAUUUGUUAUCAAUAAAAU-AAAUUAAGCUGGUCCCAAGGCGACGCCAGGGGAUCAGCCC
...--------------.((((((...)----)))))(((.(....).)))((((((((........)))-)))))..(((((((((..(((...)))..))))))))).. ( -34.80)
>DroAna_CAF1 91881 111 - 1
UUUUGUUCGUUUUCGUUAUGCAGUUAUGGCUCUUGCCCGGCCGCGAGACAUAAUUUGUAAUCAAUAAAAUGAAAUUAAGCUCGUCUCCAGGUGACGCCCGGCGAUGAGCUC
.....((((((((.((((((.(((((((..((((((......)))))))))))))))))))....))))))))....((((((((.((.((.....)).)).)))))))). ( -34.90)
>consensus
UUG______________AUGCCGCUUCG____CUGCAGUGCCGCGAGACAUAAUUUGUUAUCAAUAAAAUCAAAUUAAGCUGGUCCCCAGGCGACGCCAGGAGAUCAGCCC
..................(((.((...............)).))).((((.....))))...................(((((((.((.(((...))).)).))))))).. (-19.52 = -18.83 +  -0.69)

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 09:33:40 2006