Locus 360

Sequence ID 2L_DroMel_CAF1
Location 1,126,937 – 1,127,056
Length 119
Max. P 0.655428
window567 window568

overview

Window 7

Location 1,126,937 – 1,127,056
Length 119
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.79
Mean single sequence MFE -29.88
Consensus MFE -20.85
Energy contribution -21.85
Covariance contribution 1.00
Combinations/Pair 1.20
Mean z-score -1.23
Structure conservation index 0.70
SVM decision value 0.12
SVM RNA-class probability 0.595480
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1126937 119 + 22407834
AUGAACCGUGAGACCGUGUAGCUCUGGCAGACGAAGCUGAUUGCAAAUCGUCUGAUGCAAUAUGCUAAUCAUUCGCAAAUGUGCGAGCUAAGCGCAAUAGUUCGCAACUGACCAACUUU
..(((((....)..(((.((((((...(((((((.((.....))...)))))))..(((...(((.........)))....))))))))).))).....))))................ ( -32.70)
>DroSec_CAF1 13551 99 + 1
GUGAA------------------CUGGCAGACGAAGCUGAUUGCAAAUCGUCUGAUGCAAUAUGCGAAUCAUUCGCAAAUGUGCGAGCUAAGCGCA--AGUUUGCAACUGACCAACUUU
.....------------------.((((((((((.((.....))...))))))).(((((..((((.....((((((....)))))).....))))--...))))).....)))..... ( -30.90)
>DroSim_CAF1 13384 101 + 1
GUGAG------------------CUGGCAGACGAAGCUGAUUGCAAAUCGUCUGAUGCAAUAUGCUAAUCAUUCGCAAAUGUGCGAGCUAAGCGCAAUAGUUUGCAACUGGCCAACUUU
((..(------------------(..((((((((.((.....))...))))))).(((((...((((.....(((((....)))))((.....))..))))))))).)..))..))... ( -31.10)
>DroEre_CAF1 13987 117 + 1
GUGAAC--UGAGACUGUGUAGCUCUGGCAGACGAAGCUGAUUGCAAAUCGUCUGAUGCAAUAUGCUAAUCAUUCGCAAAUGUGCGAGCUAAGCGCAAUAGUUUGCAACUGGCCAACUUU
(..(((--((....((((((((((...(((((((.((.....))...)))))))..(((...(((.........)))....))))))))..))))).)))))..).............. ( -34.70)
>DroYak_CAF1 14245 117 + 1
GUGAAC--UGAGACUGUGUAGCUCUGGCAGACGAAGCCGAUUGCAAAUCGUCUGAUGCAAUAUGCUAAUCAUUCGCAAAUGUGCGAGCUAAGCGCAAUAGUUUGCAACCGGCCAACUUU
(..(((--((....((((((((((...(((((((.((.....))...)))))))..(((...(((.........)))....))))))))..))))).)))))..).............. ( -33.50)
>DroAna_CAF1 14157 101 + 1
GUGAAA--UGG-AACGCGUAACUCUAGCAGACGAAGCUGAUUGCAAACAGUCUGAUGCAAUAUGCUAAUCGAUCGCAAAUAUGUAGACGAAGCUAAAUACUUUU---------------
(((...--...-..)))(((....((((......(((..((((((..........))))))..)))..(((.(((((....))).))))).))))..)))....--------------- ( -16.40)
>consensus
GUGAAC__UGA_AC_GUGUAGCUCUGGCAGACGAAGCUGAUUGCAAAUCGUCUGAUGCAAUAUGCUAAUCAUUCGCAAAUGUGCGAGCUAAGCGCAAUAGUUUGCAACUGGCCAACUUU
(((((......................(((((((.((.....))...)))))))..((.....))......))))).....(((((((((.......)))))))))............. (-20.85 = -21.85 +   1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,126,937 – 1,127,056
Length 119
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.79
Mean single sequence MFE -29.63
Consensus MFE -18.67
Energy contribution -20.42
Covariance contribution 1.75
Combinations/Pair 1.15
Mean z-score -1.59
Structure conservation index 0.63
SVM decision value 0.26
SVM RNA-class probability 0.655428
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1126937 119 - 22407834
AAAGUUGGUCAGUUGCGAACUAUUGCGCUUAGCUCGCACAUUUGCGAAUGAUUAGCAUAUUGCAUCAGACGAUUUGCAAUCAGCUUCGUCUGCCAGAGCUACACGGUCUCACGGUUCAU
...((((((((.(((((((....((((.......))))..))))))).)))))))).........(((((((...((.....)).)))))))...((((....((......)))))).. ( -33.10)
>DroSec_CAF1 13551 99 - 1
AAAGUUGGUCAGUUGCAAACU--UGCGCUUAGCUCGCACAUUUGCGAAUGAUUCGCAUAUUGCAUCAGACGAUUUGCAAUCAGCUUCGUCUGCCAG------------------UUCAC
...((..((((.(((((((..--((((.......))))..))))))).))))..))..((((...(((((((...((.....)).))))))).)))------------------).... ( -30.00)
>DroSim_CAF1 13384 101 - 1
AAAGUUGGCCAGUUGCAAACUAUUGCGCUUAGCUCGCACAUUUGCGAAUGAUUAGCAUAUUGCAUCAGACGAUUUGCAAUCAGCUUCGUCUGCCAG------------------CUCAC
..(((((((..(.(((((.....(((..(((..(((((....))))).)))...)))..))))).)((((((...((.....)).)))))))))))------------------))... ( -33.10)
>DroEre_CAF1 13987 117 - 1
AAAGUUGGCCAGUUGCAAACUAUUGCGCUUAGCUCGCACAUUUGCGAAUGAUUAGCAUAUUGCAUCAGACGAUUUGCAAUCAGCUUCGUCUGCCAGAGCUACACAGUCUCA--GUUCAC
.....((((..(.(((((.....(((..(((..(((((....))))).)))...)))..))))).)((((((...((.....)).))))))))))(((((..........)--)))).. ( -31.80)
>DroYak_CAF1 14245 117 - 1
AAAGUUGGCCGGUUGCAAACUAUUGCGCUUAGCUCGCACAUUUGCGAAUGAUUAGCAUAUUGCAUCAGACGAUUUGCAAUCGGCUUCGUCUGCCAGAGCUACACAGUCUCA--GUUCAC
..((..(((((((((((((.....((.....))(((((....))))).((((..((.....)))))).....)))))))))))))....))....(((((..........)--)))).. ( -32.30)
>DroAna_CAF1 14157 101 - 1
---------------AAAAGUAUUUAGCUUCGUCUACAUAUUUGCGAUCGAUUAGCAUAUUGCAUCAGACUGUUUGCAAUCAGCUUCGUCUGCUAGAGUUACGCGUU-CCA--UUUCAC
---------------....(((((((((.((((..........))))..(((.(((..((((((..........))))))..)))..))).))))))..))).....-...--...... ( -17.50)
>consensus
AAAGUUGGCCAGUUGCAAACUAUUGCGCUUAGCUCGCACAUUUGCGAAUGAUUAGCAUAUUGCAUCAGACGAUUUGCAAUCAGCUUCGUCUGCCAGAGCUACAC_GU_UCA__GUUCAC
....(((((..(.(((((.....(((.......(((((....))))).......)))..))))).)((((((...((.....)).)))))))))))....................... (-18.67 = -20.42 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:54 2006