Locus 887

Sequence ID 3R_DroMel_CAF1
Location 3,002,015 – 3,002,112
Length 97
Max. P 0.592637
window1406 window1407

overview

Window 6

Location 3,002,015 – 3,002,112
Length 97
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 79.42
Mean single sequence MFE -21.85
Consensus MFE -12.17
Energy contribution -13.50
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.56
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3002015 97 + 27905053
CCAUCGGGCACU-UUGAAUUUCAAUA-AUUGCUACACGCUUUUUUUUUUUUGCGUCUGUCCAAGUGUGACGUGUUCAUCAAACGUUGCACUCGGUUCUC
((...(((((..-(((.....)))..-........((((............)))).))))).((((..((((.........))))..)))).))..... ( -23.20)
>DroVir_CAF1 44181 84 + 1
CCAGCGUCUAAU------AUCCAUUA-AUUGCUACACGCCU------UUGUGCGUCAGGCCGAGUGUGACGUGUUCAUCAAACAUUGCACCCAAGCC--
..((((..((((------....))))-..))))....((..------..((((((((.((...)).))))(((((.....))))).))))....)).-- ( -17.90)
>DroSec_CAF1 48309 93 + 1
CCAUCGGGCACU-UUGAAUUUCAAUA-AUUGCUACACGCUUUU----UUUUGCGUCUGUCCAAGUGUGACGUGUUCAUCAAACGUUGCACUCGGUUCUC
((...(((((..-(((.....)))..-........((((....----....)))).))))).((((..((((.........))))..)))).))..... ( -24.30)
>DroSim_CAF1 48762 93 + 1
CCAUCGAGCACU-UUGAAUUUCAAUA-AUUGCAACACGCUUUU----UUUUGCGUCUGUCCAAGUGUGACGUGUUCAUCAAACGUUGCACUCGGUUCUC
.......(((..-(((.....)))..-..)))...((((....----....))))....((.((((..((((.........))))..)))).))..... ( -22.50)
>DroEre_CAF1 47601 91 + 1
CCGGCUGAUCAU-UUGAAUUUCAAUA-AUUGCUACACGCCU------UUUUGCGUUUGUCCGAGUGUGACGUGUUCAUCAAACGUUGCACUCGGUUCUC
..(((.(((...-(((.....)))..-))))))..((((..------....))))....(((((((..((((.........))))..)))))))..... ( -26.70)
>DroAna_CAF1 41293 90 + 1
---UCGUGCAAUUUAAAAUUUCAAUAAAUUUCUGCACGCUU------UUGUGCGUCUGUCCGACUGUGACGUGUUCAUCAAACAUUGCACUCCAUCUUG
---..(((((((.....................(((((...------.)))))((.((...(((........)))...)).)))))))))......... ( -16.50)
>consensus
CCAUCGGGCAAU_UUGAAUUUCAAUA_AUUGCUACACGCUU______UUUUGCGUCUGUCCAAGUGUGACGUGUUCAUCAAACGUUGCACUCGGUUCUC
...................................((((............))))....((.((((..((((.........))))..)))).))..... (-12.17 = -13.50 +   1.33) 

alignment

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secondary structure

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dotplot

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Window 7

Location 3,002,015 – 3,002,112
Length 97
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -21.83
Consensus MFE -15.04
Energy contribution -14.43
Covariance contribution -0.61
Combinations/Pair 1.31
Mean z-score -1.22
Structure conservation index 0.69
SVM decision value 0.12
SVM RNA-class probability 0.592637
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3002015 97 - 27905053
GAGAACCGAGUGCAACGUUUGAUGAACACGUCACACUUGGACAGACGCAAAAAAAAAAAAGCGUGUAGCAAU-UAUUGAAAUUCAA-AGUGCCCGAUGG
.....(((((((..((((.(.....).))))..)))))))..(.((((............)))).).(((..-..(((.....)))-..)))....... ( -19.90)
>DroVir_CAF1 44181 84 - 1
--GGCUUGGGUGCAAUGUUUGAUGAACACGUCACACUCGGCCUGACGCACAA------AGGCGUGUAGCAAU-UAAUGGAU------AUUAGACGCUGG
--((((.(((((.......(((((....))))))))))))))..((((....------..)))).((((..(-((((....------)))))..)))). ( -20.91)
>DroSec_CAF1 48309 93 - 1
GAGAACCGAGUGCAACGUUUGAUGAACACGUCACACUUGGACAGACGCAAAA----AAAAGCGUGUAGCAAU-UAUUGAAAUUCAA-AGUGCCCGAUGG
.....(((((((..((((.(.....).))))..)))))))..(.((((....----....)))).).(((..-..(((.....)))-..)))....... ( -21.00)
>DroSim_CAF1 48762 93 - 1
GAGAACCGAGUGCAACGUUUGAUGAACACGUCACACUUGGACAGACGCAAAA----AAAAGCGUGUUGCAAU-UAUUGAAAUUCAA-AGUGCUCGAUGG
......((((((((((((.(((((....))))).))........((((....----....)))))))))...-..(((.....)))-...))))).... ( -23.40)
>DroEre_CAF1 47601 91 - 1
GAGAACCGAGUGCAACGUUUGAUGAACACGUCACACUCGGACAAACGCAAAA------AGGCGUGUAGCAAU-UAUUGAAAUUCAA-AUGAUCAGCCGG
.....(((((((..((((.(.....).))))..)))))))....((((....------..))))...((.((-((((........)-)))))..))... ( -22.80)
>DroAna_CAF1 41293 90 - 1
CAAGAUGGAGUGCAAUGUUUGAUGAACACGUCACAGUCGGACAGACGCACAA------AAGCGUGCAGAAAUUUAUUGAAAUUUUAAAUUGCACGA---
.........((((..((((((((............))))))))...))))..------...(((((((((((((....)))))))....)))))).--- ( -23.00)
>consensus
GAGAACCGAGUGCAACGUUUGAUGAACACGUCACACUCGGACAGACGCAAAA______AAGCGUGUAGCAAU_UAUUGAAAUUCAA_AGUGCCCGAUGG
.....(((((((..((((.(.....).))))..)))))))....((((............))))................................... (-15.04 = -14.43 +  -0.61) 

alignment

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secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:36 2006