Locus 196

Sequence ID 4_DroMel_CAF1
Location 1,268,369 – 1,268,520
Length 151
Max. P 0.875207
window316 window317 window318

overview

Window 6

Location 1,268,369 – 1,268,480
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.04
Mean single sequence MFE -27.43
Consensus MFE -19.44
Energy contribution -20.33
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -2.02
Structure conservation index 0.71
SVM decision value 0.08
SVM RNA-class probability 0.571670
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1268369 111 - 1281640
CAAAGUCGACUCUAGCACAGACAUAAGUUUACCGCUUAGACCUUGUGUCAUAGCUACAUUCGCUUUGUCGAUUUGGUCAUCAAUUUUCGCAUGAAACUUGUACUAA---------AUGGA
(((((.(((.(.((((...((((((((((((.....)))).))))))))...)))).).))))))))((.(((((((...(((.((((....)))).))).)))))---------)).)) ( -30.30)
>DroVir_CAF1 12000 120 - 1
CAAAGUCGACUCUAGCACUGACAUAAGUUUGCCACUUAAUCCUUGUGUCAUCGCUACAUUCGCUUUGUCGAUUUGAUCAUCGAUUUUUGCGUGGAAUUUGUACUGUUUUUUUAUUUUGAU
((((.((.((..((((..(((((((((..(........)..)))))))))..)))).....((...((((((......))))))....)))).)).)))).................... ( -28.10)
>DroGri_CAF1 14130 111 - 1
CAAAGUCGACUCCAGCACUGACAUAAGUUUGCCACUGAGGCCUUGUGUCAUCGCCACAUUCGCUUUGUCAAUUUGAUCAUCAAUUUUCGCAUGAAAUUUGUACUAC---------AAUAA
(((((.(((.....((..(((((((((...(((.....))))))))))))..)).....)))))))).....(((.....(((.((((....)))).))).....)---------))... ( -25.70)
>DroWil_CAF1 54426 111 - 1
CAAAGUCGACUCUAGCACUGACAUAAGUUUACCGCUCAGCCCUUGUGUCAUGGCUACAUUCGCCUUGUCGAUUUGAUCGUCGAUUUUUGCGUGAAAUUUGUACUGC---------AUGCA
.(((((((((..((((..(((((((((..(........)..)))))))))..))))((.(((......)))..))...)))))))))((((((............)---------))))) ( -29.30)
>DroMoj_CAF1 13710 111 - 1
CAAAGUCGACUCCAGCACUGACAUAAGUUUUCCACUUAAACCUUGUGUCAUGGCUACAUUCGCUUUGUCGAUUUGUUCAUCGAUUCUUGCAUGGAAUUUGUACUAA---------AAGAU
...((((((.((((((..(((((((((.(((......))).)))))))))..)))......((...((((((......))))))....))..)))..))).)))..---------..... ( -26.80)
>DroPer_CAF1 27325 107 - 1
CAAAGUCGACUCUAGCACUGACAUAAGUUUACCACUUAGCCCUUGUGUCAUCGCUACAUUCGCUUUGUCGAUUUGGUCGUCGAUUUUUGCAUGGAAUUUAUACUAG-------------G
(((((.(((.(.((((..(((((((((..(........)..)))))))))..)))).).))))))))(((((......))))).......................-------------. ( -24.40)
>consensus
CAAAGUCGACUCUAGCACUGACAUAAGUUUACCACUUAGACCUUGUGUCAUCGCUACAUUCGCUUUGUCGAUUUGAUCAUCGAUUUUUGCAUGAAAUUUGUACUAA_________AUGAA
(((((.(((.(.((((..(((((((((..(........)..)))))))))..)))).).))))))))(((((......)))))..................................... (-19.44 = -20.33 +   0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,268,400 – 1,268,520
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -38.24
Consensus MFE -28.19
Energy contribution -27.72
Covariance contribution -0.47
Combinations/Pair 1.23
Mean z-score -2.60
Structure conservation index 0.74
SVM decision value 0.01
SVM RNA-class probability 0.536459
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1268400 120 + 1281640
AUGACCAAAUCGACAAAGCGAAUGUAGCUAUGACACAAGGUCUAAGCGGUAAACUUAUGUCUGUGCUAGAGUCGACUUUGUCUAAGCUAGCACGAUACGAUGAAGGUAGCUUGAUCGGCU
....((.....((((((((((.(.((((...((((.(((..((....))....))).))))...)))).).))).)))))))(((((((.(.............).)))))))...)).. ( -33.52)
>DroVir_CAF1 12040 120 + 1
AUGAUCAAAUCGACAAAGCGAAUGUAGCGAUGACACAAGGAUUAAGUGGCAAACUUAUGUCAGUGCUAGAGUCGACUUUGUCGAAGUUGGCGCGUUACGAUGAAGGUAGCCUCAUUGGCU
..(.((((.((((((((((((.(.(((((.(((((.(((..............))).))))).))))).).))).)))))))))..)))))......((((((.((...))))))))... ( -38.44)
>DroGri_CAF1 14161 120 + 1
AUGAUCAAAUUGACAAAGCGAAUGUGGCGAUGACACAAGGCCUCAGUGGCAAACUUAUGUCAGUGCUGGAGUCGACUUUGUCAAAAUUGGCCCGUUACGAUGAAGGUAGCCUAAUUGGCU
...(((...((((((((((((.(.(((((.(((((.((((((.....)))...))).))))).))))).).))).))))))))).((((........))))...)))((((.....)))) ( -39.00)
>DroWil_CAF1 54457 120 + 1
ACGAUCAAAUCGACAAGGCGAAUGUAGCCAUGACACAAGGGCUGAGCGGUAAACUUAUGUCAGUGCUAGAGUCGACUUUGUCAAAAUUGGCCCGCUAUGAUGAGGGCAGCCUAAUUGGUU
..((((((...((((((((((.(.((((..(((((.(((.(((....)))...))).)))))..)))).).))).))))))).......((((.(......).)))).......)))))) ( -40.90)
>DroMoj_CAF1 13741 120 + 1
AUGAACAAAUCGACAAAGCGAAUGUAGCCAUGACACAAGGUUUAAGUGGAAAACUUAUGUCAGUGCUGGAGUCGACUUUGUCGAAGUUAGGGCGUUACGAUGAGGGCAGUCUCAUUGGAU
...(((...((((((((((((.(.((((..(((((..((((((.......)))))).)))))..)))).).))).))))))))).((....))))).((((((((....))))))))... ( -39.20)
>DroPer_CAF1 27352 120 + 1
ACGACCAAAUCGACAAAGCGAAUGUAGCGAUGACACAAGGGCUAAGUGGUAAACUUAUGUCAGUGCUAGAGUCGACUUUGUCAAAAUUAGCUCGAUACGACGAAGGAAGCUUGAUUGGUU
..((((((.((((((((((((.(.(((((.(((((.(((.(((....)))...))).))))).))))).).))).)))))))......((((((...)))(....)..))).)))))))) ( -38.40)
>consensus
AUGAUCAAAUCGACAAAGCGAAUGUAGCGAUGACACAAGGGCUAAGUGGUAAACUUAUGUCAGUGCUAGAGUCGACUUUGUCAAAAUUAGCCCGUUACGAUGAAGGUAGCCUAAUUGGCU
...........((((((((((.(.((((..(((((.(((..............))).)))))..)))).).))).)))))))...............((((.(((....))).))))... (-28.19 = -27.72 +  -0.47)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,268,400 – 1,268,520
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.67
Mean single sequence MFE -35.64
Consensus MFE -26.81
Energy contribution -27.03
Covariance contribution 0.22
Combinations/Pair 1.18
Mean z-score -3.54
Structure conservation index 0.75
SVM decision value 0.89
SVM RNA-class probability 0.875207
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1268400 120 - 1281640
AGCCGAUCAAGCUACCUUCAUCGUAUCGUGCUAGCUUAGACAAAGUCGACUCUAGCACAGACAUAAGUUUACCGCUUAGACCUUGUGUCAUAGCUACAUUCGCUUUGUCGAUUUGGUCAU
.(((((((((((((....(((......))).)))))).(((((((.(((.(.((((...((((((((((((.....)))).))))))))...)))).).)))))))))))).)))))... ( -36.60)
>DroVir_CAF1 12040 120 - 1
AGCCAAUGAGGCUACCUUCAUCGUAACGCGCCAACUUCGACAAAGUCGACUCUAGCACUGACAUAAGUUUGCCACUUAAUCCUUGUGUCAUCGCUACAUUCGCUUUGUCGAUUUGAUCAU
((((.....))))..................(((..(((((((((.(((.(.((((..(((((((((..(........)..)))))))))..)))).).)))))))))))).)))..... ( -37.80)
>DroGri_CAF1 14161 120 - 1
AGCCAAUUAGGCUACCUUCAUCGUAACGGGCCAAUUUUGACAAAGUCGACUCCAGCACUGACAUAAGUUUGCCACUGAGGCCUUGUGUCAUCGCCACAUUCGCUUUGUCAAUUUGAUCAU
((((.....))))...............(..(((..(((((((((.(((.....((..(((((((((...(((.....))))))))))))..)).....)))))))))))).)))..).. ( -38.20)
>DroWil_CAF1 54457 120 - 1
AACCAAUUAGGCUGCCCUCAUCAUAGCGGGCCAAUUUUGACAAAGUCGACUCUAGCACUGACAUAAGUUUACCGCUCAGCCCUUGUGUCAUGGCUACAUUCGCCUUGUCGAUUUGAUCGU
..((.....))..((((.(......).))))(((..(((((((.(.(((.(.((((..(((((((((..(........)..)))))))))..)))).).)))).))))))).)))..... ( -32.50)
>DroMoj_CAF1 13741 120 - 1
AUCCAAUGAGACUGCCCUCAUCGUAACGCCCUAACUUCGACAAAGUCGACUCCAGCACUGACAUAAGUUUUCCACUUAAACCUUGUGUCAUGGCUACAUUCGCUUUGUCGAUUUGUUCAU
.....(((((......)))))...........(((.(((((((((.(((....(((..(((((((((.(((......))).)))))))))..)))....))))))))))))...)))... ( -34.00)
>DroPer_CAF1 27352 120 - 1
AACCAAUCAAGCUUCCUUCGUCGUAUCGAGCUAAUUUUGACAAAGUCGACUCUAGCACUGACAUAAGUUUACCACUUAGCCCUUGUGUCAUCGCUACAUUCGCUUUGUCGAUUUGGUCGU
.(((((((.(((((.............)))))......(((((((.(((.(.((((..(((((((((..(........)..)))))))))..)))).).)))))))))))).)))))... ( -34.72)
>consensus
AGCCAAUCAGGCUACCUUCAUCGUAACGCGCCAACUUUGACAAAGUCGACUCUAGCACUGACAUAAGUUUACCACUUAGACCUUGUGUCAUCGCUACAUUCGCUUUGUCGAUUUGAUCAU
...(((...(((.................)))....(((((((((.(((.(.((((..(((((((((..(........)..)))))))))..)))).).)))))))))))).)))..... (-26.81 = -27.03 +   0.22)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:02 2006