Locus 8435

Sequence ID X_DroMel_CAF1
Location 20,939,089 – 20,939,317
Length 228
Max. P 0.960087
window13856 window13857 window13858 window13859 window13860

overview

Window 6

Location 20,939,089 – 20,939,185
Length 96
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 82.18
Mean single sequence MFE -31.73
Consensus MFE -19.32
Energy contribution -20.19
Covariance contribution 0.87
Combinations/Pair 1.08
Mean z-score -2.05
Structure conservation index 0.61
SVM decision value 0.41
SVM RNA-class probability 0.726063
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20939089 96 - 22224390
UGUAAAAUGGUUAUUUGCGAGCGCCUUAUCAGCUCCAUUCCCGC----UCGUCACGGCGUCAGGGAAUCUAAGCUGAUAAUUACAAGGUAGUCU-------GCGAAU
............(((((((..(((((((((((((..((((((..----.(((....)))...))))))...))))))))......)))).)..)-------)))))) ( -33.10)
>DroSec_CAF1 11311 99 - 1
UGUAA-AUGGUUAUUUGCGAGCGGCUUAUCAGCUCCAUUCCCGCUCGCUCGUCACGGCGUCAGGGACUUUAAGCUGAUAAUUACAAGGUAGUCU-------GCGAAU
.....-......(((((((..(.(((((((((((....((((...((((......))))...)))).....)))))))).......))).)..)-------)))))) ( -29.91)
>DroEre_CAF1 9797 91 - 1
----C-AUGGUUACUGGCGAGCGUCUUAUCAGCUGCAUUCCCGC----UCGCCACGGCAGUAGGGAAUUUGAGCUGAUAAUUGCAAGGUAGUCG-------CCGAAU
----.-.((((.((((.(..(((..(((((((((..((((((((----(.((....))))).))))))...))))))))).)))..).)))).)-------)))... ( -37.60)
>DroYak_CAF1 10985 102 - 1
UGUAA-AUGGUUAUUUGCGAGCGGCUUAUCAGCUACAUUCCCGC----UCGUCGCGGCAGUAGGAAAUUUAAGCUGAUAAUUACAAGGUAGUCGUUAGUCUCCGAAU
.((((-((....)))))).(((((((((((((((...((((..(----(.((....))))..)))).....))))))))..........)))))))........... ( -26.30)
>consensus
UGUAA_AUGGUUAUUUGCGAGCGGCUUAUCAGCUCCAUUCCCGC____UCGUCACGGCAGCAGGGAAUUUAAGCUGAUAAUUACAAGGUAGUCG_______CCGAAU
........(..(((((.........(((((((((..((((((.......(((....)))...))))))...))))))))).....)))))..).............. (-19.32 = -20.19 +   0.87)

alignment

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secondary structure

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Window 7

Location 20,939,145 – 20,939,265
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.45
Mean single sequence MFE -34.20
Consensus MFE -23.66
Energy contribution -24.48
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.83
Structure conservation index 0.69
SVM decision value 0.46
SVM RNA-class probability 0.745932
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20939145 120 + 22224390
GAAUGGAGCUGAUAAGGCGCUCGCAAAUAACCAUUUUACACCAUGUACGACUAUAUGCAUAGUAUAUUUGGCCCAGUUUUAUGCCGGCGGGAAACUAGAGCGAUCGGUUCACGCAACAUU
.....((((((((....(((((.((((((.......(((.....)))..(((((....))))).))))))(((..((.....)).)))((....)).))))))))))))).......... ( -29.30)
>DroSec_CAF1 11371 119 + 1
GAAUGGAGCUGAUAAGCCGCUCGCAAAUAACCAU-UUACACCAUCUACGACUAUGUACAUAGUAUAUUUGGCCCAGUUUUCUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUU
.((((..(((((...((((.(((...........-.....(((......(((((....))))).....))).(((((((((((....)))))))))))..))).))))))).))..)))) ( -36.40)
>DroEre_CAF1 9853 102 + 1
GAAUGCAGCUGAUAAGACGCUCGCCAGUAACCAU-G-----CG------AG------UAUAGUAUAGUUGGCCCAGUUUUCUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCCACAUU
((((.((((((.((..(..(((((..........-)-----))------))------..)..))))))))..(((((((((((....)))))))))))........)))).......... ( -32.50)
>DroYak_CAF1 11048 109 + 1
GAAUGUAGCUGAUAAGCCGCUCGCAAAUAACCAU-UUACACCA------AG----UAUAUAGUAUAGUUGGCCCAGUUUUCCGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUU
.(((((.(((((...((((.(((...........-.....(((------(.----((((...)))).)))).(((((((((((....)))))))))))..))).))))))).)).))))) ( -38.60)
>consensus
GAAUGGAGCUGAUAAGCCGCUCGCAAAUAACCAU_UUACACCA______AC____UACAUAGUAUAGUUGGCCCAGUUUUCUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUU
.((((..(((((...((((.(((.......(((...................................))).(((((((((((....)))))))))))..))).))))))).))..)))) (-23.66 = -24.48 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,939,145 – 20,939,265
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.45
Mean single sequence MFE -33.67
Consensus MFE -22.72
Energy contribution -25.09
Covariance contribution 2.37
Combinations/Pair 1.05
Mean z-score -1.50
Structure conservation index 0.67
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20939145 120 - 22224390
AAUGUUGCGUGAACCGAUCGCUCUAGUUUCCCGCCGGCAUAAAACUGGGCCAAAUAUACUAUGCAUAUAGUCGUACAUGGUGUAAAAUGGUUAUUUGCGAGCGCCUUAUCAGCUCCAUUC
...((((.((((..((.((((.(((((((((....))....)))))))((((..(((((((((.((......)).)))))))))...)))).....)))).))..))))))))....... ( -28.90)
>DroSec_CAF1 11371 119 - 1
AAUGUUGCGUGAACCGAUCGUUCCAGUUUCCCGCCGGCAGAAAACUGGGCCAAAUAUACUAUGUACAUAGUCGUAGAUGGUGUAA-AUGGUUAUUUGCGAGCGGCUUAUCAGCUCCAUUC
...((((.((((.(((.((((.(((((((.(.(....).).)))))))((((..((((((((.(((......))).)))))))).-.)))).....)))).))).))))))))....... ( -37.20)
>DroEre_CAF1 9853 102 - 1
AAUGUGGCGUGAACCGAUCGUUCCAGUUUCCCGCCGGCAGAAAACUGGGCCAACUAUACUAUA------CU------CG-----C-AUGGUUACUGGCGAGCGUCUUAUCAGCUGCAUUC
((((..((.(((...((.(((((((((((.(.(....).).)))))).((((.....(((((.------..------..-----.-)))))...)))))))))))...)))))..)))). ( -29.70)
>DroYak_CAF1 11048 109 - 1
AAUGUUGCGUGAACCGAUCGUUCCAGUUUCCCGCCGGCGGAAAACUGGGCCAACUAUACUAUAUA----CU------UGGUGUAA-AUGGUUAUUUGCGAGCGGCUUAUCAGCUACAUUC
(((((.((((((.(((.((((.(((((((.(((....))).)))))))((((..(((((((....----..------))))))).-.)))).....)))).))).))))..)).))))). ( -38.90)
>consensus
AAUGUUGCGUGAACCGAUCGUUCCAGUUUCCCGCCGGCAGAAAACUGGGCCAAAUAUACUAUAUA____CU______UGGUGUAA_AUGGUUAUUUGCGAGCGGCUUAUCAGCUCCAUUC
((((..((((((.(((.((((.(((((((.(.(....).).)))))))((((..((((((((..............))))))))...)))).....)))).))).))))..))..)))). (-22.72 = -25.09 +   2.37)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,939,185 – 20,939,299
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 87.24
Mean single sequence MFE -32.55
Consensus MFE -30.06
Energy contribution -30.00
Covariance contribution -0.06
Combinations/Pair 1.12
Mean z-score -1.38
Structure conservation index 0.92
SVM decision value 0.25
SVM RNA-class probability 0.654923
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20939185 114 + 22224390
CCAUGUACGACUAUAUGCAUAGUAUAUUUGGCCCAGUUUUAUGCCGGCGGGAAACUAGAGCGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCUCCG
(((.(((..(((((....))))).))).)))..............(((((....)).((((.....))))...........)))((((((..(((........))).)))))). ( -25.10)
>DroSec_CAF1 11410 114 + 1
CCAUCUACGACUAUGUACAUAGUAUAUUUGGCCCAGUUUUCUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCG
.........(((((....)))))......(((.((((((((((....))))))))))((((.....))))...........)))((((((..(((........))).)))))). ( -35.00)
>DroEre_CAF1 9888 101 + 1
-CG------AG------UAUAGUAUAGUUGGCCCAGUUUUCUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCCACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCG
-..------..------............((((((((((((((....))))))))))).......(((....)))......)))((((((..(((........))).)))))). ( -34.30)
>DroYak_CAF1 11087 104 + 1
CCA------AG----UAUAUAGUAUAGUUGGCCCAGUUUUCCGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCG
(((------(.----((((...)))).)))).(((((((((((....))))))))))).......((((...........))))((((((..(((........))).)))))). ( -35.80)
>consensus
CCA______AC____UACAUAGUAUAGUUGGCCCAGUUUUCUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCG
.............................(((.((((((((((....))))))))))((((.....))))...........)))((((((..(((........))).)))))). (-30.06 = -30.00 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,939,225 – 20,939,317
Length 92
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 95.11
Mean single sequence MFE -32.02
Consensus MFE -30.00
Energy contribution -30.25
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -2.18
Structure conservation index 0.94
SVM decision value 1.51
SVM RNA-class probability 0.960087
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20939225 92 + 22224390
AUGCCGGCGGGAAACUAGAGCGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCUCCGCUGAUGAUGACAUUGGUU
..((((((((....)..((((.....)))).)))..(((((((.((((((..(((........))).))))))))))))).......)))). ( -29.40)
>DroSec_CAF1 11450 92 + 1
CUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCGCUGAUGAUGACAUUGGGU
..(((.((((....)..((((.....)))).)))..(((((((.((((((..(((........))).))))))))))))).........))) ( -31.90)
>DroEre_CAF1 9915 92 + 1
CUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCCACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCGCCGAUGAUGACAUUGGCU
..((((((((....)..((((.....)))).)))).(((..((.((((((..(((........))).))))))))..)))........))). ( -34.40)
>DroYak_CAF1 11117 92 + 1
CCGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCGCCGAUGAUGACAUUGGCU
.....(((((....)).((((.....))))...........)))((((((..(((........))).))))))(((((((....))))))). ( -32.40)
>consensus
CUGCCGGCGGGAAACUGGAACGAUCGGUUCACGCAACAUUAGCCGGGGAUCAAUCAAGCAUUAGAUAAUCCCCGCCGAUGAUGACAUUGGCU
..((((((((....)..((((.....)))).)))..(((((((.((((((..(((........))).))))))))))))).......)))). (-30.00 = -30.25 +   0.25)

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 13:03:58 2006