Locus 2298

Sequence ID X_DroMel_CAF1
Location 6,227,886 – 6,228,023
Length 137
Max. P 0.990573
window3718 window3719 window3720 window3721

overview

Window 8

Location 6,227,886 – 6,227,987
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.41
Mean single sequence MFE -39.58
Consensus MFE -24.74
Energy contribution -24.30
Covariance contribution -0.44
Combinations/Pair 1.27
Mean z-score -2.59
Structure conservation index 0.63
SVM decision value 2.22
SVM RNA-class probability 0.990573
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6227886 101 + 22224390
UUUUCAAACAUUUUGCGCGUAAAGGUUUCC----UGUGGCGAAAUGACCUCUGA--CCGGGCGGAGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUA-------------
(((((..(((((((((.((...(((...))----).)))))))))(((((((((--((.....).))))))))))))..((((...........)))))))))....------------- ( -33.10)
>DroSec_CAF1 2274 116 + 1
UUUUCAACCAUUUUGCGCGUAAAGGUUUCC----UCUGGCGAAAUUACCUCUGAGGUCAGAGGGGGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUAGUACAGUAAGCCC
...............((((.........((----((((((.......((((((....))))))..)))))))).))))((((((((((((((((.........)))))).)))))))))) ( -46.40)
>DroSim_CAF1 4338 116 + 1
UUUUCAACCAUUUUGCGCGUAAAGGUUUCC----UCUGGCGAAAUGACCUCUGAGGUCAGAGGGGGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUAGUACAGUAAGCCC
...............((((.........((----((((((.......((((((....))))))..)))))))).))))((((((((((((((((.........)))))).)))))))))) ( -46.40)
>DroYak_CAF1 9912 102 + 1
UUUUCA-UCACCUUGC---UGAAGGUUUCCAUCAUCUGGU---AUGACCGC---------CAGGGGUCAGAGGUCGUGGGACUUACCGACUGAUGGCCGAAAAAUUAGUACAGUAAGC--
......-....(((((---((..((((.(((.....))).---..))))((---------((..((((.((((((....))))).).))))..)))).............))))))).-- ( -32.40)
>consensus
UUUUCAACCAUUUUGCGCGUAAAGGUUUCC____UCUGGCGAAAUGACCUCUGA__UCAGAGGGGGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUAGUACAGUAAGC__
(((((....(((((.......)))))...........(((.......((((((....)))))).(((((((((((....))))).))))))....))))))))................. (-24.74 = -24.30 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,227,886 – 6,227,987
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.41
Mean single sequence MFE -32.98
Consensus MFE -18.16
Energy contribution -20.10
Covariance contribution 1.94
Combinations/Pair 1.07
Mean z-score -2.41
Structure conservation index 0.55
SVM decision value 1.09
SVM RNA-class probability 0.914168
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6227886 101 - 22224390
-------------UAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACUCCGCCCGG--UCAGAGGUCAUUUCGCCACA----GGAAACCUUUACGCGCAAAAUGUUUGAAAA
-------------....((((((..(((..((..(((((......(((((((((((......))--))))))))).((((......----))))...)))))..))...)))..)))))) ( -28.00)
>DroSec_CAF1 2274 116 - 1
GGGCUUACUGUACUAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACCCCCUCUGACCUCAGAGGUAAUUUCGCCAGA----GGAAACCUUUACGCGCAAAAUGGUUGAAAA
((((((((((.(((...............)))))))))))))..(((((........((((((....))))))...((((((.(((----((...)))))..))).)))..))))).... ( -38.96)
>DroSim_CAF1 4338 116 - 1
GGGCUUACUGUACUAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACCCCCUCUGACCUCAGAGGUCAUUUCGCCAGA----GGAAACCUUUACGCGCAAAAUGGUUGAAAA
((((((((((.(((...............)))))))))))))..(((((..(((((...((((....)))))))))((((((.(((----((...)))))..))).)))..))))).... ( -39.16)
>DroYak_CAF1 9912 102 - 1
--GCUUACUGUACUAAUUUUUCGGCCAUCAGUCGGUAAGUCCCACGACCUCUGACCCCUG---------GCGGUCAU---ACCAGAUGAUGGAAACCUUCA---GCAAGGUGA-UGAAAA
--...............((((((.((((((...((((.(((....)))...(((((....---------..))))))---)))...))))))..(((((..---..)))))..-)))))) ( -25.80)
>consensus
__GCUUACUGUACUAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACCCCCUCUGA__UCAGAGGUCAUUUCGCCAGA____GGAAACCUUUACGCGCAAAAUGGUUGAAAA
.................(((((((((((..((..((((((.....(((((((((............))))))))).....))........(....)..))))..))...))))))))))) (-18.16 = -20.10 +   1.94)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,227,922 – 6,228,023
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.79
Mean single sequence MFE -38.30
Consensus MFE -21.76
Energy contribution -26.32
Covariance contribution 4.56
Combinations/Pair 1.11
Mean z-score -2.84
Structure conservation index 0.57
SVM decision value 2.10
SVM RNA-class probability 0.987931
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6227922 101 + 22224390
GAAAUGACCUCUGA--CCGGGCGGAGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUA-----------------CUAAGACUGACAAUUAGAUAAUGCGAGACGGGCUUA
.....(((((((((--((.....).))))))))))((.((.....)).))....(.(((....((((-----------------((((.........)))).))))......))).)... ( -28.00)
>DroSec_CAF1 2310 120 + 1
GAAAUUACCUCUGAGGUCAGAGGGGGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUAGUACAGUAAGCCCCGCACUAAGACUGACAAUUAGAUAAUGCGAGGCGGGCUUA
.......((((((....))))))..(((((.(((.(((((((((((((((((((.........)))))).))))))))))))))))....)))))...........((.......))... ( -48.90)
>DroSim_CAF1 4374 120 + 1
GAAAUGACCUCUGAGGUCAGAGGGGGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUAGUACAGUAAGCCCCGCACUAAGACUGACAAUUAGAUAAUGCGAGGCGGGCUUA
.....(((((((((..((....))..)))))))))(((((((((((((((((((.........)))))).)))))))))))))..((((.(((...(((....)))......))).)))) ( -49.30)
>DroYak_CAF1 9948 96 + 1
---AUGACCGC---------CAGGGGUCAGAGGUCGUGGGACUUACCGACUGAUGGCCGAAAAAUUAGUACAGUAAGC------------CUGAUAAUUAGAUAAUGCGAGGCUGGCUUA
---......((---------(((.(((((..(((((.(.......))))))..)))))....(((((...(((.....------------))).))))).............)))))... ( -27.00)
>consensus
GAAAUGACCUCUGA__UCAGAGGGGGUCAGAGGUCGUGGGGCUUACUGACUGAUGGCCGAAAAAUUAGUACAGUAAGC______CUAAGACUGACAAUUAGAUAAUGCGAGGCGGGCUUA
.......((((((....))))))(((((.(...(((((((((((((((((((((.........)))))).))))))))))).........((((...)))).....))))..).))))). (-21.76 = -26.32 +   4.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,227,922 – 6,228,023
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.79
Mean single sequence MFE -32.01
Consensus MFE -16.16
Energy contribution -21.16
Covariance contribution 5.00
Combinations/Pair 1.08
Mean z-score -2.95
Structure conservation index 0.50
SVM decision value 1.51
SVM RNA-class probability 0.960210
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6227922 101 - 22224390
UAAGCCCGUCUCGCAUUAUCUAAUUGUCAGUCUUAG-----------------UAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACUCCGCCCGG--UCAGAGGUCAUUUC
.......((...((.(((.((.((((...(((..((-----------------.....))..)))...)))).)))))))...))(((((((((((......))--)))))))))..... ( -25.90)
>DroSec_CAF1 2310 120 - 1
UAAGCCCGCCUCGCAUUAUCUAAUUGUCAGUCUUAGUGCGGGGCUUACUGUACUAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACCCCCUCUGACCUCAGAGGUAAUUUC
...((.......))...........(((((......((.(((((((((((.(((...............)))))))))))))).))....)))))..((((((....))))))....... ( -38.96)
>DroSim_CAF1 4374 120 - 1
UAAGCCCGCCUCGCAUUAUCUAAUUGUCAGUCUUAGUGCGGGGCUUACUGUACUAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACCCCCUCUGACCUCAGAGGUCAUUUC
............((((((.((.......))...))))))(((((((((((.(((...............))))))))))))))..(((((((((............)))))))))..... ( -42.06)
>DroYak_CAF1 9948 96 - 1
UAAGCCAGCCUCGCAUUAUCUAAUUAUCAG------------GCUUACUGUACUAAUUUUUCGGCCAUCAGUCGGUAAGUCCCACGACCUCUGACCCCUG---------GCGGUCAU---
...((((((((.................))------------)))..................((((...(((((...(((....)))..)))))...))---------)))))...--- ( -21.13)
>consensus
UAAGCCCGCCUCGCAUUAUCUAAUUGUCAGUCUUAG______GCUUACUGUACUAAUUUUUCGGCCAUCAGUCAGUAAGCCCCACGACCUCUGACCCCCUCUGA__UCAGAGGUCAUUUC
...((.......)).........................(((((((((((.(((...............))))))))))))))..(((((((((............)))))))))..... (-16.16 = -21.16 +   5.00)

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 10:30:54 2006