Locus 237

Sequence ID 3L_DroMel_CAF1
Location 642,798 – 643,081
Length 283
Max. P 0.945580
window351 window352 window353 window354

overview

Window 1

Location 642,798 – 642,899
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.97
Mean single sequence MFE -34.83
Consensus MFE -12.74
Energy contribution -15.30
Covariance contribution 2.56
Combinations/Pair 1.12
Mean z-score -2.05
Structure conservation index 0.37
SVM decision value 0.87
SVM RNA-class probability 0.871453
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 642798 101 - 23771897
UCGGCA--------------GCCAACGAGUCUAUCAAGGCUUGACAACAUUUGCAUCUGGUCCG----GGCCAACUUG-AGAUAACUCGACCACAUCAUGGGGCAAGUUGCAGCGGCUGC
...(((--------------(((..(((((((....))))))).......(((((.((.((((.----(......(((-((....)))))........).)))).)).))))).)))))) ( -34.34)
>DroSec_CAF1 9950 101 - 1
UCGGCA--------------GCCAACGAGUCUAUCAAGACUUGACAACAUUUGCAUCUGGUCCG----GGCCAACUUG-AGAUAACUCGACCAGAUCAUGGGGCAAGUUGCAGCGGCUGC
...(((--------------(((..(((((((....))))))).((((..((((((((((((.(----(.....)).(-((....)))))))))))......))))))))....)))))) ( -36.60)
>DroEre_CAF1 12968 101 - 1
UCGGCA--------------GCCAACAAGUCUAUCAAGGCAUGACAACAUUUGCAUCUGGUCCG----GGCCAACUUG-AGAUAACUCGACCACAUCAUGUGGCAAGUUGCAGCGGCUGC
...(((--------------(((..........((((((((..........)))...((((...----.)))).))))-)(.(((((.(.((((.....))))).))))))...)))))) ( -32.30)
>DroWil_CAF1 10214 109 - 1
UUGGCAACCAUUUGGUUACUGCCAACAAGUCUAUCAAGACCUGACGACAUUUGCCUCCUAUCUGUUGUAGCCAGCUUGCAGCCUGGUGGGCCACUUUAG------UGUUGUAACU-----
(((((((((....)))...))))))((.((((....)))).))((((((((.....((((((.(((((((.....)))))))..)))))).......))------))))))....----- ( -33.50)
>DroYak_CAF1 10252 101 - 1
UCGGCA--------------GCCAACAAGUCUAUCAAGACUUGACAACAUUUGCAUCUGGACGG----GGCCAACUCG-AGAUAACUCGACCACAUCGUGGGGCAACUUGCUGCGGCUGC
...(((--------------(((..(((((((....))))))).........(((...(.(.(.----.(((...(((-((....)))))((((...)))))))..).).)))))))))) ( -37.40)
>consensus
UCGGCA______________GCCAACAAGUCUAUCAAGACUUGACAACAUUUGCAUCUGGUCCG____GGCCAACUUG_AGAUAACUCGACCACAUCAUGGGGCAAGUUGCAGCGGCUGC
..(((...............)))..(((((((....))))))).((((..((((...(((((......))))).................(((.....))).)))))))).......... (-12.74 = -15.30 +   2.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 642,838 – 642,939
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 95.05
Mean single sequence MFE -37.08
Consensus MFE -32.49
Energy contribution -33.30
Covariance contribution 0.81
Combinations/Pair 1.06
Mean z-score -1.55
Structure conservation index 0.88
SVM decision value 0.06
SVM RNA-class probability 0.562093
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 642838 101 + 23771897
UCAAGUUGGCCCGGACCAGAUGCAAAUGUUGUCAAGCCUUGAUAGACUCGUUGGCUGCCGACGCGAUUUGUCAACGACUCCACGGCGGCUGGUUUGGGUUG
.......((((((((((((.(((...((..(((.....(((((((((.((((((...)))))).).)))))))).)))..))..))).)))))))))))). ( -39.60)
>DroSec_CAF1 9990 101 + 1
UCAAGUUGGCCCGGACCAGAUGCAAAUGUUGUCAAGUCUUGAUAGACUCGUUGGCUGCCGACGCGAUUUGUCAACGACUCCACGGCGGCUGGUUUGGGUUG
.......((((((((((((.......((((((..(((((((((((((.((((((...)))))).).)))))))).))))..)))))).)))))))))))). ( -42.80)
>DroEre_CAF1 13008 101 + 1
UCAAGUUGGCCCGGACCAGAUGCAAAUGUUGUCAUGCCUUGAUAGACUUGUUGGCUGCCGACGCGAUUUGUCAACGACUCCACGGCGGCUGGUUUGAAUUG
(((((..((((..(((.(.((....)).).)))..(((.((...((.(((((((((((....)))....)))))))).)))).)))))))..))))).... ( -30.10)
>DroYak_CAF1 10292 101 + 1
UCGAGUUGGCCCCGUCCAGAUGCAAAUGUUGUCAAGUCUUGAUAGACUUGUUGGCUGCCGACGCGAUUUGUCAACGACUCCGCGGCGGCUGGUUUGGAUUG
.............((((((((...........(((((((....)))))))..((((((((.((.((.(((....))).)))))))))))).)))))))).. ( -35.80)
>consensus
UCAAGUUGGCCCGGACCAGAUGCAAAUGUUGUCAAGCCUUGAUAGACUCGUUGGCUGCCGACGCGAUUUGUCAACGACUCCACGGCGGCUGGUUUGGAUUG
.......((((((((((((.(((...((..(((.....(((((((((.((((((...)))))).).)))))))).)))..))..))).)))))))))))). (-32.49 = -33.30 +   0.81)

alignment

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secondary structure

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dotplot

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Window 3

Location 642,873 – 642,973
Length 100
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 79.14
Mean single sequence MFE -17.15
Consensus MFE -16.37
Energy contribution -15.93
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -0.50
Structure conservation index 0.95
SVM decision value 1.35
SVM RNA-class probability 0.945580
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 642873 100 - 23771897
UGCCCUCACCACAUCACUCCACUCCAAACUU-AAGCAACCCAAACCAGCCGCCGUGGAGUCGUUGACAAAUCGCGUCGGCAGCCAACGAGUCUAUCAAGGC
.((((((........(((((((.........-.....................))))))).((((((.......)))))).......)))........))) ( -18.41)
>DroEre_CAF1 13043 80 - 1
UCAC---------------CACUCCAAA------CCAAUUCAAACCAGCCGCCGUGGAGUCGUUGACAAAUCGCGUCGGCAGCCAACAAGUCUAUCAAGGC
....---------------.........------.............((((.(((((.(((...)))...))))).)))).(((..............))) ( -15.44)
>DroYak_CAF1 10327 101 - 1
UCACCUGACCACUUUACUCCACUCCAAACCAAAACCAAUCCAAACCAGCCGCCGCGGAGUCGUUGACAAAUCGCGUCGGCAGCCAACAAGUCUAUCAAGAC
...............................................((((.(((((.(((...)))...))))).)))).........((((....)))) ( -17.60)
>consensus
UCACCU_ACCAC_U_ACUCCACUCCAAAC___AACCAAUCCAAACCAGCCGCCGUGGAGUCGUUGACAAAUCGCGUCGGCAGCCAACAAGUCUAUCAAGGC
...............................................((((.(((((.(((...)))...))))).)))).........((((....)))) (-16.37 = -15.93 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 642,973 – 643,081
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 66.27
Mean single sequence MFE -25.32
Consensus MFE -11.98
Energy contribution -13.29
Covariance contribution 1.31
Combinations/Pair 1.12
Mean z-score -1.67
Structure conservation index 0.47
SVM decision value 0.22
SVM RNA-class probability 0.639420
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 642973 108 - 23771897
-UGAAAUGUUUGCAAGAGGGAGUGCACUAAGCUGUAUCUGUCUAUUAUAAAACGUUCAUAG-----------GGAUAGCCCAUGCAAUGAAAACUCAGCACUCCCAAGAAUCUGGGCACC
-.........(((.(((((((((((.....(((((..((((..((........))..))))-----------..)))))........(((....))))))))))).....)))..))).. ( -27.90)
>DroSec_CAF1 10130 101 - 1
-UGAAAUGUUUGCAAGAGGGAGUGUACUAAACUGUAGCUAUCUCUA-------GUUCAUAG-----------GAAUAACCCAUGCAAAGAAAACUCAGCACUCCCAAGAAUCUGGGCACC
-.........(((.(((((((((((......(((((((((....))-------))).))))-----------................((....)).)))))))).....)))..))).. ( -22.50)
>DroEre_CAF1 13123 94 - 1
UUUAAAUGGUUGCAAUAGGGAGUGUUAUAAAAAACC---------------ACGUACAUGG-----------GAAUAGUCCAUGUAAAGACAACUCAGCACUCCCAAGAAUCUGGGCACC
.......(((.((....(((((((((..........---------------...(((((((-----------(.....))))))))..((....))))))))))).((...))..))))) ( -25.20)
>DroYak_CAF1 10428 108 - 1
------------CAAUAAGCAGGGCUAUAAAGUAUGGCUGUCUAUUAUGAAAUGUACAUGGGAAUAACACGGGAAUAACCCGUGUAAAGACAACUCAGCACUCCCUACAAUCUGAGCACC
------------......((..(((((((...))))))).............((((...((((...(((((((.....)))))))...((....)).....))))))))......))... ( -25.70)
>consensus
_UGAAAUGUUUGCAAGAGGGAGUGCAAUAAACUAUAGCUGUCUAUU_____ACGUACAUAG___________GAAUAACCCAUGCAAAGAAAACUCAGCACUCCCAAGAAUCUGGGCACC
.................((((((((.............................(((((((..................)))))))..((....)).))))))))............... (-11.98 = -13.29 +   1.31)

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 09:37:06 2006