Locus 1946

Sequence ID 2L_DroMel_CAF1
Location 5,257,869 – 5,258,004
Length 135
Max. P 0.899139
window3150 window3151 window3152

overview

Window 0

Location 5,257,869 – 5,257,977
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.53
Mean single sequence MFE -29.82
Consensus MFE -16.84
Energy contribution -18.95
Covariance contribution 2.11
Combinations/Pair 1.03
Mean z-score -2.56
Structure conservation index 0.56
SVM decision value 0.21
SVM RNA-class probability 0.636936
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5257869 108 + 22407834
--UCUGGGCCAGCUUAUUAUAGUU-----CGUAAUGAGCGUUCCCAGCUGCAUUUCUGCAGCCUAUUUGCCAAUUAAAUGAAAUUAAAGUCAUAUCUGGCAAUUGC-----UCUCAGUCG
--..((((...(((((((((....-----.)))))))))...))))((((((....))))))....((((((.....((((........))))...))))))....-----......... ( -31.90)
>DroPse_CAF1 34649 112 + 1
--------CCAUCUUAUUAAAGUCCGUUUCGUAAUGAGCAUUCCCAGCUGCAUUUCUGCAGGCCAUUUGCCAAUUAAAUGAAAUUAAAGUCAUAUCUGGCAAUUGGCAAUCCCUCCAUCU
--------....(((((((..(......)..))))))).........(((((....)))))((((.((((((.....((((........))))...)))))).))))............. ( -25.40)
>DroSec_CAF1 34667 108 + 1
--UCUGGGCCAGCUUAUUAUAGUU-----CGUAAUGAGCGUUCCCAGCUGCAUUUCUGCAACCCAUUUGCCAAUUAUAUGAAAUUAAAGUCAUAUCUGGCAAUUGC-----UCUCGCUCG
--.(((((...(((((((((....-----.)))))))))...))))).((((....))))...((.((((((...((((((........)))))).)))))).)).-----......... ( -32.30)
>DroYak_CAF1 36756 111 + 1
--UCUGGCCCAGCUUAUUAUAGUUGA--GCGUAAUGAGCGUUCCCAGCUGCAUUUCUGCAGCCUAUUUGCCAAUUAAAUGAAAUUAAAGUCAUAUCUGGCAAUUGC-----UGUCGGUCG
--...((((((((.....((((..((--((((.....))))))...((((((....))))))))))((((((.....((((........))))...))))))..))-----))..)))). ( -33.60)
>DroAna_CAF1 15984 108 + 1
GGCCUGGCCCAGCUUAUUAAAGUU-----CGUAAUGAGCGUUCCCAGCUGCAUUUCUGCAGACCAUUAGCCAAUUAAACGAAAUUAAAGUCAUAUCGGGCAAUUGC-----CGGCGA--G
((.((((....((((((((.....-----..))))))))....))))(((((....))))).))....(((.......(((.((.......)).)))(((....))-----))))..--. ( -30.30)
>DroPer_CAF1 34706 112 + 1
--------CCAUCUUAUUAAAGUCCGUUUCGUAAUGAGCAUUCCCAGCUGCAUUUCUGCAGGCCAUUUGCCAAUUAAAUGAAAUUAAAGUCAUAUCUGGCAAUUGGCAAUCCCUCCAUCU
--------....(((((((..(......)..))))))).........(((((....)))))((((.((((((.....((((........))))...)))))).))))............. ( -25.40)
>consensus
__UCUGG_CCAGCUUAUUAAAGUU_____CGUAAUGAGCGUUCCCAGCUGCAUUUCUGCAGCCCAUUUGCCAAUUAAAUGAAAUUAAAGUCAUAUCUGGCAAUUGC_____CCUCGAUCG
...((((....((((((((............))))))))....))))(((((....)))))..((.((((((.....((((........))))...)))))).))............... (-16.84 = -18.95 +   2.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,257,869 – 5,257,977
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.53
Mean single sequence MFE -31.07
Consensus MFE -18.68
Energy contribution -19.02
Covariance contribution 0.33
Combinations/Pair 1.14
Mean z-score -2.09
Structure conservation index 0.60
SVM decision value 0.04
SVM RNA-class probability 0.552084
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5257869 108 - 22407834
CGACUGAGA-----GCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUAGGCUGCAGAAAUGCAGCUGGGAACGCUCAUUACG-----AACUAUAAUAAGCUGGCCCAGA--
.........-----....(((((((..((((........))))....)))))))...(((((((....)))))))(((...(((.((((..-----.....)))).)))...)))...-- ( -31.40)
>DroPse_CAF1 34649 112 - 1
AGAUGGAGGGAUUGCCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUGGCCUGCAGAAAUGCAGCUGGGAAUGCUCAUUACGAAACGGACUUUAAUAAGAUGG--------
...(((((.....((((.(((((((..((((........))))....))))))).))))(((((....))))).((((....))))............))))).........-------- ( -28.60)
>DroSec_CAF1 34667 108 - 1
CGAGCGAGA-----GCAAUUGCCAGAUAUGACUUUAAUUUCAUAUAAUUGGCAAAUGGGUUGCAGAAAUGCAGCUGGGAACGCUCAUUACG-----AACUAUAAUAAGCUGGCCCAGA--
...((....-----))..((((((.((((((........))))))...))))))...(((((((....)))))))(((...(((.((((..-----.....)))).)))...)))...-- ( -35.50)
>DroYak_CAF1 36756 111 - 1
CGACCGACA-----GCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUAGGCUGCAGAAAUGCAGCUGGGAACGCUCAUUACGC--UCAACUAUAAUAAGCUGGGCCAGA--
.(.((..((-----((..(((((((..((((........))))....)))))))((((((((((....))))))((((....))))......--....)))).....)))))).)...-- ( -32.10)
>DroAna_CAF1 15984 108 - 1
C--UCGCCG-----GCAAUUGCCCGAUAUGACUUUAAUUUCGUUUAAUUGGCUAAUGGUCUGCAGAAAUGCAGCUGGGAACGCUCAUUACG-----AACUUUAAUAAGCUGGGCCAGGCC
.--..((((-----.((((((..(((.((.......)).)))..)))))).)...(((((((((....)))((((..(((.(.((.....)-----).))))....))))))))))))). ( -30.20)
>DroPer_CAF1 34706 112 - 1
AGAUGGAGGGAUUGCCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUGGCCUGCAGAAAUGCAGCUGGGAAUGCUCAUUACGAAACGGACUUUAAUAAGAUGG--------
...(((((.....((((.(((((((..((((........))))....))))))).))))(((((....))))).((((....))))............))))).........-------- ( -28.60)
>consensus
CGAUCGAGA_____GCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUGGGCUGCAGAAAUGCAGCUGGGAACGCUCAUUACG_____AACUAUAAUAAGCUGG_CCAGA__
.....(((..........(((((((..((((........))))....))))))).(((.(((((....))))))))......)))................................... (-18.68 = -19.02 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,257,902 – 5,258,004
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.56
Mean single sequence MFE -34.30
Consensus MFE -18.85
Energy contribution -19.10
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -2.48
Structure conservation index 0.55
SVM decision value 1.01
SVM RNA-class probability 0.899139
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5257902 102 - 22407834
UCAUCA---GUCCCAGAAGGCAAGACGCG----------UCGACUGAGA-----GCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUAGGCUGCAGAAAUGCAGCUGGGAA
((.(((---(((...((..((.....)).----------))))))))))-----....(((((((..((((........))))....)))))))...(((((((....)))))))..... ( -31.80)
>DroPse_CAF1 34681 115 - 1
UCAUCA---GACCAAGGCGG--AGGCGCGGGCGAAGGCGGAGAUGGAGGGAUUGCCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUGGCCUGCAGAAAUGCAGCUGGGAA
((.(((---(.(((..(((.--...)))..((....)).....))).......((((.(((((((..((((........))))....))))))).))))(((((....))))))))))). ( -37.60)
>DroSec_CAF1 34700 102 - 1
UCAUCA---GUCCCAGAAGGCAAGACGCG----------UCGAGCGAGA-----GCAAUUGCCAGAUAUGACUUUAAUUUCAUAUAAUUGGCAAAUGGGUUGCAGAAAUGCAGCUGGGAA
......---.((((((.......(((.((----------(...((....-----))..((((((.((((((........))))))...))))))))).)))(((....)))..)))))). ( -34.80)
>DroSim_CAF1 36194 102 - 1
UCAUCA---GUCCCAGAAGGCAAGACGCG----------UCGAGCGAGA-----GCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUGGGCUGCAGAAAUGCAGCUGGGAA
......---.((((.((..((.....)).----------))..((....-----))..(((((((..((((........))))....)))))))...(((((((....))))))))))). ( -34.50)
>DroAna_CAF1 16019 102 - 1
UCAUCAUCUGUCCAA-ACUGGAGGCUGUG----------CC--UCGCCG-----GCAAUUGCCCGAUAUGACUUUAAUUUCGUUUAAUUGGCUAAUGGUCUGCAGAAAUGCAGCUGGGAA
..........(((..-....(((((...)----------))--))((((-----((....)))(((.((.......)).))).......)))....((.(((((....))))))).))). ( -29.50)
>DroPer_CAF1 34738 115 - 1
UCAUCA---GACCAAGGCGG--AGGCGCGGGCGAAGGCGGAGAUGGAGGGAUUGCCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUGGCCUGCAGAAAUGCAGCUGGGAA
((.(((---(.(((..(((.--...)))..((....)).....))).......((((.(((((((..((((........))))....))))))).))))(((((....))))))))))). ( -37.60)
>consensus
UCAUCA___GUCCAAGAAGGCAAGACGCG__________UCGAUCGAGA_____GCAAUUGCCAGAUAUGACUUUAAUUUCAUUUAAUUGGCAAAUGGGCUGCAGAAAUGCAGCUGGGAA
..........(((.............................................(((((((..((((........))))....))))))).(((.(((((....))))))))))). (-18.85 = -19.10 +   0.25)

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 10:15:41 2006