Locus 6882

Sequence ID 2L_DroMel_CAF1
Location 19,246,853 – 19,246,943
Length 90
Max. P 0.534099
window10971 window10972

overview

Window 1

Location 19,246,853 – 19,246,943
Length 90
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 80.93
Mean single sequence MFE -27.97
Consensus MFE -17.65
Energy contribution -18.04
Covariance contribution 0.39
Combinations/Pair 1.13
Mean z-score -1.48
Structure conservation index 0.63
SVM decision value -0.03
SVM RNA-class probability 0.516251
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19246853 90 + 22407834
AAGGAUGCAGGUC-CUGGCC-----------------CUACCACUGCGAGCACAUAAAAACGUAUUAAGCAUAUUAUCUAGGCAGGCACAGACGCCUGCCAGACGACG
....((((.(((.-...)))-----------------.......((((............))))....)))).(..(((.(((((((......))))))))))..).. ( -25.00)
>DroPse_CAF1 75156 107 + 1
CAGGUCGCAGGAC-GAGGCUCCAGAAUGGAAAUGGAACCAGAAUGCCGGGCCCAUAAAAACGUAUUAAGCAUAUUAUCUAGGCAGGCACAGACGCCUGCCAGACAACG
...(((...(((.-.(.(((((.....))).((((..((........))..)))).............))...)..))).(((((((......))))))).))).... ( -32.80)
>DroSec_CAF1 66753 90 + 1
-AGGAUGCAGGUCCCUGGCC-----------------CUACCACUGCGAGCACAUAAAAACGUAUUAAGCAUAUUAUCUAGGCAGGCACAGACGCCUGCCAGACGACG
-...((((.(((.....)))-----------------.......((((............))))....)))).(..(((.(((((((......))))))))))..).. ( -25.00)
>DroEre_CAF1 66100 89 + 1
-AGGAUGCAGGUC-CUGGCC-----------------CUACCACUGCGAGCACAUAAAAACGUAUUAAGCAUAUUAUCUAGGCAGGCACAGACGCCUGCCAGCCGACG
-(((((....)))-))(((.-----------------.......(((....((........)).....))).........(((((((......))))))).))).... ( -25.80)
>DroYak_CAF1 68213 89 + 1
-CGGAUGCAGGUC-CUGGCC-----------------CUACCACUGCGAGCACAUAAAAACGUAUUAAGCAUAUUAUCUAGGCAGGCACAGACGCCUGCCAGACGACG
-((.((((.(((.-...)))-----------------.......((((............))))....))))....(((.(((((((......))))))))))))... ( -25.40)
>DroPer_CAF1 78289 107 + 1
CAGGUCGCAGGAC-GAGGUUCCAGAAUGGAAAUGGAACCAGAAUGCCGGGCCCAUAAAAACGUAUUAAGCAUAUUAUCUAGGCAGGCACAGACGCCUGCCAGACAACG
..(((((((...(-..(((((((.........))))))).)..)))..))))........................(((.(((((((......))))))))))..... ( -33.80)
>consensus
_AGGAUGCAGGUC_CUGGCC_________________CUACCACUGCGAGCACAUAAAAACGUAUUAAGCAUAUUAUCUAGGCAGGCACAGACGCCUGCCAGACGACG
.....(((((.................................)))))............................(((.(((((((......))))))))))..... (-17.65 = -18.04 +   0.39)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,246,853 – 19,246,943
Length 90
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 80.93
Mean single sequence MFE -31.97
Consensus MFE -20.01
Energy contribution -19.60
Covariance contribution -0.41
Combinations/Pair 1.10
Mean z-score -1.54
Structure conservation index 0.63
SVM decision value 0.00
SVM RNA-class probability 0.534099
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19246853 90 - 22407834
CGUCGUCUGGCAGGCGUCUGUGCCUGCCUAGAUAAUAUGCUUAAUACGUUUUUAUGUGCUCGCAGUGGUAG-----------------GGCCAG-GACCUGCAUCCUU
.((..(((((((((((....)))))))).)))..)).(((....(((((....)))))...)))...((((-----------------(.....-..)))))...... ( -29.60)
>DroPse_CAF1 75156 107 - 1
CGUUGUCUGGCAGGCGUCUGUGCCUGCCUAGAUAAUAUGCUUAAUACGUUUUUAUGGGCCCGGCAUUCUGGUUCCAUUUCCAUUCUGGAGCCUC-GUCCUGCGACCUG
.(((((((((((((((....)))))))).)))))))..((((...........((((..((((....))))..))))..........)))).((-(.....))).... ( -37.20)
>DroSec_CAF1 66753 90 - 1
CGUCGUCUGGCAGGCGUCUGUGCCUGCCUAGAUAAUAUGCUUAAUACGUUUUUAUGUGCUCGCAGUGGUAG-----------------GGCCAGGGACCUGCAUCCU-
.((..(((((((((((....)))))))).)))..)).(((....(((((....)))))...)))...((((-----------------(.(....).))))).....- ( -30.00)
>DroEre_CAF1 66100 89 - 1
CGUCGGCUGGCAGGCGUCUGUGCCUGCCUAGAUAAUAUGCUUAAUACGUUUUUAUGUGCUCGCAGUGGUAG-----------------GGCCAG-GACCUGCAUCCU-
....((...(((((..((((..((((((.........(((....(((((....)))))...)))..)))))-----------------)..)))-).)))))..)).- ( -28.30)
>DroYak_CAF1 68213 89 - 1
CGUCGUCUGGCAGGCGUCUGUGCCUGCCUAGAUAAUAUGCUUAAUACGUUUUUAUGUGCUCGCAGUGGUAG-----------------GGCCAG-GACCUGCAUCCG-
.((..(((((((((((....)))))))).)))..)).(((....(((((....)))))...)))...((((-----------------(.....-..))))).....- ( -29.60)
>DroPer_CAF1 78289 107 - 1
CGUUGUCUGGCAGGCGUCUGUGCCUGCCUAGAUAAUAUGCUUAAUACGUUUUUAUGGGCCCGGCAUUCUGGUUCCAUUUCCAUUCUGGAACCUC-GUCCUGCGACCUG
.(((((((((((((((....)))))))).))))))).(((.....(((.....((((..((((....))))..))))((((.....))))...)-))...)))..... ( -37.10)
>consensus
CGUCGUCUGGCAGGCGUCUGUGCCUGCCUAGAUAAUAUGCUUAAUACGUUUUUAUGUGCUCGCAGUGGUAG_________________GGCCAG_GACCUGCAUCCU_
.(((((((((((((((....)))))))).)))).....((...(((......)))..)).............................)))................. (-20.01 = -19.60 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:01 2006