Locus 2461

Sequence ID 2R_DroMel_CAF1
Location 8,839,231 – 8,839,363
Length 132
Max. P 0.928982
window4062 window4063 window4064

overview

Window 2

Location 8,839,231 – 8,839,339
Length 108
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 92.57
Mean single sequence MFE -29.42
Consensus MFE -26.40
Energy contribution -26.48
Covariance contribution 0.08
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.90
SVM decision value 1.19
SVM RNA-class probability 0.928982
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8839231 108 + 20766785
GACAAUUGCAUUAAAUUCGCCUGCACAACGGUGCGUAUGCGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGGGUAG-----
(((....(((((((((.(((.(((((....)))))...)))....)))))).))).)))((((((((........))))))))......(((((.........)))))----- ( -31.90)
>DroPse_CAF1 94376 106 + 1
GACAAAUGCAUUAAAUUUUCCUGCACAGCAGUGCGUAUGCGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCAAGA-------
(((...((((...........))))..(((((..(.(((.(((((.....)))))))))((((((((........)))))))).....)))))..)))........------- ( -27.70)
>DroEre_CAF1 85949 108 + 1
GACAAUUGCAUUAAAUUCGCCUGCACAACGGUGCGUAUGCGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAGCCAGGAAG-----
(((....(((((((((.(((.(((((....)))))...)))....)))))).))).)))((((((((........))))))))......(((.(.....).)))....----- ( -29.00)
>DroYak_CAF1 86967 108 + 1
GACAAUUGCAUUAAAUUCGCCUGCACAACGGUGCGUAUGCGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGGCAAG-----
(((....(((((((((.(((.(((((....)))))...)))....)))))).))).)))((((((((........)))))))).......((((........))))..----- ( -32.60)
>DroAna_CAF1 84472 113 + 1
GACAAUUGCAUUAAAUUUGCCUGCACAACGGUGCGUAUGCGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGAGCUGCUUGU
(((....(((((((((.(((.(((((....)))))...)))....)))))).))).)))((((((((........))))))))........((.(((.......))))).... ( -27.60)
>DroPer_CAF1 97484 106 + 1
GACAAAUGCAUUAAAUUUUCCUGCACAGCAGUGCGUAUGCGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCAAGA-------
(((...((((...........))))..(((((..(.(((.(((((.....)))))))))((((((((........)))))))).....)))))..)))........------- ( -27.70)
>consensus
GACAAUUGCAUUAAAUUCGCCUGCACAACGGUGCGUAUGCGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCAAGAAG_____
(((....(((((((((.(((.(((((....)))))...)))....)))))).)))....((((((((........))))))))............)))............... (-26.40 = -26.48 +   0.08)

alignment

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secondary structure

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Window 3

Location 8,839,270 – 8,839,363
Length 93
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 73.41
Mean single sequence MFE -21.52
Consensus MFE -14.00
Energy contribution -14.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.65
SVM decision value 1.12
SVM RNA-class probability 0.918308
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8839270 93 + 20766785
CGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGGGUAG----------CGACCACCACCA---ACCAACUUCAC--------C
.(((((.....))))).(((((((((((........))))))))......(((((.........)))))----------.)))........---...........--------. ( -21.90)
>DroSec_CAF1 84091 95 + 1
CGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGGGUAG----------CGACC-----CC---ACCGCCUUCACCACCACC-C
.(((((.....))))).(((((((((((........))))))))......(((((.........)))))----------.))).-----..---..................-. ( -21.90)
>DroEre_CAF1 85988 84 + 1
CGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAGCCAGGAAG----------CGACCCCACCACUCC--------------------
.(((((.....))))).(((((((((((........))))))))......(((.(.....).)))....----------.)))...........-------------------- ( -18.60)
>DroYak_CAF1 87006 104 + 1
CGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGGCAAG----------CGACCCCCUCCCUCCCCCGCCCUCUCCACUCCCAU
.(((((.....))))).(((((((((((........)))))))).......((((........))))..----------.)))............................... ( -22.20)
>DroAna_CAF1 84511 99 + 1
CGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGAGCUGCUUGUAGCUGCGGCUCCUACCCU---------GUACUA------U
.(((((.....)))))....((((((((........))))))))..........(((......(((((((........))))))).....))---------).....------. ( -27.20)
>DroPer_CAF1 97523 76 + 1
CGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCAAGA---------------CUACACCUC-----------------------
.(((((.....)))))....((((((((........))))))))...........((((......))---------------)).......----------------------- ( -17.30)
>consensus
CGUAAUGUUUAAUUGCCGUCAGCAGCUUCAUUAGAAGAGCUGCUAAAUAACUGCCAGUCAACCGGGAAG__________CGACCCCAACCC__________UCAC_________
.(((((.....)))))....((((((((........))))))))...................................................................... (-14.00 = -14.00 +   0.00)

alignment

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secondary structure

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Window 4

Location 8,839,270 – 8,839,363
Length 93
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 73.41
Mean single sequence MFE -27.60
Consensus MFE -18.02
Energy contribution -17.97
Covariance contribution -0.05
Combinations/Pair 1.16
Mean z-score -1.05
Structure conservation index 0.65
SVM decision value 0.00
SVM RNA-class probability 0.535964
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8839270 93 - 20766785
G--------GUGAAGUUGGU---UGGUGGUGGUCG----------CUACCCGGUUGACUGGCAGUUAUUUAGCAGCUCUUCUAAUGAAGCUGCUGACGGCAAUUAAACAUUACG
.--------((((.((..((---(((((((....)----------))))).....)))..)).(((..(((((((((..((....))))))))))).))).........)))). ( -29.50)
>DroSec_CAF1 84091 95 - 1
G-GGUGGUGGUGAAGGCGGU---GG-----GGUCG----------CUACCCGGUUGACUGGCAGUUAUUUAGCAGCUCUUCUAAUGAAGCUGCUGACGGCAAUUAAACAUUACG
.-.((((((.((..(((..(---.(-----(((..----------..)))).)..).))..))(((..(((((((((..((....))))))))))).))).......)))))). ( -30.20)
>DroEre_CAF1 85988 84 - 1
--------------------GGAGUGGUGGGGUCG----------CUUCCUGGCUGACUGGCAGUUAUUUAGCAGCUCUUCUAAUGAAGCUGCUGACGGCAAUUAAACAUUACG
--------------------...((((((.(((((----------((....))).)))).((.(((....(((((((..((....)))))))))))).)).......)))))). ( -26.70)
>DroYak_CAF1 87006 104 - 1
AUGGGAGUGGAGAGGGCGGGGGAGGGAGGGGGUCG----------CUUGCCGGUUGACUGGCAGUUAUUUAGCAGCUCUUCUAAUGAAGCUGCUGACGGCAAUUAAACAUUACG
.....((((..((..((.(..(((.((.....)).----------)))(((((....)))))......(((((((((..((....)))))))))))).))..))...))))... ( -29.50)
>DroAna_CAF1 84511 99 - 1
A------UAGUAC---------AGGGUAGGAGCCGCAGCUACAAGCAGCUCGGUUGACUGGCAGUUAUUUAGCAGCUCUUCUAAUGAAGCUGCUGACGGCAAUUAAACAUUACG
.------..(((.---------.(..(((..((((..((.....)).((.(((....)))))......(((((((((..((....)))))))))))))))..)))..)..))). ( -29.00)
>DroPer_CAF1 97523 76 - 1
-----------------------GAGGUGUAG---------------UCUUGGUUGACUGGCAGUUAUUUAGCAGCUCUUCUAAUGAAGCUGCUGACGGCAAUUAAACAUUACG
-----------------------.....((((---------------(.(((((((.(((........(((((((((..((....)))))))))))))))))))))..))))). ( -20.70)
>consensus
_________GUGA__________GGGGGGGGGUCG__________CUUCCCGGUUGACUGGCAGUUAUUUAGCAGCUCUUCUAAUGAAGCUGCUGACGGCAAUUAAACAUUACG
...............................((((..............((((....)))).......(((((((((..((....))))))))))))))).............. (-18.02 = -17.97 +  -0.05)

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 10:30:37 2006