Locus 3238

Sequence ID 2L_DroMel_CAF1
Location 9,306,334 – 9,306,458
Length 124
Max. P 0.977741
window5144 window5145 window5146

overview

Window 4

Location 9,306,334 – 9,306,437
Length 103
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 85.01
Mean single sequence MFE -28.40
Consensus MFE -23.47
Energy contribution -23.50
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -1.49
Structure conservation index 0.83
SVM decision value -0.06
SVM RNA-class probability 0.505296
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9306334 103 + 22407834
UCUGGCCGC--UGCAUUGUUGCCGCUUUUCUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCCCCUGUUCUCACCCAUU--
...(((.((--((.....((((((......))))))(((....(((....)))(((((....)))))))).........)))).)))..................-- ( -28.90)
>DroSec_CAF1 135798 101 + 1
UCUGGCCGC--UGCAUUGUUGCCGCUUUUCUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCC-CCU-UCUCGCCCAUU--
...(((.((--((.....((((((......))))))(((....(((....)))(((((....)))))))).........)))).)))..-...-...........-- ( -28.90)
>DroSim_CAF1 138896 102 + 1
UCUGGCCGC--UGCAUUGUUGCCGCUUUUCUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCCCCCG-UCUCACCCAUU--
...(((.((--((.....((((((......))))))(((....(((....)))(((((....)))))))).........)))).)))......-...........-- ( -28.90)
>DroEre_CAF1 148021 103 + 1
UCUGGGCGC--UGCAUUGUUGCCGCUCUUCUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCCACCGCCCC-CCG-UUUCAACCAUUUC
...(((((.--((.....((((((......))))))(((....(((....)))(((((....))))))))..........)).))))).-...-............. ( -28.60)
>DroYak_CAF1 144285 90 + 1
UCUGGCCGC--UGCAUUGUUGCCGCUUUUCUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUCCCU---------------UUUCACCCAUUUC
..(((((((--((((...((((((......))))))......((((....))))..)).)))).)))))..........---------------............. ( -26.10)
>DroAna_CAF1 136505 95 + 1
UCUGGCCGCAUUGCAUUGUUGCCGCUUUUCUGGCAAAUGUUGCGCUGUCAAGCGCCUGUCGACGGGCCAAGCUUUUCCCCAGAUUUCCC----------CUCAUU--
(((((..(((.((((...((((((......))))))....)))).))).(((((((((....)))))...))))....)))))......----------......-- ( -29.00)
>consensus
UCUGGCCGC__UGCAUUGUUGCCGCUUUUCUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCC_CCG_UCUCACCCAUU__
..((((.((...(((((..(((((......))))))))))...)).)))).(.(((((....))))))....................................... (-23.47 = -23.50 +   0.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,306,361 – 9,306,458
Length 97
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 75.84
Mean single sequence MFE -19.96
Consensus MFE -16.87
Energy contribution -17.07
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -0.64
Structure conservation index 0.85
SVM decision value 0.14
SVM RNA-class probability 0.601579
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9306361 97 + 22407834
CUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCCCCUGUUCUCACCCAUU------------------UCCCACCUGCCACAUGUCUCU---
..((((.......((((....))))..(((.((((((..(((........(((........)))........))).------------------.....)))))))))))))...--- ( -20.09)
>DroSec_CAF1 135825 95 + 1
CUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCC-CCU-UCUCGCCCAUU------------------UCCCACCUGCCACAUGUCUCU---
.(((((..((...((((....))))......(((.(((..((........))))))))..-...-...........------------------...))..))))).........--- ( -19.40)
>DroSim_CAF1 138923 96 + 1
CUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCCCCCG-UCUCACCCAUU------------------UCCCACCUGCCACAUGUCUCU---
.(((((..((...((((....))))...(.(((..(((..((........))...)))...)))-.).........------------------...))..))))).........--- ( -19.70)
>DroEre_CAF1 148048 113 + 1
CUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCCACCGCCCC-CCG-UUUCAACCAUUUCCACCAUUUCCACCAUUUCCCACCUGCCACAUGUCUCU---
.(((((..((....(((....)))(((((....)))))......................-...-................................))..))))).........--- ( -18.90)
>DroAna_CAF1 136534 87 + 1
CUGGCAAAUGUUGCGCUGUCAAGCGCCUGUCGACGGGCCAAGCUUUUCCCCAGAUUUCCC----------CUCAUU------------------UUCCACCUGCCACAUGUCUCU---
.(((((..((..(((((....)))))(((..((..(((...)))..))..))).......----------......------------------...))..))))).........--- ( -21.70)
>DroPer_CAF1 161155 87 + 1
CUGGCAAAUGUUACGCUGUCAAACGCCUGUCGGCAUGCAAUGGC-----------GCUGU-GCU-UUCCUUUUAUU------------------UUCCACCUGCCACAUGUCUCGGCG
.(((((..........)))))..((((....((((((...((((-----------(..((-(..-...........------------------...))).)))))))))))..)))) ( -19.99)
>consensus
CUGGCAAAUGUUACGCUGUCAAGCGCCUGUCGGCAGGCCAUGUUUUUCCUCAGCCGCCCC_CCG_UCUCACCCAUU__________________UCCCACCUGCCACAUGUCUCU___
.(((((..((....(((....)))(((((....)))))...........................................................))..)))))............ (-16.87 = -17.07 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,306,361 – 9,306,458
Length 97
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 75.84
Mean single sequence MFE -31.08
Consensus MFE -22.83
Energy contribution -23.83
Covariance contribution 1.00
Combinations/Pair 1.18
Mean z-score -1.98
Structure conservation index 0.73
SVM decision value 1.80
SVM RNA-class probability 0.977741
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9306361 97 - 22407834
---AGAGACAUGUGGCAGGUGGGA------------------AAUGGGUGAGAACAGGGGGGCGGCUGAGGAAAAACAUGGCCUGCCGACAGGCGCUUGACAGCGUAACAUUUGCCAG
---.........(((((((((...------------------...............(..((((((((.(......).))))).)))..)..(((((....)))))..))))))))). ( -31.00)
>DroSec_CAF1 135825 95 - 1
---AGAGACAUGUGGCAGGUGGGA------------------AAUGGGCGAGA-AGG-GGGGCGGCUGAGGAAAAACAUGGCCUGCCGACAGGCGCUUGACAGCGUAACAUUUGCCAG
---.........(((((((((..(------------------..((..((((.-..(-..((((((((.(......).))))).)))..).....)))).))...)..))))))))). ( -31.40)
>DroSim_CAF1 138923 96 - 1
---AGAGACAUGUGGCAGGUGGGA------------------AAUGGGUGAGA-CGGGGGGGCGGCUGAGGAAAAACAUGGCCUGCCGACAGGCGCUUGACAGCGUAACAUUUGCCAG
---.........(((((((((...------------------...........-...(..((((((((.(......).))))).)))..)..(((((....)))))..))))))))). ( -31.00)
>DroEre_CAF1 148048 113 - 1
---AGAGACAUGUGGCAGGUGGGAAAUGGUGGAAAUGGUGGAAAUGGUUGAAA-CGG-GGGGCGGUGGAGGAAAAACAUGGCCUGCCGACAGGCGCUUGACAGCGUAACAUUUGCCAG
---.........(((((((((.....((((...(((.((....)).)))...)-)((-.((((.(((.........))).)))).))..)).(((((....)))))..))))))))). ( -38.30)
>DroAna_CAF1 136534 87 - 1
---AGAGACAUGUGGCAGGUGGAA------------------AAUGAG----------GGGAAAUCUGGGGAAAAGCUUGGCCCGUCGACAGGCGCUUGACAGCGCAACAUUUGCCAG
---.........(((((((((...------------------..(((.----------(((....(..((......))..)))).)))....(((((....)))))..))))))))). ( -30.70)
>DroPer_CAF1 161155 87 - 1
CGCCGAGACAUGUGGCAGGUGGAA------------------AAUAAAAGGAA-AGC-ACAGC-----------GCCAUUGCAUGCCGACAGGCGUUUGACAGCGUAACAUUUGCCAG
............(((((((((...------------------.......(...-...-.).((-----------((..(((.(((((....))))).)))..))))..))))))))). ( -24.10)
>consensus
___AGAGACAUGUGGCAGGUGGGA__________________AAUGGGUGAGA_CGG_GGGGCGGCUGAGGAAAAACAUGGCCUGCCGACAGGCGCUUGACAGCGUAACAUUUGCCAG
............(((((((((.......................................(((((((..(......)..)))).))).....(((((....)))))..))))))))). (-22.83 = -23.83 +   1.00)

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 10:47:44 2006