Locus 1369

Sequence ID 2L_DroMel_CAF1
Location 3,639,518 – 3,639,665
Length 147
Max. P 0.952065
window2237 window2238 window2239 window2240

overview

Window 7

Location 3,639,518 – 3,639,628
Length 110
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 79.68
Mean single sequence MFE -45.08
Consensus MFE -27.64
Energy contribution -28.68
Covariance contribution 1.04
Combinations/Pair 1.29
Mean z-score -1.76
Structure conservation index 0.61
SVM decision value 0.19
SVM RNA-class probability 0.624726
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3639518 110 + 22407834
GGUGAUACA---GCACCGGACUUCCUUGGCUGGUGUACAGGCCCUGCGUCUGCGCCUGAAGCUGCUGCAAUUGCUGAUAGCGCUGCUGUAGCUGCAGCUCCUGUUGGUGCAGA
((.(.....---(((((((.((.....))))))))).....)))....((((((((...((..((((((...(((.(((((...))))))))))))))..))...)))))))) ( -44.80)
>DroGri_CAF1 129137 113 + 1
GAUAGUGCACCGGCACUGGACUACCGGAUGCGGUAUAGAUGCCCUGUGUCUGUGCCUGCAACUGUUGCAAUUGCUGAUAGCGCUGCUGCAGCACCAGCUCCUGCUGAUGCAGC
(((((((((...(((((((....)))).)))(((((((((((...)))))))))))))).))))))(((..(((((.((((...))))))))).((((....)))).)))... ( -46.50)
>DroWil_CAF1 159504 110 + 1
GCUGGUAUA---GAACCGGACUCCCUGUGGCCGUAUAGAAACCUUGUGUCUGCGCCUGCAAUUGCUGCAAUUGUUGAUAGCGUUGCUGCAACUGCAGUUCCUGUUGAUGCAGC
((.((..((---((..(((.....(((((....))))).....)))..))))..)).))....((((((....(..((((.(..(((((....))))).)))))..))))))) ( -32.70)
>DroYak_CAF1 112429 110 + 1
GAUGGUACA---GCACCGGACUGCCUUGGCUGGUGUACAGACCUUGGGUCUGUGCCUGCAGUUGUUGCAAUUGCUGAUAGCGCUGCUGCAGCUGCAGCUCCUGUUGGUGCAGU
..((((...---..)))).(((((.(..((.((.(((((((((...)))))))))((((((((((.(((..(((.....))).))).))))))))))..)).))..).))))) ( -49.90)
>DroAna_CAF1 116752 110 + 1
GGUGGUACA---GCACCGGACUACCCUGGGCGGUGUACAGGCCCUGGGUCUGGGCCUGGAGCUGUUGCAGUUGCUGGUAGCGCUGCUGCAGUUGCAGCUCCUGUUGGUGCAAC
.........---(((((((.((((((.((((.(....)..)))).))))..)).)).((((((((((((((.((.......)).))))))...))))))))....)))))... ( -51.50)
>consensus
GAUGGUACA___GCACCGGACUACCUUGGGCGGUGUACAGGCCCUGGGUCUGCGCCUGCAGCUGUUGCAAUUGCUGAUAGCGCUGCUGCAGCUGCAGCUCCUGUUGGUGCAGC
...(((......((((((............))))))....)))......(((((((.((((..((((((...((((.((((...))))))))))))))..)))).))))))). (-27.64 = -28.68 +   1.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,639,518 – 3,639,628
Length 110
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 79.68
Mean single sequence MFE -40.49
Consensus MFE -19.88
Energy contribution -21.76
Covariance contribution 1.88
Combinations/Pair 1.21
Mean z-score -2.23
Structure conservation index 0.49
SVM decision value 0.72
SVM RNA-class probability 0.831678
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3639518 110 - 22407834
UCUGCACCAACAGGAGCUGCAGCUACAGCAGCGCUAUCAGCAAUUGCAGCAGCUUCAGGCGCAGACGCAGGGCCUGUACACCAGCCAAGGAAGUCCGGUGC---UGUAUCACC
(((((.((....((((((((.(((.....)))((.....)).......)))))))).)).))))).((((.(((.(.((.((......))..))).))).)---)))...... ( -38.70)
>DroGri_CAF1 129137 113 - 1
GCUGCAUCAGCAGGAGCUGGUGCUGCAGCAGCGCUAUCAGCAAUUGCAACAGUUGCAGGCACAGACACAGGGCAUCUAUACCGCAUCCGGUAGUCCAGUGCCGGUGCACUAUC
((.((((((((....)))))))).))....(((((....(((((((...))))))).(((((.(((...((....)).(((((....))))))))..))))))))))...... ( -46.30)
>DroWil_CAF1 159504 110 - 1
GCUGCAUCAACAGGAACUGCAGUUGCAGCAACGCUAUCAACAAUUGCAGCAAUUGCAGGCGCAGACACAAGGUUUCUAUACGGCCACAGGGAGUCCGGUUC---UAUACCAGC
.((((.((.....)).((((((((((.((((............)))).))))))))))..))))......(((.......(((((....))...)))....---...)))... ( -30.94)
>DroYak_CAF1 112429 110 - 1
ACUGCACCAACAGGAGCUGCAGCUGCAGCAGCGCUAUCAGCAAUUGCAACAACUGCAGGCACAGACCCAAGGUCUGUACACCAGCCAAGGCAGUCCGGUGC---UGUACCAUC
((.(((((....((.(((((....))))).((((.....))..(((((.....)))))))(((((((...)))))))...)).((....)).....)))))---.))...... ( -40.60)
>DroAna_CAF1 116752 110 - 1
GUUGCACCAACAGGAGCUGCAACUGCAGCAGCGCUACCAGCAACUGCAACAGCUCCAGGCCCAGACCCAGGGCCUGUACACCGCCCAGGGUAGUCCGGUGC---UGUACCACC
...(((((....(((((((....(((((..((.......))..))))).))))))).((.(...((((.((((.........)))).)))).).)))))))---......... ( -45.90)
>consensus
GCUGCACCAACAGGAGCUGCAGCUGCAGCAGCGCUAUCAGCAAUUGCAACAGCUGCAGGCACAGACACAGGGCCUGUACACCGCCCAAGGUAGUCCGGUGC___UGUACCACC
((((((.........(((((.......)))))((.....))...))))))...(((((((.(........))))))))..........((....))(((((....)))))... (-19.88 = -21.76 +   1.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,639,550 – 3,639,665
Length 115
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 77.03
Mean single sequence MFE -47.02
Consensus MFE -26.08
Energy contribution -26.84
Covariance contribution 0.76
Combinations/Pair 1.34
Mean z-score -1.79
Structure conservation index 0.55
SVM decision value 0.24
SVM RNA-class probability 0.649282
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3639550 115 + 22407834
UACAGGCCCUGCGUCUGCGCCUGAAGCUGCUGCAAUUGCUGAUAGCGCUGCUGUAGCUGCAGCUCCUGUUGGUGCAGAAGGCUUCGGGGAUCCUGGUUCAAUUGCUG---GGCGCCCG
..((((((.....((((((((...((..((((((...(((.(((((...))))))))))))))..))...)))))))).))))).)(((..((..((......))..---))..))). ( -51.40)
>DroGri_CAF1 129172 112 + 1
UAGAUGCCCUGUGUCUGUGCCUGCAACUGUUGCAAUUGCUGAUAGCGCUGCUGCAGCACCAGCUCCUGCUGAUGCAGCAGACUGCGUUGAUCUGUGUGC------UGUGGUGUACCCG
.((((((...))))))(((((..((......(((...((.((((((((..((((.(((.((((....)))).))).))))...))))).))).)).)))------))..).))))... ( -39.30)
>DroWil_CAF1 159536 118 + 1
UAGAAACCUUGUGUCUGCGCCUGCAAUUGCUGCAAUUGUUGAUAGCGUUGCUGCAACUGCAGUUCCUGUUGAUGCAGCAGACUCCUGGGAUCUGUGUGUAACUGCUGCAGCGUACCAC
.(((..((..(.((((((..(((((.((((.(((((.((.....))))))).)))).)))))....(((....))))))))).)..))..)))(((.(((...((....)).)))))) ( -39.90)
>DroYak_CAF1 112461 115 + 1
UACAGACCUUGGGUCUGUGCCUGCAGUUGUUGCAAUUGCUGAUAGCGCUGCUGCAGCUGCAGCUCCUGUUGGUGCAGUAGGCUGCGGGGAUCCUGGUUCAGUUGCUG---GGCGCCCG
.(((((((...)))))))(((.((((..((((((...((((.((((...))))))))))))))..)))).)))((((....)))).(((..((..((......))..---))..))). ( -53.50)
>DroAna_CAF1 116784 115 + 1
UACAGGCCCUGGGUCUGGGCCUGGAGCUGUUGCAGUUGCUGGUAGCGCUGCUGCAGUUGCAGCUCCUGUUGGUGCAACAAACUACGUGGAUCCUGGUGGAGUUGCUG---GGCACCCG
..(((((((.......))))))).((((((.(((((.((.....))))))).))))))(((((((((((((...))))).((((.(.....).)))))))))))).(---(....)). ( -51.00)
>consensus
UACAGGCCCUGGGUCUGCGCCUGCAGCUGUUGCAAUUGCUGAUAGCGCUGCUGCAGCUGCAGCUCCUGUUGGUGCAGCAGACUGCGGGGAUCCUGGUGCAAUUGCUG___GGCACCCG
..(((((.....)))))..(((((((((((((((...((((.((((...))))))))..((((....)))).)))))))).))))))).............................. (-26.08 = -26.84 +   0.76)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,639,550 – 3,639,665
Length 115
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 77.03
Mean single sequence MFE -41.34
Consensus MFE -18.36
Energy contribution -19.96
Covariance contribution 1.60
Combinations/Pair 1.25
Mean z-score -2.30
Structure conservation index 0.44
SVM decision value 1.42
SVM RNA-class probability 0.952065
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3639550 115 - 22407834
CGGGCGCC---CAGCAAUUGAACCAGGAUCCCCGAAGCCUUCUGCACCAACAGGAGCUGCAGCUACAGCAGCGCUAUCAGCAAUUGCAGCAGCUUCAGGCGCAGACGCAGGGCCUGUA
(((((.((---..((..(((..((.((....))(((((.(((((......)))))(((((((((.....)))((.....))...)))))).))))).))..)))..)).))))))).. ( -41.80)
>DroGri_CAF1 129172 112 - 1
CGGGUACACCACA------GCACACAGAUCAACGCAGUCUGCUGCAUCAGCAGGAGCUGGUGCUGCAGCAGCGCUAUCAGCAAUUGCAACAGUUGCAGGCACAGACACAGGGCAUCUA
.((.....))...------((.....(((...(((.(.((((.((((((((....)))))))).))))).)))..))).(((((((...)))))))..)).................. ( -37.00)
>DroWil_CAF1 159536 118 - 1
GUGGUACGCUGCAGCAGUUACACACAGAUCCCAGGAGUCUGCUGCAUCAACAGGAACUGCAGUUGCAGCAACGCUAUCAACAAUUGCAGCAAUUGCAGGCGCAGACACAAGGUUUCUA
((((((.((((...))))))).)))(((..((..(.((((((.((.((.....)).((((((((((.((((............)))).)))))))))))))))))).)..))..))). ( -43.30)
>DroYak_CAF1 112461 115 - 1
CGGGCGCC---CAGCAACUGAACCAGGAUCCCCGCAGCCUACUGCACCAACAGGAGCUGCAGCUGCAGCAGCGCUAUCAGCAAUUGCAACAACUGCAGGCACAGACCCAAGGUCUGUA
..(((((.---......(((.....((....))((((....)))).....)))..(((((....))))).)))))....((...((((.....)))).))(((((((...))))))). ( -41.20)
>DroAna_CAF1 116784 115 - 1
CGGGUGCC---CAGCAACUCCACCAGGAUCCACGUAGUUUGUUGCACCAACAGGAGCUGCAACUGCAGCAGCGCUACCAGCAACUGCAACAGCUCCAGGCCCAGACCCAGGGCCUGUA
..(((((.---.(((((((((....)))........).))))))))))....(((((((....(((((..((.......))..))))).)))))))((((((.......))))))... ( -43.40)
>consensus
CGGGUGCC___CAGCAACUGCACCAGGAUCCCCGCAGUCUGCUGCACCAACAGGAGCUGCAGCUGCAGCAGCGCUAUCAGCAAUUGCAACAGCUGCAGGCACAGACACAGGGCCUGUA
.................................((((.((((((((.........(((((.......)))))((.....))...))))))))))))((((.(........)))))... (-18.36 = -19.96 +   1.60)

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 10:00:52 2006