Locus 1579

Sequence ID 3L_DroMel_CAF1
Location 4,609,903 – 4,610,050
Length 147
Max. P 0.988147
window2448 window2449 window2450 window2451

overview

Window 8

Location 4,609,903 – 4,610,012
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.56
Mean single sequence MFE -41.65
Consensus MFE -23.98
Energy contribution -24.48
Covariance contribution 0.50
Combinations/Pair 1.05
Mean z-score -2.65
Structure conservation index 0.58
SVM decision value 2.11
SVM RNA-class probability 0.988147
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4609903 109 + 23771897
-----CCGGUUCGGGAUCAGGUUCCGGUGCC------GGGGCCAAGGGCGCCAAGGAGAACAACAUUUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCGAAGUA
-----..(.((((((.((.(((((((....)------))))))..((.(((((.(..(((.....)))..).))))).))((((((((((.....))))))))..)))).).))))).). ( -43.80)
>DroVir_CAF1 221407 97 + 1
--------------GC---GGCGCCUCGUCG------GCGUCGAAGGGCGCCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUA
--------------(.---((((((.(((((------(((((....))))))..(.....).......)))).)))((.(((((((((((.....))))))))..))).))))))..... ( -44.40)
>DroGri_CAF1 207721 111 + 1
UGUGGCAACAACGGGU---GGCGCCUCCGCG------ACUAAGGGGGGCGCCAAGGAGAACAACAUUUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUA
..((....)).(...(---(((((((((.(.------.....))))))))))).).........(((((....(((((.(((((((((((.....))))))))..))).)))))))))). ( -46.30)
>DroWil_CAF1 165548 106 + 1
-----CUGCAGCUGGG---GGCAACUCAUCG------AGCACUAAGGGCGCCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAACGUCCGCCCAAGUA
-----.(((.(((.((---(....)))....------))).....((((((((.(...............).))))((.((.((((((((.....))))))))...)).))))))..))) ( -32.46)
>DroMoj_CAF1 245025 104 + 1
GGUGGCA-------GU---GGUGCCGCCGCU------GCAUCGAAGGGCGCCAAGGAGAACAAUAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUA
((((.((-------((---((.....)))))------)))))...((((((((.(...............).))))((.(((((((((((.....))))))))..))).))))))..... ( -42.46)
>DroAna_CAF1 196771 115 + 1
-----CUGGCUCGGGCUCAGGAUCCGGAUCCGGAACUGGCGCCAAGGGCACCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAACGACCGCCGAAGUA
-----...((((.(((((((..((((....)))).)))).)))..)))).......................((((((.((.((((((((.....))))))))...)).))))))..... ( -40.50)
>consensus
_____CAG___CGGGC___GGCGCCGCAGCG______GCCACGAAGGGCGCCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUA
...................(((.((.....................)).))).....................(((((.(((((((((((.....))))))))..))).)))))...... (-23.98 = -24.48 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,609,903 – 4,610,012
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.56
Mean single sequence MFE -37.91
Consensus MFE -25.33
Energy contribution -25.14
Covariance contribution -0.19
Combinations/Pair 1.10
Mean z-score -1.91
Structure conservation index 0.67
SVM decision value 1.43
SVM RNA-class probability 0.953462
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4609903 109 - 23771897
UACUUCGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAAAUGUUGUUCUCCUUGGCGCCCUUGGCCCC------GGCACCGGAACCUGAUCCCGAACCGG-----
......(((((((((..((((((.........)))))))))))))))..(((((............)))))(((...))).((------((..(.(((......))).)..))))----- ( -37.10)
>DroVir_CAF1 221407 97 - 1
UAUUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGCGCCCUUCGACGC------CGACGAGGCGCC---GC--------------
......(((((((((..((((((.........))))))))))))))).....................(((((((.(((....------))).).))))))---..-------------- ( -40.20)
>DroGri_CAF1 207721 111 - 1
UAUUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAAAUGUUGUUCUCCUUGGCGCCCCCCUUAGU------CGCGGAGGCGCC---ACCCGUUGUUGCCACA
(((((((((((((((..((((((.........)))))))))))))))....))))))..........(((((((.(((.....------.).)).))))))---)............... ( -41.00)
>DroWil_CAF1 165548 106 - 1
UACUUGGGCGGACGUUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGCGCCCUUAGUGCU------CGAUGAGUUGCC---CCCAGCUGCAG-----
......(((((.(((..((((((.........))))))))).))))).........((((..(((.(((((((.....)))).------))).))).....---..)))).....----- ( -28.30)
>DroMoj_CAF1 245025 104 - 1
UAUUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUAUUGUUCUCCUUGGCGCCCUUCGAUGC------AGCGGCGGCACC---AC-------UGCCACC
......(((((((((..((((((.........)))))))))))))))..((((..............))))(((((.......------)).)))((((..---..-------))))... ( -35.84)
>DroAna_CAF1 196771 115 - 1
UACUUCGGCGGUCGUUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGUGCCCUUGGCGCCAGUUCCGGAUCCGGAUCCUGAGCCCGAGCCAG-----
......(((((((((..((((((.........)))))))))))))))............((((....(((((((...)))))))((((.((((....)))).))))..))))...----- ( -45.00)
>consensus
UACUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGCGCCCUUCGACCC______CGAGGAGGCGCC___ACCCG___CAG_____
......(((((((((..((((((.........))))))))))))))).(((((..............)))))................................................ (-25.33 = -25.14 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,609,932 – 4,610,050
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.33
Mean single sequence MFE -35.48
Consensus MFE -24.69
Energy contribution -25.47
Covariance contribution 0.78
Combinations/Pair 1.10
Mean z-score -1.57
Structure conservation index 0.70
SVM decision value 0.10
SVM RNA-class probability 0.581837
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4609932 118 + 23771897
GCCAAGGGCGCCAAGGAGAACAACAUUUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCGAAGUACAAGCCACCGGAUUUCACCUAGUGUCG--UCUCAUUCCCG
.....(((.......((((...(((((.(....(((((.(((((((((((.....))))))))..))).)))))(((((.(........).)))))..).)))))..--))))...))). ( -36.00)
>DroVir_CAF1 221424 106 + 1
UCGAAGGGCGCCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUACAAGCCGCCGGACUUUACCUAGCGCC--------------
......(((((..(((...............(.(((((.(((((((((((.....))))))))..))).))))))......(((((...)).)))..))).)))))-------------- ( -34.40)
>DroGri_CAF1 207752 117 + 1
AAGGGGGGCGCCAAGGAGAACAACAUUUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUAUAAACCGCCCGAUUUUACCUAAUCCCG--GGAAAUUCCG-
..(((((((((((.(..(((.....)))..).))))((.(((((((((((.....))))))))..))).))))))............((((..............))--))....))).- ( -37.64)
>DroWil_CAF1 165574 120 + 1
ACUAAGGGCGCCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAACGUCCGCCCAAGUACAAGCCGCCAGAUUUUACCUAGCGUCUAACCUAAAUCCUC
.....((((((..(((((((((.....))...(((((((...((((((((.....))))))))....((.(......).))..)))))))..)))).))).))))))............. ( -31.90)
>DroMoj_CAF1 245049 106 + 1
UCGAAGGGCGCCAAGGAGAACAAUAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUACAAGCCGCCGGAUUUUACCUAGCAUA--------------
.....((((((((.(...............).))))((.(((((((((((.....))))))))..))).))))))...........((..(.......)..))...-------------- ( -30.66)
>DroAna_CAF1 196806 118 + 1
GCCAAGGGCACCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAACGACCGCCGAAGUACAAGCCGCCGGACUUCCCCUAGCGGCG--UGUACCUUCCC
(((...))).....((((..............((((((.((.((((((((.....))))))))...)).))))))..(((((.(((((..(.......)..))))).--))))).)))). ( -42.30)
>consensus
ACGAAGGGCGCCAAGGAGAACAACAUAUGACGUGGCGGCCGCAAUUGGUUAUAGAAGCCAAUUAAGCGACCGCCCAAAUACAAGCCGCCGGAUUUUACCUAGCGUCG____UAA_UCC__
......(((((..(((.(((((.....))....(((((.(((((((((((.....))))))))..))).)))))...................))).))).))))).............. (-24.69 = -25.47 +   0.78)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,609,932 – 4,610,050
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.33
Mean single sequence MFE -40.93
Consensus MFE -30.48
Energy contribution -30.09
Covariance contribution -0.39
Combinations/Pair 1.27
Mean z-score -1.83
Structure conservation index 0.74
SVM decision value 0.44
SVM RNA-class probability 0.737479
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4609932 118 - 23771897
CGGGAAUGAGA--CGACACUAGGUGAAAUCCGGUGGCUUGUACUUCGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAAAUGUUGUUCUCCUUGGCGCCCUUGGC
.(((((..(((--((.((((.((......))))))...........(((((((((..((((((.........))))))))))))))).)))).....)..)))))......(((...))) ( -40.40)
>DroVir_CAF1 221424 106 - 1
--------------GGCGCUAGGUAAAGUCCGGCGGCUUGUAUUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGCGCCCUUCGA
--------------(((((((((...((..(((((...((....(((((((((((..((((((.........))))))))))))))).)).))..)))))..)).)))))))))...... ( -44.70)
>DroGri_CAF1 207752 117 - 1
-CGGAAUUUCC--CGGGAUUAGGUAAAAUCGGGCGGUUUAUAUUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAAAUGUUGUUCUCCUUGGCGCCCCCCUU
-.((......)--)(((....(((...)))((((............(((((((((..((((((.........)))))))))))))))..(((((............)))))))))))).. ( -39.80)
>DroWil_CAF1 165574 120 - 1
GAGGAUUUAGGUUAGACGCUAGGUAAAAUCUGGCGGCUUGUACUUGGGCGGACGUUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGCGCCCUUAGU
((((...(((((.((.((((((((...)))))))).))...)))))(((((.(((..((((((.........))))))))).))))).(((((..............))))).))))... ( -37.84)
>DroMoj_CAF1 245049 106 - 1
--------------UAUGCUAGGUAAAAUCCGGCGGCUUGUAUUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUAUUGUUCUCCUUGGCGCCCUUCGA
--------------...(((.((......)))))(((.........(((((((((..((((((.........)))))))))))))))..((((..............)))))))...... ( -34.84)
>DroAna_CAF1 196806 118 - 1
GGGAAGGUACA--CGCCGCUAGGGGAAGUCCGGCGGCUUGUACUUCGGCGGUCGUUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGUGCCCUUGGC
(((.(((((((--.((((((.(((....))))))))).))))))).(((((((((..((((((.........))))))))))))))).........................)))..... ( -48.00)
>consensus
__GGA_UUA____CGACGCUAGGUAAAAUCCGGCGGCUUGUACUUGGGCGGUCGCUUAAUUGGCUUCUAUAACCAAUUGCGGCCGCCACGUCAUAUGUUGUUCUCCUUGGCGCCCUUCGA
.............................((((.(((.........(((((((((..((((((.........)))))))))))))))..((((..............))))))).)))). (-30.48 = -30.09 +  -0.39)

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 10:11:09 2006