Locus 1304

Sequence ID 3R_DroMel_CAF1
Location 3,828,229 – 3,828,482
Length 253
Max. P 0.895231
window2137 window2138 window2139 window2140

overview

Window 7

Location 3,828,229 – 3,828,322
Length 93
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 85.80
Mean single sequence MFE -23.70
Consensus MFE -15.44
Energy contribution -15.92
Covariance contribution 0.48
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.65
SVM decision value 0.53
SVM RNA-class probability 0.771735
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3828229 93 - 27905053
CAAAAGAAGUGGACGCAGCUCAAGUAGACCACGAUCAAGGAAAUGAGCUGC------AAUCAAUUAAAAAUGUUCUGUUUUUUCGUUCUUUUCUAUAUC
....(((((.((((((((((((......((........))...))))))))------........((((((.....))))))..)))).)))))..... ( -21.90)
>DroSec_CAF1 841 93 - 1
CAGAAGAAGUGGACGCAGCUCAAGUAGACCACGAUCAAGGAAAUGAGCUGC------AAUAAAUUUAAAAAGUUUUGUUAUUUCGUUCUUUUCUAUAUC
....(((((.((((((((((((......((........))...))))))))------((((((..........)))))).....)))).)))))..... ( -22.20)
>DroSim_CAF1 589 93 - 1
CAGAAGAAGUGGACGCAGCUCAAGUAGACCACGAUCAAGGAAAUGAGCUGC------AAUCAAUUAAAGAAGUUUUGUUAUUUCGUUCUUUUCUAUAUC
....(((((.((((((((((((......((........))...))))))))------...........(((((......))))))))).)))))..... ( -24.60)
>DroEre_CAF1 1701 99 - 1
CAGAAGAAGUGAACGCAGCUCAAAUAGACCACGAUCAAGGAAAUGAGCUGCGGAGCAAAUCAGUUAAAAAAUUGUUGUUAUAUCGUUCAUUUCUAUAUU
....((((((((((((((((((......((........))...))))))))..(((((..(((((....)))))))))).....))))))))))..... ( -30.40)
>DroYak_CAF1 1668 99 - 1
CAGAAGAAGUGGACGCAGCUCAAAUAGACCACAAUCAAGGAAAUUAGCUAAGGAGCAAAUCAGUUUAAAAAGUUGUGUUAUUUCGUUCGCUUAUGUAUU
..(((((((((.((((((((.((((.((((........))......(((....)))...)).))))....)))))))))))))).)))........... ( -19.40)
>consensus
CAGAAGAAGUGGACGCAGCUCAAGUAGACCACGAUCAAGGAAAUGAGCUGC______AAUCAAUUAAAAAAGUUUUGUUAUUUCGUUCUUUUCUAUAUC
....(((((.((((((((((((......((........))...)))))))).........................(......))))).)))))..... (-15.44 = -15.92 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,828,264 – 3,828,362
Length 98
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 83.92
Mean single sequence MFE -30.50
Consensus MFE -27.79
Energy contribution -27.10
Covariance contribution -0.69
Combinations/Pair 1.40
Mean z-score -1.56
Structure conservation index 0.91
SVM decision value 0.53
SVM RNA-class probability 0.770087
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3828264 98 + 27905053
AUUGAUU------GCAGCUCAUUUCCUUGAUCGUGGUCUACUUGAGCUGCGUCCACUUCUUUUGGAGGCCAGAGAAUAGUGCCCACUUCGUGGUCGCCGGACAA
.......------((((((((...((........))......))))))))((((..((((((.((...))))))))..(((.((((...)))).))).)))).. ( -32.90)
>DroSec_CAF1 876 98 + 1
AUUUAUU------GCAGCUCAUUUCCUUGAUCGUGGUCUACUUGAGCUGCGUCCACUUCUUCUGGAAGCCAGAGAACAGUGCCCACUUCGUGGUCGCCGGACAG
.......------((((((((...((........))......))))))))((((..((((.((((...))))))))..(((.((((...)))).))).)))).. ( -35.40)
>DroSim_CAF1 624 98 + 1
AUUGAUU------GCAGCUCAUUUCCUUGAUCGUGGUCUACUUGAGCUGCGUCCACUUCUUCUGGAAGCCAGAGAACAGUGCCCACUUCGUGGUCGCCGGACAA
.......------((((((((...((........))......))))))))((((..((((.((((...))))))))..(((.((((...)))).))).)))).. ( -35.40)
>DroEre_CAF1 1736 104 + 1
ACUGAUUUGCUCCGCAGCUCAUUUCCUUGAUCGUGGUCUAUUUGAGCUGCGUUCACUUCUUCUGGAAGCCAGAGAACAGUGCACACUUCGUGAUCGCCGGACAG
.......((.(((((((((((...((........))......))))))))((.(((((((.((((...)))))))..)))).))..............))))). ( -30.80)
>DroYak_CAF1 1703 104 + 1
ACUGAUUUGCUCCUUAGCUAAUUUCCUUGAUUGUGGUCUAUUUGAGCUGCGUCCACUUCUUCUGGAAGCCAGAGAACAGUGCCCACUUUGUGGUCGCCGGACAG
........((((..((((((...((...))...))).)))...))))...((((..((((.((((...))))))))..(((.((((...)))).))).)))).. ( -27.60)
>DroAna_CAF1 586 98 + 1
UUUAAUU------ACAGCUAAUUUCUCUGGUGAUUAUAUACUUGAGUUGUGUCCACUUUUUCUGGAAGCCGGAAAACAGCGCUCACUUUGUUGUUGCUGGCCAA
.......------.((((......(((.((((......)))).)))..(((..(.((((((((((...)))))))).)).)..))).........))))..... ( -20.90)
>consensus
AUUGAUU______GCAGCUCAUUUCCUUGAUCGUGGUCUACUUGAGCUGCGUCCACUUCUUCUGGAAGCCAGAGAACAGUGCCCACUUCGUGGUCGCCGGACAA
.............((((((((.......(((....)))....))))))))((((..((((.((((...))))))))..(((.((((...)))).))).)))).. (-27.79 = -27.10 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,828,322 – 3,828,442
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.06
Mean single sequence MFE -43.35
Consensus MFE -28.74
Energy contribution -27.92
Covariance contribution -0.83
Combinations/Pair 1.48
Mean z-score -1.27
Structure conservation index 0.66
SVM decision value 0.19
SVM RNA-class probability 0.624899
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3828322 120 + 27905053
GAGGCCAGAGAAUAGUGCCCACUUCGUGGUCGCCGGACAAUCCAUGUGGAUAGCUGUAGCGGGCUAUCUGAGUAGCUUUCUUGGCGCCCUGCAGGUGCCGGUAUUUCUACUGGUUAUGAC
..((((((((((....(.((((...)))).)(((((((.((((....))))..((((((.((((((...(((.....))).)))).)))))))))).)))))..)))).))))))..... ( -43.90)
>DroVir_CAF1 673 120 + 1
GAAGCCAGAGAAUAGCGCACGUUUCGUUGUCGCCGGCCAGUCCAUGUGGAUAGCCAUUGCCGGCUAUUUGUGCAGUUUUCUGGGCGCGUUUCAGGUGCCUGUUUUCCUGCUGGUCAUGGG
..(((..((((((((.((((.(..(((....(((((((.((((....)))).).....)))))).....((.(((....))).)))))....).))))))))))))..)))......... ( -40.70)
>DroGri_CAF1 1457 120 + 1
GAAACCGGAGAAUAGCUCGCAUUUCGUUAUCGCUGGCCAAACUAUGUGGAUAGCCAUUGCUGGCUAUUUGUGCAGCUUUUUGGGCGCUCUUCAAGUGCCCGUCUUUCUGCUGGUGAUGGG
....((((.((.((((.........)))))).))))(((.((((.(..((((((((....))))))))..)((((.....((((((((.....)))))))).....))))))))..))). ( -42.70)
>DroWil_CAF1 6786 120 + 1
GCGGCCAGAGAACCGAGCACAUUUUGUAGUUGCCGGUCAAUCCAUGUGGAUAGCCAUAGCCGGAUAUCUGUGCAGCUUUUUAGGAGCUCUUCAAGUACCAGUAUUCCUGCUGGUUAUGGC
...((((..(((..((((.(.......(((((((((...((((.(((((....)))))...))))..))).))))))......).)))))))....(((((((....)))))))..)))) ( -39.12)
>DroMoj_CAF1 1530 120 + 1
GAAGCCGGAGAACAAAGCGCACUUCGUAGUUGCCGGGCAGUCUAUGUGGAUAGCCAUUGCCAGCUAUUUGUGCAGCUUUCUGGGCGCCCUUCAGGUGCCGGCUCUGCUGCUUGUCAUGAG
.(((((((((...(((((((((...((((((((..(((.((((....)))).)))...).)))))))..)))).)))))...((((((.....))))))..)))))..))))........ ( -45.90)
>DroAna_CAF1 644 120 + 1
GAAGCCGGAAAACAGCGCUCACUUUGUUGUUGCUGGCCAAACCAUGUGGGUAGCCAUCGCUGGCUACUUGAGCAGUUUUCUGGGUGCCCUUCAGGUGCCCGUUUUCCUGCUGGUUAUGGC
...(((((..(((((((.......))))))).)))))((((((....(((((((((....))))))))).(((((.....((((..((.....))..)))).....))))))))).)).. ( -47.80)
>consensus
GAAGCCAGAGAACAGCGCACACUUCGUUGUCGCCGGCCAAUCCAUGUGGAUAGCCAUUGCCGGCUAUUUGUGCAGCUUUCUGGGCGCCCUUCAGGUGCCCGUUUUCCUGCUGGUUAUGGC
...(((((........((((..............((.....))....((((((((......)))))))))))).......((((((((.....))))))))........)))))...... (-28.74 = -27.92 +  -0.83)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,828,362 – 3,828,482
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.22
Mean single sequence MFE -40.25
Consensus MFE -27.95
Energy contribution -27.04
Covariance contribution -0.91
Combinations/Pair 1.40
Mean z-score -1.59
Structure conservation index 0.69
SVM decision value 0.99
SVM RNA-class probability 0.895231
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3828362 120 + 27905053
UCCAUGUGGAUAGCUGUAGCGGGCUAUCUGAGUAGCUUUCUUGGCGCCCUGCAGGUGCCGGUAUUUCUACUGGUUAUGACCUAUGUAACAGCAUCUACGGCAUAUCAUCUGCAAACCCUA
....(((((((.(((((.((((((...(..((.......))..).)))).))(((((((((((....)))))))....)))).....))))))))))))(((.......)))........ ( -39.80)
>DroVir_CAF1 713 120 + 1
UCCAUGUGGAUAGCCAUUGCCGGCUAUUUGUGCAGUUUUCUGGGCGCGUUUCAGGUGCCUGUUUUCCUGCUGGUCAUGGGCUACGUGCUUGUCUCCACGGCGUAUCAUCUGCAGACGAGU
..(((((((....((((.((((((........(((....)))(((((.......))))).........)))))).)))).)))))))(((((((.((.((.......)))).))))))). ( -39.20)
>DroGri_CAF1 1497 120 + 1
ACUAUGUGGAUAGCCAUUGCUGGCUAUUUGUGCAGCUUUUUGGGCGCUCUUCAAGUGCCCGUCUUUCUGCUGGUGAUGGGCUACGUUUGCGUCUCAACGGCGUAUCAUUUACAGACGAGC
.....(..((((((((....))))))))..)...((((...(((((((.....))))))).....((((..(((((((.((((((....)))......))).)))))))..)))).)))) ( -43.40)
>DroWil_CAF1 6826 120 + 1
UCCAUGUGGAUAGCCAUAGCCGGAUAUCUGUGCAGCUUUUUAGGAGCUCUUCAAGUACCAGUAUUCCUGCUGGUUAUGGCCUAUGUAACGGCCUCGACGGCGUAUCAUCUACAGAUUAGC
....(((((((.(((.((((.(((...(((((((((((.....)))))......))).)))...))).))))(((..((((........))))..)))))).....)))))))....... ( -38.00)
>DroMoj_CAF1 1570 120 + 1
UCUAUGUGGAUAGCCAUUGCCAGCUAUUUGUGCAGCUUUCUGGGCGCCCUUCAGGUGCCGGCUCUGCUGCUUGUCAUGAGCUACGUCAUUGCAUCCACAGCGUAUCAUCUACAGACGACU
(((.(((((((.((.((.((.((((...((.(((((....(.((((((.....)))))).)....)))))....))..))))..)).)).)))))))))..(((.....))))))..... ( -38.80)
>DroAna_CAF1 684 120 + 1
ACCAUGUGGGUAGCCAUCGCUGGCUACUUGAGCAGUUUUCUGGGUGCCCUUCAGGUGCCCGUUUUCCUGCUGGUUAUGGCAUAUGUUACGGCAUCGACGGCAUAUCACCUGCAGACAAGA
....((..(((.(((((.((..((.....((((((....))(((..((.....))..)))))))....))..)).)))))((((((..((.......)))))))).)))..))....... ( -42.30)
>consensus
UCCAUGUGGAUAGCCAUUGCCGGCUAUUUGUGCAGCUUUCUGGGCGCCCUUCAGGUGCCCGUUUUCCUGCUGGUUAUGGCCUACGUAACGGCAUCCACGGCGUAUCAUCUACAGACGAGA
.(((((.((((((((......))))))))..((((.....((((((((.....)))))))).....))))....)))))..(((((.............)))))................ (-27.95 = -27.04 +  -0.91)

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 10:06:20 2006