Locus 1075

Sequence ID 3R_DroMel_CAF1
Location 3,298,692 – 3,298,881
Length 189
Max. P 0.939144
window1736 window1737 window1738

overview

Window 6

Location 3,298,692 – 3,298,802
Length 110
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 80.83
Mean single sequence MFE -25.38
Consensus MFE -18.65
Energy contribution -17.93
Covariance contribution -0.72
Combinations/Pair 1.43
Mean z-score -1.81
Structure conservation index 0.73
SVM decision value 0.71
SVM RNA-class probability 0.828267
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3298692 110 - 27905053
ACCAACAGCCAGGGAU--CAAGACUAUUAUCUGUCAUUGAGUCCUAGACAGAUAGUUUAGUCUCUGGUUUACAGAACACCCAAAUGGAAAUGAAACAC-GCGCUUUUGUCGAC
..(((.((((.(((..--...((((((((((((((...........))))))))))..))))((((.....))))...)))..((....)).......-).))).)))..... ( -27.60)
>DroVir_CAF1 1057 107 - 1
AGCAA-UGCCAUUUAAUGCUAGACUGUUAUUUGUCAUUAAG-UCAAGACAAAUGAUUUAGGCUUGGGCGUACAAUC-UUUAU-UUUUUAUUGAAAC--AGUGCUAUUGUCGCC
..(((-.(((.((((....))))..((((((((((......-....))))))))))...))))))((((.(((((.-..(((-(.(((....))).--))))..))))))))) ( -21.70)
>DroSec_CAF1 3143 109 - 1
ACCAAUAGCCAGGGAU--CAAGACUAUUAUCUGUCCUUAAGUUCUAGACAGGUAGUUUAGUCUCUGUCUUACAGAACACCCAAAU-GAAAUGAAACAC-GCGCUAUUGUCGAC
..((((((((.(((..--...((((((((((((((...........))))))))))..))))((((.....))))...)))...(-(........)).-).)))))))..... ( -29.10)
>DroSim_CAF1 1543 109 - 1
ACCAACAGCCAGGGAU--CAAGACUAUUAUCUGUCCUUAAGUCCUAGACAGAUAGUUUAGUCUCUGGCUUACAGAACACCCAAAA-GAAAUGAAACAC-GCGCUAUUGUCGAC
..(((.((((.(((..--...((((((((((((((...........))))))))))..))))((((.....))))...)))...(-....).......-).))).)))..... ( -26.20)
>DroEre_CAF1 500 110 - 1
ACCACAUGCCAGGUAU--CAAGACUAUUAUCUGUCCUUAAGUCCUAGACAGAUAGUUUAGUUUCUGGCUUACAGAACACCCAACUAGAAAUGAAACAC-GCACUAUUGUCGAC
(((........)))..--...(((...((((((((...........))))))))((((.((((((((................)))))))).))))..-........)))... ( -22.29)
>DroYak_CAF1 6270 110 - 1
ACCAAAAGCCAGGUAU--CAAGACUAUUGUCUGUCCUUAAGUCCUAGACAGAUAGUUUAGUUUCUGGCUUACAGAACACCAAAAUAAAAAUGAAACAC-GCACUUUUGUUGAC
.....((((((((...--(.(((((((((((((..(....)..).))))).))))))).)..))))))))............(((((((.((......-.)).)))))))... ( -25.40)
>consensus
ACCAAAAGCCAGGGAU__CAAGACUAUUAUCUGUCCUUAAGUCCUAGACAGAUAGUUUAGUCUCUGGCUUACAGAACACCCAAAU_GAAAUGAAACAC_GCGCUAUUGUCGAC
......((((((........(((((((((((((((...........))))))))))..)))))))))))............................................ (-18.65 = -17.93 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,298,729 – 3,298,841
Length 112
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 76.30
Mean single sequence MFE -35.98
Consensus MFE -22.54
Energy contribution -20.60
Covariance contribution -1.94
Combinations/Pair 1.52
Mean z-score -1.92
Structure conservation index 0.63
SVM decision value 1.30
SVM RNA-class probability 0.939144
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3298729 112 - 27905053
GCACUCCAGAAU-UUGCAGUGGCCGUAAGGCCAGCGGGACACCAACAGCCAGGGAU--CAAGACUAUUAUCUGUCAUUGAGUCCUAGACAGAUAGUUUAGUCUCUGGUUUACAGA
(((((.(((...-))).)))((((....)))).))((....))...((((((((((--..((((((...((((((...........)))))))))))).))))))))))...... ( -38.70)
>DroVir_CAF1 1091 113 - 1
GGCUCAGAGCAUGUAGCGGUUGCUGUAAGGCCAACGGAACAGCAA-UGCCAUUUAAUGCUAGACUGUUAUUUGUCAUUAAG-UCAAGACAAAUGAUUUAGGCUUGGGCGUACAAU
.(((((((((((.....(((((((((..(.....)...)))))).-.))).....)))))...((((((((((((......-....))))))))))..))..))))))....... ( -31.60)
>DroSec_CAF1 3179 112 - 1
GCACUCCAGACU-UUGCAGUGGCCGUAAGGCCAGCGGGACACCAAUAGCCAGGGAU--CAAGACUAUUAUCUGUCCUUAAGUUCUAGACAGGUAGUUUAGUCUCUGUCUUACAGA
((..........-..((..(((((....)))))))((....))....))..(((((--..(((((((((((((((...........))))))))))..)))))..)))))..... ( -35.40)
>DroEre_CAF1 537 112 - 1
GCACUCCAGAAU-UGGCAGUAGCCGUAAGGCCAGCGGGACACCACAUGCCAGGUAU--CAAGACUAUUAUCUGUCCUUAAGUCCUAGACAGAUAGUUUAGUUUCUGGCUUACAGA
.....(((((.(-(((((((.(((....)))..))((....))...))))))....--...((((((((((((((...........))))))))))..)))))))))........ ( -35.00)
>DroYak_CAF1 6307 112 - 1
GCCCUCCAGAAU-UGGCAGUGGCCGUAAGGCCAGCGGAACACCAAAAGCCAGGUAU--CAAGACUAUUGUCUGUCCUUAAGUCCUAGACAGAUAGUUUAGUUUCUGGCUUACAGA
((.((((.....-.)).))(((((....)))))))((....))..((((((((...--(.(((((((((((((..(....)..).))))).))))))).)..))))))))..... ( -37.90)
>DroMoj_CAF1 722 113 - 1
GCCUCGGAGUAUGCGGCGGUUGCUGUAAGGCCAACGGAACAGCAA-UGCCAUUUAACGCUAGACUGUUGUUUGCCAUCGAG-UCAAGGCAGAUGAUUUAGGCGUGGGCGCACAAU
((((..........((((.(((((((..(.....)...)))))))-)))).....(((((.....((..((((((......-....))))))..))...)))))))))....... ( -37.30)
>consensus
GCACUCCAGAAU_UGGCAGUGGCCGUAAGGCCAGCGGAACACCAA_AGCCAGGUAU__CAAGACUAUUAUCUGUCAUUAAGUCCUAGACAGAUAGUUUAGUCUCUGGCUUACAGA
..................((((((....(((....((....))....)))...........((((((((((((((...........))))))))))..))))...)))).))... (-22.54 = -20.60 +  -1.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,298,768 – 3,298,881
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.57
Mean single sequence MFE -34.12
Consensus MFE -25.18
Energy contribution -24.52
Covariance contribution -0.66
Combinations/Pair 1.38
Mean z-score -1.23
Structure conservation index 0.74
SVM decision value 0.86
SVM RNA-class probability 0.868107
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3298768 113 - 27905053
UCUAGCAAAUCUAGUUUCAUCCGUUGUAAUCUUUGCUGCUGCACUCCAGAAU-UUGCAGUGGCCGUAAGGCCAGCGGGACACCAAC---AGCCAGG-GAU--CAAGACUAUUAUCUGUCA
...........((((((.(((((((((.......(((((((((.........-.))))))((((....)))))))((....)).))---)))...)-)))--..)))))).......... ( -32.70)
>DroVir_CAF1 1129 113 - 1
AAUAGCACA--CAGUUUCGUUCGUUGUAAUCUUAGCGGCUGGCUCAGAGCAUGUAGCGGUUGCUGUAAGGCCAACGGAACAGCAA----UGCCAUU-UAAUGCUAGACUGUUAUUUGUCA
..(((((..--..((((((((.(((.......(((((((((.((((.....)).)))))))))))...))).)))))))).((..----.))....-...)))))(((........))). ( -30.20)
>DroGri_CAF1 1485 118 - 1
AAAAGCACA--CAGUUUCGUCCGUUGUAAUCUUAGCGGCCGUCUCGGAGCAUGCGGCGGUCGCUGUAAGGCCAGCGGAACAACAAACGCUGCCAUUUUUACGCUAGACUGUUGUUUGUCG
..(((((.(--((((((.((.....((((...(((((((((((.((.....)).)))))))))))...(((.((((..........)))))))....)))))).)))))))))))).... ( -41.50)
>DroEre_CAF1 576 113 - 1
UUUAGCAAAUUUAGUUUCAUCCGUUGUAAUCUUUGCUGCUGCACUCCAGAAU-UGGCAGUAGCCGUAAGGCCAGCGGGACACCACA---UGCCAGG-UAU--CAAGACUAUUAUCUGUCC
....(((.((.((((((...((((((.......(((((((............-.)))))))(((....)))))))))((.(((...---.....))-).)--).))))))..)).))).. ( -30.32)
>DroYak_CAF1 6346 113 - 1
UCCAGCAAAUUUUGUUUCAUCCGUUGUAAUCUUUGCUGCUGCCCUCCAGAAU-UGGCAGUGGCCGUAAGGCCAGCGGAACACCAAA---AGCCAGG-UAU--CAAGACUAUUGUCUGUCC
..((((((.(((((.....((((((............((((((.........-.))))))((((....))))))))))..(((...---.....))-)..--)))))...))).)))... ( -32.60)
>DroMoj_CAF1 760 113 - 1
AAUAGCACA--AGGUUUCGUCCGCUGUAAUCUUAGCGGCCGCCUCGGAGUAUGCGGCGGUUGCUGUAAGGCCAACGGAACAGCAA----UGCCAUU-UAACGCUAGACUGUUGUUUGCCA
....(((..--..(((((((..(((.......(((((((((((.((.....)).)))))))))))...)))..))))))).....----)))....-....((.((((....)))))).. ( -37.40)
>consensus
AAUAGCAAA__UAGUUUCAUCCGUUGUAAUCUUAGCGGCUGCCCCCCAGAAU_UGGCAGUGGCCGUAAGGCCAGCGGAACACCAAA___UGCCAGG_UAA__CAAGACUAUUAUCUGUCA
....(((............(((((((...((((.(((((((((...........)))))))))...)))).)))))))...........))).............(((........))). (-25.18 = -24.52 +  -0.66)

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 09:59:54 2006