Locus 1315

Sequence ID 2R_DroMel_CAF1
Location 5,095,388 – 5,095,585
Length 197
Max. P 0.924378
window2281 window2282 window2283 window2284

overview

Window 1

Location 5,095,388 – 5,095,505
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.31
Mean single sequence MFE -27.63
Consensus MFE -11.98
Energy contribution -13.94
Covariance contribution 1.96
Combinations/Pair 1.30
Mean z-score -1.87
Structure conservation index 0.43
SVM decision value 0.23
SVM RNA-class probability 0.642188
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5095388 117 - 20766785
AGAGCUUUGAGCAGCAGCUGGAAGACCUGAAGCAGAAACUGGAGCUGCUAAA---GAACCAACCCAGAGAGCAGGAAACACAAGGGAAAGUGGUGGAUAAAUCUCUAGGGGAAAUGUAAG
....((((.(((....))).))))..((..(((((.........)))))..)---)......((((((((........(((........))).........))))).))).......... ( -27.63)
>DroSec_CAF1 1804 117 - 1
AGAACUUCAAGCAGCAGCUGGAAGAACUGAAGCAGAAACUGGAGCUGCUGAA---GAACCAACCCAAAGAGCAGGAAACGCUAGCGAAAGUGGUGGAUAAAUCUCUAGGGAAAAUGUAAG
....(((((.(((((..(..(.....(((...)))...)..).)))))))))---)......(((..((((.......(((((.(....)))))).......)))).))).......... ( -30.54)
>DroSim_CAF1 1763 117 - 1
AGAACUUUCAGCAGCAGCUGGAAGACCUGAAGCAGAAACUGGAGCUGCUAAA---GAACCAACCCAAAGAGCAGGAAACGCAAGCGAAAGUGGUGGAUAAAUCUCUAGGGGAAAUGUAAG
....((((((((....))))))))..((..(((((.........)))))..)---)......(((..((((.......(((..((....)).))).......))))..)))......... ( -32.84)
>DroYak_CAF1 1769 117 - 1
AGAGCUUUCAGCAGCAGCUGGAGAAGCUGAAGCAGAAACUGGAUCUACUAAA---GAACCAACCCAAAGAGCAGGAAACUCAAGAGAAAGUGGAGGAGAAGGCUUUAGGGGAAAUGUAAG
..((.((((.((..(((((.....)))))..)).))))))((.(((.....)---)).))..(((..(((((......(((...........)))......)))))..)))......... ( -29.40)
>DroAna_CAF1 1630 120 - 1
AAUCUUUUCUUCAGCAAUUGGAAAACUUAAAGAACGAAUUGGAGAUACUGAAACGGAAGGAAGCGGAUGCCACCGCAUCGCAACAAAAACAAGAUAUUAAAAGCUUAGAAAAAAUGUAUG
..(((((((((((((((((.(.............).)))))......)))))..))))))).(((.((((....)))))))....................................... ( -17.72)
>consensus
AGAACUUUCAGCAGCAGCUGGAAGACCUGAAGCAGAAACUGGAGCUGCUAAA___GAACCAACCCAAAGAGCAGGAAACGCAAGAGAAAGUGGUGGAUAAAUCUCUAGGGGAAAUGUAAG
....((((((((....))))))))......(((((.........))))).............(((..((((.......(((...........))).......))))..)))......... (-11.98 = -13.94 +   1.96)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,095,428 – 5,095,545
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.95
Mean single sequence MFE -33.88
Consensus MFE -18.64
Energy contribution -18.45
Covariance contribution -0.19
Combinations/Pair 1.46
Mean z-score -2.16
Structure conservation index 0.55
SVM decision value 1.16
SVM RNA-class probability 0.924378
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5095428 117 + 20766785
UGUUUCCUGCUCUCUGGGUUGGUUC---UUUAGCAGCUCCAGUUUCUGCUUCAGGUCUUCCAGCUGCUGCUCAAAGCUCUCUUUAAGCUGCAGCUGCCCGAGAUAAUCCAAAUGCUCCUC
........((....((((((....(---(..(((((.........)))))..))(((((.(((((((.(((.((((....)))).))).)))))))...)))))))))))...))..... ( -34.10)
>DroSec_CAF1 1844 117 + 1
CGUUUCCUGCUCUUUGGGUUGGUUC---UUCAGCAGCUCCAGUUUCUGCUUCAGUUCUUCCAGCUGCUGCUUGAAGUUCUCCUUAAGCUGCAGCUGCCCGAGAUGUUCCAAAUGCUCCUC
........((..((((((.....((---((..((((((.((((((..(....((..((((.(((....))).))))..)).)..)))))).))))))..))))...)))))).))..... ( -35.50)
>DroSim_CAF1 1803 117 + 1
CGUUUCCUGCUCUUUGGGUUGGUUC---UUUAGCAGCUCCAGUUUCUGCUUCAGGUCUUCCAGCUGCUGCUGAAAGUUCUCCUUAAGCUGCAGCUGCCCGAGAUGUUCCAAAUGCUCCUC
........((..((((((.....((---((..((((((.((((((..(....((..(((.((((....)))).)))..)).)..)))))).))))))..))))...)))))).))..... ( -35.20)
>DroEre_CAF1 1820 117 + 1
UGUUUCCUGCUCGUUGGCUUGGUUC---UUGAGUAGCUCCAGUUUCUGCUUCAGGUUGUCCAGCUGCUGUUGGAAGCUCUCGUUAAGCUUCAGCUUCUCCAGACAAUCCAAGUGCUCCUC
................((((((.((---(.(((.((((..(((((..((....((((.((((((....))))))))))...)).)))))..)))).))).)))....))))))....... ( -31.80)
>DroYak_CAF1 1809 117 + 1
AGUUUCCUGCUCUUUGGGUUGGUUC---UUUAGUAGAUCCAGUUUCUGCUUCAGCUUCUCCAGCUGCUGCUGAAAGCUCUCGUUGAGCUGCAGCUGCUCUAGACAAUCCAAGUGUUCCUC
........((.(((.((((((...(---(..((((((.......))))))..))..(((..(((.(((((....(((((.....)))))))))).)))..)))))))))))).))..... ( -36.90)
>DroAna_CAF1 1670 120 + 1
CGAUGCGGUGGCAUCCGCUUCCUUCCGUUUCAGUAUCUCCAAUUCGUUCUUUAAGUUUUCCAAUUGCUGAAGAAAAGAUUCAUUUAAUUGCAUCUGCUCCAAGCUGGAGAGAUGCUUUUC
.((.((((.(((....))).....)))).)).........((((..(((((((.((.........)))))))))..)))).........((((((.((((.....))))))))))..... ( -29.80)
>consensus
CGUUUCCUGCUCUUUGGGUUGGUUC___UUUAGCAGCUCCAGUUUCUGCUUCAGGUCUUCCAGCUGCUGCUGAAAGCUCUCCUUAAGCUGCAGCUGCCCGAGACAAUCCAAAUGCUCCUC
....(((........)))((((..........((((((.((((((.......((..(((.((((....)))).)))..))....)))))).))))))..........))))......... (-18.64 = -18.45 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,095,428 – 5,095,545
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.95
Mean single sequence MFE -35.72
Consensus MFE -13.96
Energy contribution -14.77
Covariance contribution 0.81
Combinations/Pair 1.31
Mean z-score -2.51
Structure conservation index 0.39
SVM decision value 0.75
SVM RNA-class probability 0.841750
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5095428 117 - 20766785
GAGGAGCAUUUGGAUUAUCUCGGGCAGCUGCAGCUUAAAGAGAGCUUUGAGCAGCAGCUGGAAGACCUGAAGCAGAAACUGGAGCUGCUAAA---GAACCAACCCAGAGAGCAGGAAACA
.....((.(((((......((((((((((((.((((((((....)))))))).))))))).....)))))(((((.........)))))...---........)))))..)).(....). ( -41.50)
>DroSec_CAF1 1844 117 - 1
GAGGAGCAUUUGGAACAUCUCGGGCAGCUGCAGCUUAAGGAGAACUUCAAGCAGCAGCUGGAAGAACUGAAGCAGAAACUGGAGCUGCUGAA---GAACCAACCCAAAGAGCAGGAAACG
.....((.(((((......((...(((((((.(((((((.....))).)))).)))))))...)).((..(((((.........)))))..)---).......)))))..)).(....). ( -36.50)
>DroSim_CAF1 1803 117 - 1
GAGGAGCAUUUGGAACAUCUCGGGCAGCUGCAGCUUAAGGAGAACUUUCAGCAGCAGCUGGAAGACCUGAAGCAGAAACUGGAGCUGCUAAA---GAACCAACCCAAAGAGCAGGAAACG
.....((.(((((....(((..(((((((.((((((.(((....((((((((....)))))))).))).))))......)).)))))))..)---))......)))))..)).(....). ( -40.90)
>DroEre_CAF1 1820 117 - 1
GAGGAGCACUUGGAUUGUCUGGAGAAGCUGAAGCUUAACGAGAGCUUCCAACAGCAGCUGGACAACCUGAAGCAGAAACUGGAGCUACUCAA---GAACCAAGCCAACGAGCAGGAAACA
.....((.(((((.((((((.(((.(((((((((((.....)))))))...(((...(((............)))...))).)))).))).)---))..))).)))).).)).(....). ( -32.10)
>DroYak_CAF1 1809 117 - 1
GAGGAACACUUGGAUUGUCUAGAGCAGCUGCAGCUCAACGAGAGCUUUCAGCAGCAGCUGGAGAAGCUGAAGCAGAAACUGGAUCUACUAAA---GAACCAACCCAAAGAGCAGGAAACU
.........((((....(((..(((.((((((((((.....)))))....))))).)))..))).((....))......(((.(((.....)---)).)))..)))).....((....)) ( -31.40)
>DroAna_CAF1 1670 120 - 1
GAAAAGCAUCUCUCCAGCUUGGAGCAGAUGCAAUUAAAUGAAUCUUUUCUUCAGCAAUUGGAAAACUUAAAGAACGAAUUGGAGAUACUGAAACGGAAGGAAGCGGAUGCCACCGCAUCG
.....((((((((((.....)))).))))))........((.(((((((((((((((((.(.............).)))))......)))))..))))))).((((......)))).)). ( -31.92)
>consensus
GAGGAGCAUUUGGAUUAUCUCGAGCAGCUGCAGCUUAACGAGAGCUUUCAGCAGCAGCUGGAAAACCUGAAGCAGAAACUGGAGCUACUAAA___GAACCAACCCAAAGAGCAGGAAACG
.........((((.........((.((((.(((...........((((((((....))))))))..(((...)))...))).)))).)).........)))).((........))..... (-13.96 = -14.77 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,095,465 – 5,095,585
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.72
Mean single sequence MFE -36.48
Consensus MFE -19.77
Energy contribution -20.70
Covariance contribution 0.93
Combinations/Pair 1.41
Mean z-score -1.84
Structure conservation index 0.54
SVM decision value 0.16
SVM RNA-class probability 0.612108
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5095465 120 + 20766785
AGUUUCUGCUUCAGGUCUUCCAGCUGCUGCUCAAAGCUCUCUUUAAGCUGCAGCUGCCCGAGAUAAUCCAAAUGCUCCUCUAGCGAAGCAAUCUUCUUCAGCUUCCAGGCGCAGAAGGCC
......((((((..(((((.(((((((.(((.((((....)))).))).)))))))...))))).........(((.....))))))))).((((((...(((....)))..)))))).. ( -40.00)
>DroSec_CAF1 1881 120 + 1
AGUUUCUGCUUCAGUUCUUCCAGCUGCUGCUUGAAGUUCUCCUUAAGCUGCAGCUGCCCGAGAUGUUCCAAAUGCUCCUCCAGCGAAGCGAUCUUCUUCAGCUUCCAGGCGCAGUAGGCC
.((((((((............((((((.((((((........)))))).))))))(((.(((..((.......))..)))..(.(((((((......)).)))))).))))))).)))). ( -38.90)
>DroSim_CAF1 1840 120 + 1
AGUUUCUGCUUCAGGUCUUCCAGCUGCUGCUGAAAGUUCUCCUUAAGCUGCAGCUGCCCGAGAUGUUCCAAAUGCUCCUCCAGCGAAGCGAUCUUUUUCAGCUUCCAGGCGCAGUAGGCC
.((((((((.....(((((.(((((((.(((..(((.....))).))).)))))))...)))))...((....(((.....)))(((((((......)).)))))..)).)))).)))). ( -37.70)
>DroEre_CAF1 1857 120 + 1
AGUUUCUGCUUCAGGUUGUCCAGCUGCUGUUGGAAGCUCUCGUUAAGCUUCAGCUUCUCCAGACAAUCCAAGUGCUCCUCCAGCAAAGCAAUCUUUUCCAGCUUCCAGGCGCAGUAGGCC
.((((((((...(((((((.....(((((..(((.(((((.(..((((....))))..).)))..........)))))..)))))..)))))))......(((....))))))).)))). ( -32.10)
>DroYak_CAF1 1846 120 + 1
AGUUUCUGCUUCAGCUUCUCCAGCUGCUGCUGAAAGCUCUCGUUGAGCUGCAGCUGCUCUAGACAAUCCAAGUGUUCCUCCAGGGAAGCAAUAUUUUUCAGCUCCCAGGCGCAGUAGGCC
.((((((((....(((((.(((((.(((((....(((((.....)))))))))).)))...((((.......))))......)))))))...........(((....))))))).)))). ( -38.70)
>DroAna_CAF1 1710 120 + 1
AAUUCGUUCUUUAAGUUUUCCAAUUGCUGAAGAAAAGAUUCAUUUAAUUGCAUCUGCUCCAAGCUGGAGAGAUGCUUUUCCAGGACAUCCAGGUCCUCUAGCUUCCAGGCGCAAUGUGCC
((((..(((((((.((.........)))))))))..)))).........((((((.((((.....))))))))))......(((((......)))))..........(((((...))))) ( -31.50)
>consensus
AGUUUCUGCUUCAGGUCUUCCAGCUGCUGCUGAAAGCUCUCCUUAAGCUGCAGCUGCCCGAGACAAUCCAAAUGCUCCUCCAGCGAAGCAAUCUUCUUCAGCUUCCAGGCGCAGUAGGCC
....(((((.....((((..(((((((.(((.((........)).))).)))))))....))))........(((.(((.....(((((...........))))).))).)))))))).. (-19.77 = -20.70 +   0.93)

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 10:02:02 2006