Locus 2688

Sequence ID 2R_DroMel_CAF1
Location 9,493,593 – 9,493,747
Length 154
Max. P 0.983520
window4426 window4427 window4428

overview

Window 6

Location 9,493,593 – 9,493,707
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.56
Mean single sequence MFE -38.00
Consensus MFE -24.49
Energy contribution -25.85
Covariance contribution 1.36
Combinations/Pair 1.28
Mean z-score -2.47
Structure conservation index 0.64
SVM decision value 1.59
SVM RNA-class probability 0.966214
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9493593 114 + 20766785
GCACAUCGGUCGUGGAGGCGAUUCCCCGCAAUCGGUGCUGUUCGUCCAGCAAAUUGAACUUCUCCUUGCGAAAGUCCAUCAAGGAGAAGUUUUUGAUGCGAUAGUUGGGGUUUC
((.(((.....)))...))((..((((((.((((.(((((......)))))....((((((((((((((....).....)))))))))))))......)))).).)))))..)) ( -40.90)
>DroPse_CAF1 5940 111 + 1
GCUCAGUGAUAGU---CACUCCAUCCCUCAGACGAUGCCUCUCAUCGAUCGCAUUAAUCUUCUCCCUGCGAAACUCCAUCAAGGAGAAGCUCUUAAUGCGAUAGUUGGAGCUUC
((((((((.....---))))........(((.(((((.....)))))((((((((((.(((((((.((...........)).)))))))...))))))))))..)))))))... ( -34.40)
>DroSec_CAF1 5950 114 + 1
GCACAUCGGUCGUGGAGGCGAUACCCUGCAAUCGGUGCUGUUCGUCCAGCAAAUUGAACUUCUCCUUGCGAAAAUCAAUCAAGGAGAAGUUCUUGAUGCGAUAGUUGAGAUUUC
((((((((((.(..(.((.....)))..).))))))).))).......(((....(((((((((((((...........)))))))))))))....)))............... ( -37.30)
>DroSim_CAF1 6020 114 + 1
GCACAUCGGUCGUGGAGGCGAUACCCUGCAAUCGGUGCUGUUCGUCCAGCAAAUUGAACUUCUCCUUGCGGAAAUCAAUCAAGGAGAAGUUCUUGAUGCGAUAGUUGGGAUUUC
........(((((....))))).(((.((.((((.(((((......)))))....(((((((((((((..(....)...)))))))))))))......)))).)).)))..... ( -41.40)
>DroYak_CAF1 6230 114 + 1
GCGCAUUGGCCGUGGAGGCGGCAUCCCGACGUCGGUGCUCCUCAUCCAGCAAAUCGAACUUAUCCUUGCGAAAGUGCAUCAAGGAGAAGUUCUUGAUGCGAUAGUUGGAGUUUC
.(((.......)))((((.((((..(((....))))))))))).((((((..(((............((....))((((((((((....))))))))))))).))))))..... ( -39.60)
>DroPer_CAF1 5923 111 + 1
GCUCAGUGAUAGU---CACUCCAUCCCUCAGACGAUGCCUCUCAUCGAUCGCAUUAAUCUUCUCCCUGCGAAACUCCAUCAAGGAGAAGCUCUUAAUGCGAUAGUUGGAGCUUC
((((((((.....---))))........(((.(((((.....)))))((((((((((.(((((((.((...........)).)))))))...))))))))))..)))))))... ( -34.40)
>consensus
GCACAUCGGUCGUGGAGGCGACACCCCGCAAUCGGUGCUGCUCAUCCAGCAAAUUGAACUUCUCCUUGCGAAAAUCCAUCAAGGAGAAGUUCUUGAUGCGAUAGUUGGAGUUUC
........(((((....))))).(((.((.((((.(((((......)))))....(((((((((((((...........)))))))))))))......)))).)).)))..... (-24.49 = -25.85 +   1.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,493,593 – 9,493,707
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.56
Mean single sequence MFE -39.68
Consensus MFE -21.78
Energy contribution -21.98
Covariance contribution 0.20
Combinations/Pair 1.29
Mean z-score -3.04
Structure conservation index 0.55
SVM decision value 1.95
SVM RNA-class probability 0.983520
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9493593 114 - 20766785
GAAACCCCAACUAUCGCAUCAAAAACUUCUCCUUGAUGGACUUUCGCAAGGAGAAGUUCAAUUUGCUGGACGAACAGCACCGAUUGCGGGGAAUCGCCUCCACGACCGAUGUGC
..............((((((...((((((((((((.(((....))))))))))))))).....(((((......)))))..(.(((.((((......)))).))).))))))). ( -38.50)
>DroPse_CAF1 5940 111 - 1
GAAGCUCCAACUAUCGCAUUAAGAGCUUCUCCUUGAUGGAGUUUCGCAGGGAGAAGAUUAAUGCGAUCGAUGAGAGGCAUCGUCUGAGGGAUGGAGUG---ACUAUCACUGAGC
...((((...((((((((((((...((((((((((.(((....))))))))))))).)))))))((.(((((.....))))))).....)))))((((---.....)))))))) ( -43.90)
>DroSec_CAF1 5950 114 - 1
GAAAUCUCAACUAUCGCAUCAAGAACUUCUCCUUGAUUGAUUUUCGCAAGGAGAAGUUCAAUUUGCUGGACGAACAGCACCGAUUGCAGGGUAUCGCCUCCACGACCGAUGUGC
..............((((((..(((((((((((((...(.....).)))))))))))))....(((((......))))).((..((.(((......))).))))...)))))). ( -37.40)
>DroSim_CAF1 6020 114 - 1
GAAAUCCCAACUAUCGCAUCAAGAACUUCUCCUUGAUUGAUUUCCGCAAGGAGAAGUUCAAUUUGCUGGACGAACAGCACCGAUUGCAGGGUAUCGCCUCCACGACCGAUGUGC
..............((((((..(((((((((((((...(....)..)))))))))))))....(((((......))))).((..((.(((......))).))))...)))))). ( -37.80)
>DroYak_CAF1 6230 114 - 1
GAAACUCCAACUAUCGCAUCAAGAACUUCUCCUUGAUGCACUUUCGCAAGGAUAAGUUCGAUUUGCUGGAUGAGGAGCACCGACGUCGGGAUGCCGCCUCCACGGCCAAUGCGC
..............(((((...((((((.((((((.((......)))))))).)))))).....((((...((((.((((((....)))..)))..))))..))))..))))). ( -36.60)
>DroPer_CAF1 5923 111 - 1
GAAGCUCCAACUAUCGCAUUAAGAGCUUCUCCUUGAUGGAGUUUCGCAGGGAGAAGAUUAAUGCGAUCGAUGAGAGGCAUCGUCUGAGGGAUGGAGUG---ACUAUCACUGAGC
...((((...((((((((((((...((((((((((.(((....))))))))))))).)))))))((.(((((.....))))))).....)))))((((---.....)))))))) ( -43.90)
>consensus
GAAACCCCAACUAUCGCAUCAAGAACUUCUCCUUGAUGGACUUUCGCAAGGAGAAGUUCAAUUUGCUGGACGAACAGCACCGACUGCGGGAUAUCGCCUCCACGACCAAUGUGC
.....(((.....(((......(((((((((((((.(((....)))))))))))))))).....(((........)))..))).....)))..(((......)))......... (-21.78 = -21.98 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,493,627 – 9,493,747
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.56
Mean single sequence MFE -39.67
Consensus MFE -19.54
Energy contribution -20.43
Covariance contribution 0.89
Combinations/Pair 1.38
Mean z-score -2.70
Structure conservation index 0.49
SVM decision value 1.33
SVM RNA-class probability 0.942813
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9493627 120 - 20766785
CUGCUGCAUAGGACGAACUUUCUAAUCAACACGCCUCGUGGAAACCCCAACUAUCGCAUCAAAAACUUCUCCUUGAUGGACUUUCGCAAGGAGAAGUUCAAUUUGCUGGACGAACAGCAC
.(((((..(((((......))))).......((((...(((.....)))......(((.....((((((((((((.(((....))))))))))))))).....))).)).))..))))). ( -34.50)
>DroVir_CAF1 8166 120 - 1
CUAUUGCAGCGUACAAACUUCUUGAUGAACACACCGCGUGGCGACUCCAAUUACCGCAUCAAGAGUCUAGCUCUGAUGGAGUUCCGCAAGGAGAAGUAUAAUGCAAUUGACGAAAAGCAG
(.((((((..((((...(((((((..((((...((..((((..(......)..))))((((.(((.....))))))))).))))..)))))))..))))..)))))).)........... ( -33.20)
>DroPse_CAF1 5971 120 - 1
CUGAUGCAACGAACCAACUUCCUGGUGAACACGCCGCGGGGAAGCUCCAACUAUCGCAUUAAGAGCUUCUCCUUGAUGGAGUUUCGCAGGGAGAAGAUUAAUGCGAUCGAUGAGAGGCAU
...((((..........((((((.(((.......))).))))))(((((.(.((((((((((...((((((((((.(((....))))))))))))).)))))))))).).)).))))))) ( -49.90)
>DroYak_CAF1 6264 120 - 1
CUGCUGCACAGGACGAACUUUCUAAUCAACACGCCGCGUGGAAACUCCAACUAUCGCAUCAAGAACUUCUCCUUGAUGCACUUUCGCAAGGAUAAGUUCGAUUUGCUGGAUGAGGAGCAC
.((((.(.(((.(((((((..........((((...))))...........((((((((((((........)))))))).....(....)))))))))))...).))).....).)))). ( -30.70)
>DroAna_CAF1 6272 120 - 1
UUGUUGCAUCGGACAAACUUUUUGAUCAAUACGCCGCGGGGGAACCCUAACUAUCGCAUCAAGAACUUUGCCUUGAUGGAGUUCCGUAAGGAGAAGUUCAAUGCGAUCGAUGAGAAGCAU
.((((.((((((.........................(((....)))......((((((...((((((..((((.((((....))))))))..)))))).))))))))))))...)))). ( -39.80)
>DroPer_CAF1 5954 120 - 1
CUGAUGCAACGAACCAACUUCCUGGUGAACACGCCGCGGGGAAGCUCCAACUAUCGCAUUAAGAGCUUCUCCUUGAUGGAGUUUCGCAGGGAGAAGAUUAAUGCGAUCGAUGAGAGGCAU
...((((..........((((((.(((.......))).))))))(((((.(.((((((((((...((((((((((.(((....))))))))))))).)))))))))).).)).))))))) ( -49.90)
>consensus
CUGAUGCAACGGACAAACUUCCUGAUCAACACGCCGCGGGGAAACUCCAACUAUCGCAUCAAGAACUUCUCCUUGAUGGAGUUUCGCAAGGAGAAGUUCAAUGCGAUCGAUGAGAAGCAU
....(((................................((.....))......(((((...(((((((((((((.(((....)))))))))))))))).)))))...........))). (-19.54 = -20.43 +   0.89)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:27 2006