Locus 2700

Sequence ID 2L_DroMel_CAF1
Location 7,559,737 – 7,559,869
Length 132
Max. P 0.986665
window4290 window4291 window4292

overview

Window 0

Location 7,559,737 – 7,559,831
Length 94
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 76.49
Mean single sequence MFE -15.14
Consensus MFE -9.93
Energy contribution -10.68
Covariance contribution 0.75
Combinations/Pair 1.07
Mean z-score -1.70
Structure conservation index 0.66
SVM decision value 0.39
SVM RNA-class probability 0.718223
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7559737 94 + 22407834
UUAAGGUUUUUUUUUUUGUUUUUUACAUUUUCGUGC-CACACGCCAUUUUCAUGGCGUAGCCCC-------AUAGCCCCUGCUGGCCGAAAAACGUUGCUCU
.(((.((.........(((.....)))((((((.((-(..(((((((....)))))))......-------..(((....)))))))))))))).))).... ( -22.40)
>DroSec_CAF1 59450 83 + 1
-------------UUUUGUAUUUCACAUUUUCGUGC-CACACGCCAUUUUCAUGGCAUAGCCCC-----ACCUACCCCCUGCUAAACGAAAAACGUUGCUCU
-------------..............(((((((..-.....(((((....))))).((((...-----...........)))).))))))).......... ( -13.94)
>DroSim_CAF1 64160 89 + 1
-------------UUUUGUUUUUUACAUUUUCGUGCCCACACGCCAUUUUCAUGGCAUAGCCCCCCCCCCCCUACCCCCUGCUGAACGAAAAACGUUGCUCU
-------------..............(((((((........(((((....))))).((((...................)))).))))))).......... ( -13.31)
>DroEre_CAF1 58626 74 + 1
-------------UUCUGUUUUUCACAAUUUCGUGC-CACACGCCAUUUUCAUGCGAUACCC--------------CCCUGCUGGCCGAAAAUCGUUGCUCU
-------------...............(((((.((-(((((((.........)))......--------------...)).)))))))))........... ( -10.90)
>consensus
_____________UUUUGUUUUUCACAUUUUCGUGC_CACACGCCAUUUUCAUGGCAUAGCCCC_______CUACCCCCUGCUGAACGAAAAACGUUGCUCU
.................(((((((........(((....)))(((((....)))))...............................)))))))........ ( -9.93 = -10.68 +   0.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,559,737 – 7,559,831
Length 94
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 76.49
Mean single sequence MFE -22.23
Consensus MFE -15.02
Energy contribution -14.52
Covariance contribution -0.50
Combinations/Pair 1.21
Mean z-score -2.24
Structure conservation index 0.68
SVM decision value 2.05
SVM RNA-class probability 0.986665
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7559737 94 - 22407834
AGAGCAACGUUUUUCGGCCAGCAGGGGCUAU-------GGGGCUACGCCAUGAAAAUGGCGUGUG-GCACGAAAAUGUAAAAAACAAAAAAAAAAACCUUAA
......(((((((.((((((.....((((..-------..))))(((((((....))))))).))-)).)))))))))........................ ( -28.80)
>DroSec_CAF1 59450 83 - 1
AGAGCAACGUUUUUCGUUUAGCAGGGGGUAGGU-----GGGGCUAUGCCAUGAAAAUGGCGUGUG-GCACGAAAAUGUGAAAUACAAAA-------------
..(((..((..(.((.((.....)).)).)..)-----)..)))..(((((....)))))((((.-.(((......)))..))))....------------- ( -22.30)
>DroSim_CAF1 64160 89 - 1
AGAGCAACGUUUUUCGUUCAGCAGGGGGUAGGGGGGGGGGGGCUAUGCCAUGAAAAUGGCGUGUGGGCACGAAAAUGUAAAAAACAAAA-------------
...((.((((((..(.(((.((.....))...))).)..)))).(((((((....)))))))))..)).....................------------- ( -21.30)
>DroEre_CAF1 58626 74 - 1
AGAGCAACGAUUUUCGGCCAGCAGGG--------------GGGUAUCGCAUGAAAAUGGCGUGUG-GCACGAAAUUGUGAAAAACAGAA-------------
......(((((((.((((((.((.((--------------(....)).(((....))).).))))-)).)))))))))...........------------- ( -16.50)
>consensus
AGAGCAACGUUUUUCGGCCAGCAGGGGGUAG_______GGGGCUAUGCCAUGAAAAUGGCGUGUG_GCACGAAAAUGUAAAAAACAAAA_____________
......(((((((.((.((....))..................((((((((....))))))))......)))))))))........................ (-15.02 = -14.52 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,559,764 – 7,559,869
Length 105
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 80.37
Mean single sequence MFE -23.68
Consensus MFE -12.76
Energy contribution -13.37
Covariance contribution 0.61
Combinations/Pair 1.05
Mean z-score -2.11
Structure conservation index 0.54
SVM decision value 0.23
SVM RNA-class probability 0.645257
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7559764 105 - 22407834
UCAAGAAUUAUGAAAAAUGUGUUGCAAAAAAAAAAUAGAGAGCAACG---UUUUUCGGCCAGCAGGGGCUAU-------GGGGCUACGCCAUGAAAAUGGCGUGUG-GCACGAAAA
.................(((((..(...............(((..((---(.....((((......))))))-------)..)))(((((((....))))))))..-))))).... ( -32.30)
>DroSec_CAF1 59464 103 - 1
UCAAGAAUUAUGAAAAAUGUGUUGCAAA----AAAUAGAGAGCAACG---UUUUUCGUUUAGCAGGGGGUAGGU-----GGGGCUAUGCCAUGAAAAUGGCGUGUG-GCACGAAAA
((..(....(((((((((((..(((...----.........))))))---))))))))....).........((-----(..((.(((((((....))))))))).-.)))))... ( -26.80)
>DroSim_CAF1 64174 109 - 1
UCAAGAAUUAUGAAAAAUGUGUUGCAAA----AAAUAGAGAGCAACG---UUUUUCGUUCAGCAGGGGGUAGGGGGGGGGGGGCUAUGCCAUGAAAAUGGCGUGUGGGCACGAAAA
.................(((((..(...----........(((..(.---(((..((..(......)..)..)..))).)..)))(((((((....))))))))..).)))).... ( -25.40)
>DroEre_CAF1 58640 94 - 1
UCAAGAAUUAUGAAAAAUGUGUUGCAAA----AAAUAGAGAGCAACG---AUUUUCGGCCAGCAGGG--------------GGGUAUCGCAUGAAAAUGGCGUGUG-GCACGAAAU
.................(((((..((..----.....(((((.....---.))))).((((.(((.(--------------(....)).).))....)))).))..-))))).... ( -19.80)
>DroYak_CAF1 60723 94 - 1
UCAAGAAUUAUGAAAAAUGUGUUGCAAA----AAAUAGAGAGCAACG---CUAUUUGGCCAGCAGGG--------------GGGUAUCGCAUGAAAAUGGCGUGUG-GCACGAAAU
.................(((((..((..----((((((.(.....).---)))))).((((.(((.(--------------(....)).).))....)))).))..-))))).... ( -20.70)
>DroPer_CAF1 80644 94 - 1
UCAAGAAUUAUGAAAAAUGUGUUGCAAAA--AAAAUAGAGAGCAAAGGUUUUUUUUUUU-A----------G--------GUGCAGAGAAAUGAAAAUGGCGUGCG-GCACGAAAA
.................(((((((((...--((((.(((((((....))))))).))))-.----------.--------.......(..((....))..).))))-))))).... ( -17.10)
>consensus
UCAAGAAUUAUGAAAAAUGUGUUGCAAA____AAAUAGAGAGCAACG___UUUUUCGGCCAGCAGGG____G________GGGCUAUGCCAUGAAAAUGGCGUGUG_GCACGAAAA
...........((((((..((((((................))))))...)))))).................................(((....))).((((....)))).... (-12.76 = -13.37 +   0.61)

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 10:34:00 2006