Locus 7980

Sequence ID 3R_DroMel_CAF1
Location 21,392,550 – 21,392,671
Length 121
Max. P 0.994646
window12846 window12847 window12848

overview

Window 6

Location 21,392,550 – 21,392,640
Length 90
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 68.86
Mean single sequence MFE -24.56
Consensus MFE -13.14
Energy contribution -11.62
Covariance contribution -1.52
Combinations/Pair 1.33
Mean z-score -2.33
Structure conservation index 0.54
SVM decision value 2.50
SVM RNA-class probability 0.994646
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21392550 90 + 27905053
UCCUCUGUAGCAUUGCCCGUUUUGCACUUGACUACGUUUUGGGUCAAGUUGCGUAGAAUUGGUG------AUUUCGCGGAAUUGAAUUACUAUGAC
...((((..(.((..((.(((((((((((((((........))))))))...))))))).))..------)).)..))))................ ( -26.30)
>DroPse_CAF1 106862 79 + 1
U------------UUUCCAU-GUGCACUUGACUCAAUUUUGAGUCAAGUUGUUUCGUUUUGGGGCAAGCCAAUUCCUGGAAUUGA----CAGUGAC
.------------.((((((-(.((((((((((((....))))))))))(((..(.....)..))).)))).....)))))....----....... ( -23.50)
>DroSim_CAF1 83333 77 + 1
U------------UGCCCGU-UUGCACUUGACUACGUUUUGGGUCAAGUUGCGCGGGAUUGGUG------AUUUCGCGGAAUUGAAUUACUAUAAC
.------------..(((((-..((((((((((........))))))).))))))))..(((((------((((.........))))))))).... ( -25.00)
>DroYak_CAF1 86605 89 + 1
UUCUCUGUAGCGUUUCCAGU-UCGCACUUGACUACGUUUUGGGUCAAGUUGUGUAGGAUUGGUG------AUUUCGCUGAAUUGAAUUACUAUGGC
(((....(((((...(((((-((((((((((((........))))))).)))...)))))))..------....)))))....))).......... ( -24.90)
>DroPer_CAF1 129784 79 + 1
U------------UUUCCCU-UUGCACUUGACUCAAUUUUGAGUCAAGUUGUUUCGUUUUGGGGCAAGCCAAUUCCUGGAAUUGA----CAGUGAC
.------------.......-(..(((((((((((....))))))))))((((..((((..(((.........)))..)))).))----)))..). ( -23.10)
>consensus
U____________UUCCCGU_UUGCACUUGACUACGUUUUGGGUCAAGUUGUGUAGGAUUGGUG______AUUUCGCGGAAUUGAAUUACUAUGAC
................((.....((((((((((........))))))).))).........(((..........)))))................. (-13.14 = -11.62 +  -1.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,392,550 – 21,392,640
Length 90
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 68.86
Mean single sequence MFE -17.32
Consensus MFE -7.44
Energy contribution -6.84
Covariance contribution -0.60
Combinations/Pair 1.25
Mean z-score -1.73
Structure conservation index 0.43
SVM decision value 0.22
SVM RNA-class probability 0.639638
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21392550 90 - 27905053
GUCAUAGUAAUUCAAUUCCGCGAAAU------CACCAAUUCUACGCAACUUGACCCAAAACGUAGUCAAGUGCAAAACGGGCAAUGCUACAGAGGA
....(((((.......((((.(((..------......)))...(((.((((((..........)))))))))....))))...)))))....... ( -14.40)
>DroPse_CAF1 106862 79 - 1
GUCACUG----UCAAUUCCAGGAAUUGGCUUGCCCCAAAACGAAACAACUUGACUCAAAAUUGAGUCAAGUGCAC-AUGGAAA------------A
.......----....(((((....((((......)))).........((((((((((....))))))))))....-.))))).------------. ( -21.20)
>DroSim_CAF1 83333 77 - 1
GUUAUAGUAAUUCAAUUCCGCGAAAU------CACCAAUCCCGCGCAACUUGACCCAAAACGUAGUCAAGUGCAA-ACGGGCA------------A
................((((((....------.........)))(((.((((((..........)))))))))..-..)))..------------. ( -15.02)
>DroYak_CAF1 86605 89 - 1
GCCAUAGUAAUUCAAUUCAGCGAAAU------CACCAAUCCUACACAACUUGACCCAAAACGUAGUCAAGUGCGA-ACUGGAAACGCUACAGAGAA
....((((..((((.(((.(((....------)..............(((((((..........)))))))))))-).))))...))))....... ( -13.50)
>DroPer_CAF1 129784 79 - 1
GUCACUG----UCAAUUCCAGGAAUUGGCUUGCCCCAAAACGAAACAACUUGACUCAAAAUUGAGUCAAGUGCAA-AGGGAAA------------A
......(----(((((((...))))))))....(((...........((((((((((....))))))))))....-.)))...------------. ( -22.49)
>consensus
GUCAUAGUAAUUCAAUUCCGCGAAAU______CACCAAUACGACACAACUUGACCCAAAACGUAGUCAAGUGCAA_ACGGGAA____________A
................((((.(.............)...........(((((((..........)))))))......))))............... ( -7.44 =  -6.84 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,392,574 – 21,392,671
Length 97
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 69.37
Mean single sequence MFE -23.18
Consensus MFE -7.18
Energy contribution -7.18
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.31
SVM decision value 0.17
SVM RNA-class probability 0.616834
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21392574 97 - 27905053
UAAAGUCAACAGAGUGGUAAAUUCA---------GCCUCCGUCAUAGUAAUUCAAUUCCGCGAAAU------CACCAAUUCUACGCAACUUGACCCAAAACGUAGUCAAGUG
..........((((((((.(.(((.---------((.......................))))).)------.))).))))).....(((((((..........))))))). ( -13.10)
>DroPse_CAF1 106873 108 - 1
UGUAGCCACCGGAGGAGUAAAUUUAUCUCUUCUGGCCACUGUCACUG----UCAAUUCCAGGAAUUGGCUUGCCCCAAAACGAAACAACUUGACUCAAAAUUGAGUCAAGUG
((..((..(((((((((.........)))))))))...........(----(((((((...))))))))..))..))..........((((((((((....)))))))))). ( -35.00)
>DroSim_CAF1 83344 97 - 1
UAAAGUCAACAGAGUGGUAAAUUCA---------GCCUCUGUUAUAGUAAUUCAAUUCCGCGAAAU------CACCAAUCCCGCGCAACUUGACCCAAAACGUAGUCAAGUG
.......((((((((((.....)))---------..)))))))...............((((....------.........))))..(((((((..........))))))). ( -18.62)
>DroYak_CAF1 86628 85 - 1
------------AGUGGUAAAUUCU---------GCCUCCGCCAUAGUAAUUCAAUUCAGCGAAAU------CACCAAUCCUACACAACUUGACCCAAAACGUAGUCAAGUG
------------.(.((((.....)---------))).)(((...(((......)))..)))....------...............(((((((..........))))))). ( -11.20)
>DroPer_CAF1 129795 108 - 1
UGUAGCAACCAGAGGAGUAAAUUUAUCUCUUCUGGCCACUGUCACUG----UCAAUUCCAGGAAUUGGCUUGCCCCAAAACGAAACAACUUGACUCAAAAUUGAGUCAAGUG
((..(((((((((((((.........)))))))))...........(----(((((((...))))))))))))..))..........((((((((((....)))))))))). ( -38.00)
>consensus
UAAAGCCAACAGAGUGGUAAAUUCA_________GCCUCUGUCAUAGUAAUUCAAUUCCGCGAAAU______CACCAAUACGACACAACUUGACCCAAAACGUAGUCAAGUG
.......................................................................................(((((((..........))))))). ( -7.18 =  -7.18 +   0.00)

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 12:59:29 2006