Locus 5801

Sequence ID 2L_DroMel_CAF1
Location 16,453,603 – 16,453,740
Length 137
Max. P 0.992975
window9200 window9201 window9202 window9203

overview

Window 0

Location 16,453,603 – 16,453,707
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.69
Mean single sequence MFE -26.54
Consensus MFE -9.23
Energy contribution -9.87
Covariance contribution 0.64
Combinations/Pair 1.23
Mean z-score -2.48
Structure conservation index 0.35
SVM decision value 2.36
SVM RNA-class probability 0.992975
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16453603 104 + 22407834
CUUUUGGGGAGAAUUGGUUUAUUUGAUCUACAAAUGGCUUAAGCUCAAAAGAGAGCUCUUUACUUAAUGUUGACUAUCAAA--------UGCGUUAAAGAGCUCU--------AUAUAUU
((((((((.....((((.(((((((.....))))))).)))).))))))))(((((((((((.......(((.....))).--------.....)))))))))))--------....... ( -26.92)
>DroSec_CAF1 78335 103 + 1
CUU-UGGGGAGAAUUGGUUUAUUUGAUCUACAAAUGGCCUAAGCUCGAAAGAGAGCUCUUUACUUAAUUUUGAUUAUCAAA--------UGCGUUAAAGAGCUCU--------AUAAAUU
(((-(.(((....((((..((((((.....))))))..)))).))).))))(((((((((((......((((.....))))--------.....)))))))))))--------....... ( -29.70)
>DroSim_CAF1 78596 103 + 1
CUU-UGGGGAGAAUUGGUUUAUUUGAUCUACAAAUGGCCUAAGCUCGAAAGAGAGCUCUUUACUUAAUUUUGAUUAUCAAA--------UGCCUUGAAGAGCUCU--------AUAAAUU
(((-(.(((....((((..((((((.....))))))..)))).))).))))(((((((((((......((((.....))))--------.....)))))))))))--------....... ( -29.80)
>DroEre_CAF1 75196 98 + 1
------------AUUGGUUUU-UUUAUUUACAAGUGCUAUGAGCUCGAAGGAGAGCUAUUUAGUUAAUUUUCAUUAUCAUA--------UGUGUGAAA-AGCUCUCGAGCAAAAUGUUUU
------------.........-.......(((..((((..(((((.(((((..((((....))))..)))))....((((.--------...))))..-)))))...))))...)))... ( -19.40)
>DroYak_CAF1 79324 119 + 1
CUU-UGGGGAGAGUUGGUUUCCUUGAUUUACAAAUGGAAUGAGCUCGAAAAAAAGCUCUUUCUUUUAUUUUGAUUAUCAUAUGUACAUAUGUGUGAAAUAACUCUCGAGCUAAAUAUAUU
.((-(((.((((((((.......(((((.......((((.(((((........))))).))))........)))))((((((((....))))))))..))))))))...)))))...... ( -26.86)
>consensus
CUU_UGGGGAGAAUUGGUUUAUUUGAUCUACAAAUGGCAUAAGCUCGAAAGAGAGCUCUUUACUUAAUUUUGAUUAUCAAA________UGCGUUAAAGAGCUCU________AUAUAUU
.............((((((((..(.((......)).)..))))).)))...(((((((((((................................)))))))))))............... ( -9.23 =  -9.87 +   0.64)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,453,603 – 16,453,707
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.69
Mean single sequence MFE -20.06
Consensus MFE -8.67
Energy contribution -8.91
Covariance contribution 0.24
Combinations/Pair 1.27
Mean z-score -2.36
Structure conservation index 0.43
SVM decision value 2.03
SVM RNA-class probability 0.986096
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16453603 104 - 22407834
AAUAUAU--------AGAGCUCUUUAACGCA--------UUUGAUAGUCAACAUUAAGUAAAGAGCUCUCUUUUGAGCUUAAGCCAUUUGUAGAUCAAAUAAACCAAUUCUCCCCAAAAG
.......--------(((((((((((.....--------.(((.....))).......)))))))))))((((((.((....)).(((((.....)))))..............)))))) ( -21.12)
>DroSec_CAF1 78335 103 - 1
AAUUUAU--------AGAGCUCUUUAACGCA--------UUUGAUAAUCAAAAUUAAGUAAAGAGCUCUCUUUCGAGCUUAGGCCAUUUGUAGAUCAAAUAAACCAAUUCUCCCCA-AAG
.......--------(((((((((((.....--------((((.....))))......))))))))))).....(((..(.((..(((((.....)))))...)).)..)))....-... ( -21.40)
>DroSim_CAF1 78596 103 - 1
AAUUUAU--------AGAGCUCUUCAAGGCA--------UUUGAUAAUCAAAAUUAAGUAAAGAGCUCUCUUUCGAGCUUAGGCCAUUUGUAGAUCAAAUAAACCAAUUCUCCCCA-AAG
.......--------(((((((((.......--------((((.....))))........))))))))).....(((..(.((..(((((.....)))))...)).)..)))....-... ( -17.76)
>DroEre_CAF1 75196 98 - 1
AAAACAUUUUGCUCGAGAGCU-UUUCACACA--------UAUGAUAAUGAAAAUUAACUAAAUAGCUCUCCUUCGAGCUCAUAGCACUUGUAAAUAAA-AAAACCAAU------------
..........(((((((((((-..(((....--------..)))((((....)))).......)))))))....))))....................-.........------------ ( -15.90)
>DroYak_CAF1 79324 119 - 1
AAUAUAUUUAGCUCGAGAGUUAUUUCACACAUAUGUACAUAUGAUAAUCAAAAUAAAAGAAAGAGCUUUUUUUCGAGCUCAUUCCAUUUGUAAAUCAAGGAAACCAACUCUCCCCA-AAG
..............(((((((.((((...(((((....))))).........(((((.(((.((((((......)))))).)))..)))))........))))..)))))))....-... ( -24.10)
>consensus
AAUAUAU________AGAGCUCUUUAACGCA________UUUGAUAAUCAAAAUUAAGUAAAGAGCUCUCUUUCGAGCUUAGGCCAUUUGUAGAUCAAAUAAACCAAUUCUCCCCA_AAG
...............(((((((((((................................)))))))))))................................................... ( -8.67 =  -8.91 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,453,643 – 16,453,740
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.86
Mean single sequence MFE -24.20
Consensus MFE -9.77
Energy contribution -10.13
Covariance contribution 0.36
Combinations/Pair 1.28
Mean z-score -2.35
Structure conservation index 0.40
SVM decision value 1.96
SVM RNA-class probability 0.983884
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16453643 97 + 22407834
AAGCUCAAAAGAGAGCUCUUUACUUAAUGUUGACUAUCAAA--------UGCGUUAAAGAGCUCU--------AUAUAUUAGGCCUUAAGUAACUGCUAAGCCAAUUAUUGCA-------
..((.......(((((((((((.......(((.....))).--------.....)))))))))))--------........(((.(((.((....)))))))).......)).------- ( -22.92)
>DroSec_CAF1 78374 97 + 1
AAGCUCGAAAGAGAGCUCUUUACUUAAUUUUGAUUAUCAAA--------UGCGUUAAAGAGCUCU--------AUAAAUUAGGUCUUAAGUAACUGCUAAGCGAAUUACUGCA-------
.(((((....))((((((((((......((((.....))))--------.....)))))))))).--------......................)))..(((......))).------- ( -22.40)
>DroSim_CAF1 78635 97 + 1
AAGCUCGAAAGAGAGCUCUUUACUUAAUUUUGAUUAUCAAA--------UGCCUUGAAGAGCUCU--------AUAAAUUAGGCCUUAAGUAAUUGCUAAGCGAAUUACUGCA-------
..(((..(...(((((((((((......((((.....))))--------.....)))))))))))--------.....)..)))....(((((((((...)).)))))))...------- ( -24.80)
>DroEre_CAF1 75223 110 + 1
GAGCUCGAAGGAGAGCUAUUUAGUUAAUUUUCAUUAUCAUA--------UGUGUGAAA-AGCUCUCGAGCAAAAUGUUUUAGGC-UUAAGUGAGUGCUUAGCAAAUUGCUGCUCAUUAUU
((((......(((((((...........((((((.......--------...))))))-))))))).(((((..(((..(((((-..........))))))))..)))))))))...... ( -28.40)
>DroYak_CAF1 79363 113 + 1
GAGCUCGAAAAAAAGCUCUUUCUUUUAUUUUGAUUAUCAUAUGUACAUAUGUGUGAAAUAACUCUCGAGCUAAAUAUAUUAGGCCUUAAGUAAGACCUAAUCAAAUAACUGCA-------
.(((((((..(((((......)))))..........((((((((....))))))))........)))))))......((((((.(((....))).))))))............------- ( -22.50)
>consensus
AAGCUCGAAAGAGAGCUCUUUACUUAAUUUUGAUUAUCAAA________UGCGUUAAAGAGCUCU________AUAUAUUAGGCCUUAAGUAACUGCUAAGCAAAUUACUGCA_______
..((.......(((((((((((................................))))))))))).......................(((((............)))))))........ ( -9.77 = -10.13 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,453,643 – 16,453,740
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.86
Mean single sequence MFE -22.70
Consensus MFE -9.41
Energy contribution -10.97
Covariance contribution 1.56
Combinations/Pair 1.20
Mean z-score -2.20
Structure conservation index 0.41
SVM decision value 1.49
SVM RNA-class probability 0.958559
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16453643 97 - 22407834
-------UGCAAUAAUUGGCUUAGCAGUUACUUAAGGCCUAAUAUAU--------AGAGCUCUUUAACGCA--------UUUGAUAGUCAACAUUAAGUAAAGAGCUCUCUUUUGAGCUU
-------.((.......(((((((......))..)))))........--------(((((((((((.....--------.(((.....))).......))))))))))).......)).. ( -21.92)
>DroSec_CAF1 78374 97 - 1
-------UGCAGUAAUUCGCUUAGCAGUUACUUAAGACCUAAUUUAU--------AGAGCUCUUUAACGCA--------UUUGAUAAUCAAAAUUAAGUAAAGAGCUCUCUUUCGAGCUU
-------.(((((((((.((...)))))))))...............--------(((((((((((.....--------((((.....))))......))))))))))).......)).. ( -22.80)
>DroSim_CAF1 78635 97 - 1
-------UGCAGUAAUUCGCUUAGCAAUUACUUAAGGCCUAAUUUAU--------AGAGCUCUUCAAGGCA--------UUUGAUAAUCAAAAUUAAGUAAAGAGCUCUCUUUCGAGCUU
-------((((((.....)))..))).((((((((.((((.......--------((....))...)))).--------((((.....)))).)))))))).((((((......)))))) ( -20.00)
>DroEre_CAF1 75223 110 - 1
AAUAAUGAGCAGCAAUUUGCUAAGCACUCACUUAA-GCCUAAAACAUUUUGCUCGAGAGCU-UUUCACACA--------UAUGAUAAUGAAAAUUAACUAAAUAGCUCUCCUUCGAGCUC
......(((((((((..((.((.((..........-)).))...))..))))).(((((((-..(((....--------..)))((((....)))).......)))))))......)))) ( -21.80)
>DroYak_CAF1 79363 113 - 1
-------UGCAGUUAUUUGAUUAGGUCUUACUUAAGGCCUAAUAUAUUUAGCUCGAGAGUUAUUUCACACAUAUGUACAUAUGAUAAUCAAAAUAAAAGAAAGAGCUUUUUUUCGAGCUC
-------............((((((((((....))))))))))......((((((((((..(.(((...(((((....)))))....((.........))..))).)..)))))))))). ( -27.00)
>consensus
_______UGCAGUAAUUCGCUUAGCACUUACUUAAGGCCUAAUAUAU________AGAGCUCUUUAACGCA________UUUGAUAAUCAAAAUUAAGUAAAGAGCUCUCUUUCGAGCUU
........(((((((((........))))))).......................(((((((((((................................))))))))))).......)).. ( -9.41 = -10.97 +   1.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:17 2006