Locus 7723

Sequence ID X_DroMel_CAF1
Location 19,227,489 – 19,227,731
Length 242
Max. P 0.998258
window12664 window12665 window12666 window12667 window12668

overview

Window 4

Location 19,227,489 – 19,227,581
Length 92
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 65.36
Mean single sequence MFE -26.42
Consensus MFE -5.55
Energy contribution -8.63
Covariance contribution 3.08
Combinations/Pair 1.06
Mean z-score -3.22
Structure conservation index 0.21
SVM decision value 1.59
SVM RNA-class probability 0.966045
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19227489 92 + 22224390
GAUAAAUGGCAAACAUGUCAUAAAAGGACUUCAUACGCAAUGCCUCGCUCGUACUCUC--------UCCCUCUCUCUCUGUAAAGAGAGAGAGAGCGAGA-----------------
.....((((((....))))))......................((((((((......)--------....(((((((((....)))))))))))))))).----------------- ( -29.80)
>DroSec_CAF1 14543 115 + 1
GAUAAAUGGCAAACAUGUCAUAAAAGGACUUCAUACGCAAUGCCCCACUCGCCCUCUCCCUCUCUAUCUCUCACUCUGUGGAAAGAGAGAGAG--GGAGAUGGAGCGAUGGAGCGAU
.....((((((....))))))...................(((.(((.(((((((((((((((((.(((.((.(.....))).))).))))))--))))).)).))))))).))).. ( -45.60)
>DroSim_CAF1 14280 74 + 1
GAUAAAUGGCAAACAUGUCAUAAAAGGACUUCAUACGCAAUGCCUC--------------------UCUCUCACUCUCUGGAAAGAGAGAGAG--G---------------------
.....((((((....)))))).....................((((--------------------((((((..((....))..)))))))))--)--------------------- ( -22.70)
>DroEre_CAF1 12904 69 + 1
GAUAAAUGGCAAAUAUGUCAUAAAAGGACUUCAUACGCAUUGCCUCGCUC--------------------C------UUCGAAAGAGGGGACG----AG------------------
.....((((((....))))))......................((((..(--------------------(------(((....)))))..))----))------------------ ( -21.20)
>DroYak_CAF1 13538 69 + 1
GAUAAACGGCAAACAUGUCAUAAAAGGACUUCAUACGCAAUGCCUCGCUU--------------------U----CUCCCGAAAGAGAGAAAA------------------------
.......((((.....(((.......)))...........))))....((--------------------(----(((.(....).)))))).------------------------ ( -12.79)
>consensus
GAUAAAUGGCAAACAUGUCAUAAAAGGACUUCAUACGCAAUGCCUCGCUC________________UC_CUC_CUCUCUGGAAAGAGAGAGAG____AG__________________
.......((((.....(((.......)))...........)))).........................(((.((((((....)))))).)))........................ ( -5.55 =  -8.63 +   3.08)

alignment

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secondary structure

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Window 5

Location 19,227,489 – 19,227,581
Length 92
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 65.36
Mean single sequence MFE -27.96
Consensus MFE -10.04
Energy contribution -12.52
Covariance contribution 2.48
Combinations/Pair 1.13
Mean z-score -2.93
Structure conservation index 0.36
SVM decision value 2.56
SVM RNA-class probability 0.995274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19227489 92 - 22224390
-----------------UCUCGCUCUCUCUCUCUUUACAGAGAGAGAGGGA--------GAGAGUACGAGCGAGGCAUUGCGUAUGAAGUCCUUUUAUGACAUGUUUGCCAUUUAUC
-----------------((((.((((((((((((....)))))))))))).--------))))..........((((..((((.....(((.......))))))).))))....... ( -33.80)
>DroSec_CAF1 14543 115 - 1
AUCGCUCCAUCGCUCCAUCUCC--CUCUCUCUCUUUCCACAGAGUGAGAGAUAGAGAGGGAGAGGGCGAGUGGGGCAUUGCGUAUGAAGUCCUUUUAUGACAUGUUUGCCAUUUAUC
...((((((((((.((.(((((--((((((.(((((((.....).)))))).))))))))))))))))).))))))...(((......(((.......))).....)))........ ( -50.10)
>DroSim_CAF1 14280 74 - 1
---------------------C--CUCUCUCUCUUUCCAGAGAGUGAGAGA--------------------GAGGCAUUGCGUAUGAAGUCCUUUUAUGACAUGUUUGCCAUUUAUC
---------------------.--(((((((.((((....)))).))))))--------------------).((((..((((.....(((.......))))))).))))....... ( -23.10)
>DroEre_CAF1 12904 69 - 1
------------------CU----CGUCCCCUCUUUCGAA------G--------------------GAGCGAGGCAAUGCGUAUGAAGUCCUUUUAUGACAUAUUUGCCAUUUAUC
------------------.(----((..((.((....)).------)--------------------)..)))(((((...(((((..((......))..))))))))))....... ( -15.80)
>DroYak_CAF1 13538 69 - 1
------------------------UUUUCUCUCUUUCGGGAG----A--------------------AAGCGAGGCAUUGCGUAUGAAGUCCUUUUAUGACAUGUUUGCCGUUUAUC
------------------------(((((((((....)))))----)--------------------)))...((((..((((.....(((.......))))))).))))....... ( -17.00)
>consensus
__________________CU____CUCUCUCUCUUUCCAGAGAG_GAG_GA________________GAGCGAGGCAUUGCGUAUGAAGUCCUUUUAUGACAUGUUUGCCAUUUAUC
........................(((((.(((((....))))).))))).......................((((.((((((.(((....))))))).))....))))....... (-10.04 = -12.52 +   2.48)

alignment

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secondary structure

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Window 6

Location 19,227,528 – 19,227,620
Length 92
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 57.06
Mean single sequence MFE -45.33
Consensus MFE -16.62
Energy contribution -20.90
Covariance contribution 4.28
Combinations/Pair 1.09
Mean z-score -4.28
Structure conservation index 0.37
SVM decision value 3.05
SVM RNA-class probability 0.998258
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19227528 92 + 22224390
AUGCCUCGCUCGUACUCUC--------UCCCUCUCUCUCUGUAAAGAGAGAGAGAGCGAGA------------------GCGAGAUGGAAGGGGUACACCGUGGGUGGUCCUUUCGGU
..(((...((((..(((((--------.(.((((((((((....)))))))))).).))))------------------)))))..(((((((.(((.(....)))).)))))))))) ( -45.10)
>DroSec_CAF1 14582 116 + 1
AUGCCCCACUCGCCCUCUCCCUCUCUAUCUCUCACUCUGUGGAAAGAGAGAGAG--GGAGAUGGAGCGAUGGAGCGAUGGAGCGAUGGAAGGGGUACACCGUGGGAGGUCCUUUCGGU
.((((((..(((((((((((((((((.(((.((.(.....))).))).))))))--))))).)).))))....((......)).......)))))).((((.(((....)))..)))) ( -54.20)
>DroEre_CAF1 12943 69 + 1
UUGCCUCGCUC--------------------C------UUCGAAAGAGGGGACG----AG-------------------GCGAGGGGGAAGGGGUACGCCGUGGGUGGUCCUUUUGGU
((((((((..(--------------------(------(((....)))))..))----))-------------------))))...(((((((.(((.(....)))).)))))))... ( -36.70)
>consensus
AUGCCUCGCUCG__CUCUC________UC_CUC_CUCUCUGGAAAGAGAGAGAG___GAGA__________________GCGAGAUGGAAGGGGUACACCGUGGGUGGUCCUUUCGGU
....(((((.............(((((((.(.((((((((........)))))))).).))))))).............)))))..(((((((.(((.(....)))).)))))))... (-16.62 = -20.90 +   4.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,227,528 – 19,227,620
Length 92
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 57.06
Mean single sequence MFE -40.37
Consensus MFE -10.03
Energy contribution -14.87
Covariance contribution 4.84
Combinations/Pair 1.04
Mean z-score -4.67
Structure conservation index 0.25
SVM decision value 1.22
SVM RNA-class probability 0.932730
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19227528 92 - 22224390
ACCGAAAGGACCACCCACGGUGUACCCCUUCCAUCUCGC------------------UCUCGCUCUCUCUCUCUUUACAGAGAGAGAGGGA--------GAGAGUACGAGCGAGGCAU
.((....))..((((...))))...........((((((------------------((..(((((((((((((((......)))))))))--------))))))..))))))))... ( -45.10)
>DroSec_CAF1 14582 116 - 1
ACCGAAAGGACCUCCCACGGUGUACCCCUUCCAUCGCUCCAUCGCUCCAUCGCUCCAUCUCC--CUCUCUCUCUUUCCACAGAGUGAGAGAUAGAGAGGGAGAGGGCGAGUGGGGCAU
.((....))........(((((.........))))).......((((((((((.((.(((((--((((((.(((((((.....).)))))).))))))))))))))))).)))))).. ( -55.50)
>DroEre_CAF1 12943 69 - 1
ACCAAAAGGACCACCCACGGCGUACCCCUUCCCCCUCGC-------------------CU----CGUCCCCUCUUUCGAA------G--------------------GAGCGAGGCAA
.....((((...(((....).))...)))).......((-------------------((----((..((.((....)).------)--------------------)..)))))).. ( -20.50)
>consensus
ACCGAAAGGACCACCCACGGUGUACCCCUUCCAUCUCGC__________________UCUC___CUCUCUCUCUUUCCAAAGAG_GAG_GA________GAGAG__CGAGCGAGGCAU
.((....))(((......)))............((((((.............(((((((((.((((((............)))))).))))))))).............))))))... (-10.03 = -14.87 +   4.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,227,620 – 19,227,731
Length 111
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 76.52
Mean single sequence MFE -18.34
Consensus MFE -12.12
Energy contribution -12.06
Covariance contribution -0.05
Combinations/Pair 1.18
Mean z-score -2.77
Structure conservation index 0.66
SVM decision value 2.25
SVM RNA-class probability 0.991179
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19227620 111 - 22224390
UUUCCGGUUAUUAUGAAAAUUAUAAUAACCUAAAAAUCAACAUGGUCCUUGCCUCGAACCCACUGGCCUCUAUGAACCCACCCACCCAUAUGGCCCAUAUACCAUUUAACU
.....(((((((((((...)))))))))))...........(((((...((.............((((..((((............)))).))))))...)))))...... ( -19.31)
>DroPse_CAF1 52580 85 - 1
UUUUGGGUUAUUAUUAAAACGAUAAUAGCCUCAAAAUCAACAUGGUG---UCCCU--CCCCGGCCCCCCGCCCG-C------CAACC-CAAAGCCCGU-------------
(((((((((((((((.....)))))))))).)))))......(((((---.....--....(((.....)))))-)------))...-..........------------- ( -19.60)
>DroSec_CAF1 14698 89 - 1
UUUCCGGUUAUUAUGAAAAUUAUAAUAACCUAAAAAUCAACAUGGUCCUUGCCUCGAAC----------------------CCACCCAUAUGGCCCAUAUACCAUUUAACU
.....(((((((((((...)))))))))))...........(((((....(((......----------------------..........)))......)))))...... ( -15.79)
>DroSim_CAF1 14385 107 - 1
UUUCCGGUUAUUAUGAAAAUUAUAAUAACCUAAAAAUCAACAUGGUCCUUGCCUCGAACCCACUGGCCUCUACGAAC----CCACCCAUAUGGCCCAUAUACCAUUUAACU
.....(((((((((((...)))))))))))...........(((((...((.............((((.........----..........))))))...)))))...... ( -17.32)
>DroEre_CAF1 13012 107 - 1
UUUCCGGUUAUUAUGAAAAUUAUAAUAACCUAAAAAUCAACAUGGUCCUUGCCUCGAACCCACUGACCUCUCCGAAC----CCACCCAUAUGGCCCAUAUAGCAUUUAACU
...(((((((((((((...))))))))))).............((((..((.........))..)))).........----..........)).................. ( -14.30)
>DroYak_CAF1 13643 107 - 1
UUUCCGGUUAUUAUGAAAAUUAUAAUAACCCAAAAAUCAACAUGGUCCUCGCCUCGAACCCACUGGCCCCACUGAAC----CCACCCAUGUGGCCCAUAUAGGAUUUAACU
..((((((((((((((...)))))))))))...........((((.....(((...........))).((((((...----.....)).)))).))))...)))....... ( -23.70)
>consensus
UUUCCGGUUAUUAUGAAAAUUAUAAUAACCUAAAAAUCAACAUGGUCCUUGCCUCGAACCCACUGGCCUCUCCGAAC____CCACCCAUAUGGCCCAUAUACCAUUUAACU
.....(((((((((((...)))))))))))...........((((.((...........................................)).))))............. (-12.12 = -12.06 +  -0.05)

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 12:45:57 2006