Locus 1785

Sequence ID X_DroMel_CAF1
Location 4,923,765 – 4,923,939
Length 174
Max. P 0.975630
window2914 window2915 window2916

overview

Window 4

Location 4,923,765 – 4,923,862
Length 97
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 74.67
Mean single sequence MFE -25.94
Consensus MFE -13.08
Energy contribution -12.50
Covariance contribution -0.58
Combinations/Pair 1.25
Mean z-score -2.36
Structure conservation index 0.50
SVM decision value 1.75
SVM RNA-class probability 0.975630
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4923765 97 - 22224390
UUGACCACCGGCGAGGACUCAUCG---GAGUCC---UCGAAUGCCUCGCUACACCUGAACCAGCACUCCUCCACCUCAUCCUC-GCCAGC------------CUCGCAG-CACCAAG
(((......((((((((......(---(((...---..((.....))(((...........)))....))))......)))))-))).((------------......)-)..))). ( -23.50)
>DroPse_CAF1 11976 107 - 1
UUGACCACCGGUGAGGAUUCAUCCAAUGAGUCC---UCGAAUGCCUCGCUACACAAUCAGCCGCACU---CCUCCUCAUCCGCAGCCAGCAUCAGCUC----CUCGCAUUCACCAUC
.........(((((((((((((...))))))))---))((((((...............((.((...---...........)).)).(((....))).----...)))))))))... ( -28.44)
>DroEre_CAF1 10209 97 - 1
UUGACCACCGGCGAGGACUCAUCG---GAGUCC---UCGAAUGCCUCGCUACACCUGAACCAGCACUCCUCCACCUCAUCCUC-GCCAGC------------CUCGCAG-CACCAUG
.........((((((((......(---(((...---..((.....))(((...........)))....))))......)))))-))).((------------......)-)...... ( -23.40)
>DroMoj_CAF1 15265 92 - 1
UUAACCACCGGCGAGGACUCCUCCAAUGAGUCCUCAUCGAAUGCCUCGCUACAGCA---GCCGCACU------CCUCA------GCCAG------CUC----AACGCACUCACAGCA
.........(((((((((((.......))))))))...((.(((...(((.....)---)).))).)------)....------))).(------(..----...)).......... ( -25.70)
>DroAna_CAF1 10913 110 - 1
UUGACCACCGGCGAGGACUCAUCCAAUGAGUCU---UCGAAUGCCUCGCUCCACCAGCAGCAUCACUCCUCGUCCUCAUCCUC-GCCAGCAACGCAUUCAAACUCGCAA-CACCA--
..........((((((((((((...))))))).---..((((((...(((.....))).((......................-....))...))))))...)))))..-.....-- ( -26.17)
>DroPer_CAF1 11288 107 - 1
UUGACCACCGGUGAGGAUUCAUCCAAUGAGUCC---UCGAAUGCCUCGCUACACAAUCAGCCGCACU---CCUCCUCAUCCGCAGCCAGCAUCAGCUC----CUCGCAUUCACCAUC
.........(((((((((((((...))))))))---))((((((...............((.((...---...........)).)).(((....))).----...)))))))))... ( -28.44)
>consensus
UUGACCACCGGCGAGGACUCAUCCAAUGAGUCC___UCGAAUGCCUCGCUACACCAGCAGCAGCACU___CCUCCUCAUCCUC_GCCAGC_____CUC____CUCGCAG_CACCAUC
.........(((..((((((.......))))))....(((.....)))....................................))).............................. (-13.08 = -12.50 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,923,828 – 4,923,939
Length 111
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.97
Mean single sequence MFE -38.83
Consensus MFE -27.12
Energy contribution -28.20
Covariance contribution 1.08
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.70
SVM decision value 0.30
SVM RNA-class probability 0.677442
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4923828 111 + 22224390
UCGAGGACUC---CGAUGAGUCCUCGCCGGUGGUCAAGCGAUUGGUGGUUGCGUUCACAAUAUGCGAGGAG---GAGUUCAUACCGCCGCCGCUGCCAUCCUCCUCGUCCCCGCUCA
.(((((((((---....))))))))).(((.((.(..(((....((((......))))....)))((((((---((...((....((....))))...))))))))).))))).... ( -43.70)
>DroPse_CAF1 12046 96 + 1
UCGAGGACUCAUUGGAUGAAUCCUCACCGGUGGUCAAGCGAUUGGUGGUUGAGUUGACAAUAUGCGAGGAA---GAGUUCACA------------------UCCUCGUCCCCACUGA
..(((((.((((...)))).)))))..((((((((((.((((.....))))..))))).....(((((((.---(......).------------------)))))))...))))). ( -32.40)
>DroSec_CAF1 10476 111 + 1
UCGAGGACUC---CGAUGAGUCCUCGCCGGUGGUCAAGCGAUUGGUGGUUGCGUUCACAAUAUGCGAGGAG---GAGUUCAUACCGCCGCCGCUGCCAUCCUCCUCGUCCCCGCUCA
.(((((((((---....))))))))).(((.((.(..(((....((((......))))....)))((((((---((...((....((....))))...))))))))).))))).... ( -43.70)
>DroYak_CAF1 10237 111 + 1
UCGAGGACUC---CGAUGAGUCCUCGCCGGUGGUCAAGCGAUUGGUGGUUGCGUUCACAAUAUGCGAGGAG---GAAUUCAUACCGCCGCCGCUGCCAUCCUCCUCGUCCCCGCUCA
.(((((((((---....))))))))).(((.((.(..(((....((((......))))....)))((((((---((...((....((....))))...))))))))).))))).... ( -42.60)
>DroAna_CAF1 10986 105 + 1
UCGAAGACUCAUUGGAUGAGUCCUCGCCGGUGGUCAAGCGAUUGGUGGUUGCGUUCACGAUGUGCGAUGAGGAUGAGUUCAC--C----------AUAUCCUCCUCAUCCCCACUGC
.(((.(((((((...))))))).))).((((((....(((..(.((((......)))).)..)))((((((((.((......--.----------...)).)))))))).)))))). ( -38.20)
>DroPer_CAF1 11358 96 + 1
UCGAGGACUCAUUGGAUGAAUCCUCACCGGUGGUCAAGCGAUUGGUGGUUGAGUUGACAAUAUGCGAGGAA---GAGUUCACA------------------UCCUCGUCCCCACUGA
..(((((.((((...)))).)))))..((((((((((.((((.....))))..))))).....(((((((.---(......).------------------)))))))...))))). ( -32.40)
>consensus
UCGAGGACUC___CGAUGAGUCCUCGCCGGUGGUCAAGCGAUUGGUGGUUGCGUUCACAAUAUGCGAGGAG___GAGUUCACA_C__________CCAUCCUCCUCGUCCCCACUCA
..((((((((.......))))))))...(((((....(((....((((......))))....)))((((((.............................))))))....))))).. (-27.12 = -28.20 +   1.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,923,828 – 4,923,939
Length 111
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 80.97
Mean single sequence MFE -38.98
Consensus MFE -27.47
Energy contribution -27.47
Covariance contribution 0.00
Combinations/Pair 1.16
Mean z-score -1.82
Structure conservation index 0.70
SVM decision value 0.61
SVM RNA-class probability 0.800188
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4923828 111 - 22224390
UGAGCGGGGACGAGGAGGAUGGCAGCGGCGGCGGUAUGAACUC---CUCCUCGCAUAUUGUGAACGCAACCACCAAUCGCUUGACCACCGGCGAGGACUCAUCG---GAGUCCUCGA
....(((((.((((((((.(((..(((..((.((........)---).))((((.....)))).)))..)))))..)).)))).)).))).(((((((((....---))))))))). ( -44.90)
>DroPse_CAF1 12046 96 - 1
UCAGUGGGGACGAGGA------------------UGUGAACUC---UUCCUCGCAUAUUGUCAACUCAACCACCAAUCGCUUGACCACCGGUGAGGAUUCAUCCAAUGAGUCCUCGA
((.((((.(((((..(------------------(((((....---....)))))).)))))...((((.(.......).)))))))).))(((((((((((...))))))))))). ( -31.00)
>DroSec_CAF1 10476 111 - 1
UGAGCGGGGACGAGGAGGAUGGCAGCGGCGGCGGUAUGAACUC---CUCCUCGCAUAUUGUGAACGCAACCACCAAUCGCUUGACCACCGGCGAGGACUCAUCG---GAGUCCUCGA
....(((((.((((((((.(((..(((..((.((........)---).))((((.....)))).)))..)))))..)).)))).)).))).(((((((((....---))))))))). ( -44.90)
>DroYak_CAF1 10237 111 - 1
UGAGCGGGGACGAGGAGGAUGGCAGCGGCGGCGGUAUGAAUUC---CUCCUCGCAUAUUGUGAACGCAACCACCAAUCGCUUGACCACCGGCGAGGACUCAUCG---GAGUCCUCGA
.(((((.((.(((((((((...((...((....)).))...))---)))))))....((((....))))...))...))))).........(((((((((....---))))))))). ( -45.20)
>DroAna_CAF1 10986 105 - 1
GCAGUGGGGAUGAGGAGGAUAU----------G--GUGAACUCAUCCUCAUCGCACAUCGUGAACGCAACCACCAAUCGCUUGACCACCGGCGAGGACUCAUCCAAUGAGUCUUCGA
((.((((.((((((((......----------(--(....))..))))))))((.....(((........))).....))....))))..))((((((((((...)))))))))).. ( -36.90)
>DroPer_CAF1 11358 96 - 1
UCAGUGGGGACGAGGA------------------UGUGAACUC---UUCCUCGCAUAUUGUCAACUCAACCACCAAUCGCUUGACCACCGGUGAGGAUUCAUCCAAUGAGUCCUCGA
((.((((.(((((..(------------------(((((....---....)))))).)))))...((((.(.......).)))))))).))(((((((((((...))))))))))). ( -31.00)
>consensus
UCAGCGGGGACGAGGAGGAUGG__________G_UAUGAACUC___CUCCUCGCAUAUUGUGAACGCAACCACCAAUCGCUUGACCACCGGCGAGGACUCAUCC___GAGUCCUCGA
....(((((..((((((.............................))))))((.....(((........))).....))....)).))).(((((((((.......))))))))). (-27.47 = -27.47 +   0.00)

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 10:18:50 2006