Locus 7592

Sequence ID X_DroMel_CAF1
Location 18,914,402 – 18,914,581
Length 179
Max. P 0.996424
window12458 window12459 window12460 window12461

overview

Window 8

Location 18,914,402 – 18,914,507
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 61.01
Mean single sequence MFE -29.56
Consensus MFE -14.27
Energy contribution -16.98
Covariance contribution 2.71
Combinations/Pair 1.09
Mean z-score -2.77
Structure conservation index 0.48
SVM decision value 2.70
SVM RNA-class probability 0.996424
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18914402 105 + 22224390
UUAAGCGUGAUCAUUUCUAUUAAAGUAAAGUACCUGGUUAUUAAAAUGCCCAGGUA---------CACCGCCCAUUUGAUAUCCACCACUAGA-----UGAUGGUGCGAUCGCUACCUG-
......((((((.................((((((((.(((....))).)))))))---------)...(((((((...((........))..-----.))))).))))))))......- ( -29.90)
>DroSec_CAF1 147818 105 + 1
UCAAGCGUGAUCAUUUCUAUUAAAGUAAAGUACCUGGUUAUUAAAAUGCCCAGGUA---------CACCGACCAUUUGAUACCCACCACUAGA-----UGGUGGUGCGAUCGCUACCUU-
......((((((.....(((((((((...((((((((.(((....))).)))))))---------)....))..)))))))..(((((((...-----.))))))).))))))......- ( -33.70)
>DroSim_CAF1 121280 99 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---------NNCCCGCUCUUUGUU-CUCACC--CUGA-----UGGGGG--CGA-CGCUACCUU-
........................................................---------....(((((((...(-(.....--..))-----.)))))--)).-.........- (  -9.20)
>DroEre_CAF1 141974 104 + 1
UGAAGCGUGACCACUUCUAUCAAAGUAAAGUACCUGGUUAUUAAAGUGCCCAGGUA---------CACCACCCAUUUAAUGGCCACCACUAGCG------GUGGUGCGAUCGCUACCUG-
...((((((...((((......))))...((((((((.(((....))).)))))))---------)..)))..........((((((......)------)))))......))).....- ( -30.90)
>DroYak_CAF1 142927 120 + 1
UUCAGCGUGAUCAUUUCUAUUAAAGUAAAGUACCUGGUUAUUAAGAUGCCCAGGUACGAGUACUACACCACCCAUUCAAUCCCCACCACUGGUGGUGCUGGUGGUGCGAUCGCUACCUGG
..(((.((((((...........((((..((((((((.(((....))).))))))))...)))).(((((((....((....(((((...)))))))..))))))).))))))...))). ( -44.10)
>consensus
UUAAGCGUGAUCAUUUCUAUUAAAGUAAAGUACCUGGUUAUUAAAAUGCCCAGGUA_________CACCACCCAUUUGAUACCCACCACUAGA_____UGGUGGUGCGAUCGCUACCUG_
......((((((..................(((((((.(((....))).)))))))...........................(((((((.........))))))).))))))....... (-14.27 = -16.98 +   2.71)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,914,402 – 18,914,507
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 61.01
Mean single sequence MFE -30.96
Consensus MFE -12.76
Energy contribution -14.32
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -2.46
Structure conservation index 0.41
SVM decision value 1.73
SVM RNA-class probability 0.974584
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18914402 105 - 22224390
-CAGGUAGCGAUCGCACCAUCA-----UCUAGUGGUGGAUAUCAAAUGGGCGGUG---------UACCUGGGCAUUUUAAUAACCAGGUACUUUACUUUAAUAGAAAUGAUCACGCUUAA
-..((((((....)).((((((-----(...))))))).))))...((((((..(---------(((((((............))))))))..........((....))....)))))). ( -30.70)
>DroSec_CAF1 147818 105 - 1
-AAGGUAGCGAUCGCACCACCA-----UCUAGUGGUGGGUAUCAAAUGGUCGGUG---------UACCUGGGCAUUUUAAUAACCAGGUACUUUACUUUAAUAGAAAUGAUCACGCUUGA
-.....(((((((.((((((..-----....)))))).).)))...((((((..(---------(((((((............))))))))....((.....))...)))))).)))... ( -33.40)
>DroSim_CAF1 121280 99 - 1
-AAGGUAGCG-UCG--CCCCCA-----UCAG--GGUGAG-AACAAAGAGCGGGNN---------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-.........-(((--(((...-----...)--))))).-...............---------........................................................ (  -9.00)
>DroEre_CAF1 141974 104 - 1
-CAGGUAGCGAUCGCACCAC------CGCUAGUGGUGGCCAUUAAAUGGGUGGUG---------UACCUGGGCACUUUAAUAACCAGGUACUUUACUUUGAUAGAAGUGGUCACGCUUCA
-.((((((..(((((.((((------((....))))))((((...)))))))))(---------(((((((............)))))))).)))))).....((((((....)))))). ( -39.10)
>DroYak_CAF1 142927 120 - 1
CCAGGUAGCGAUCGCACCACCAGCACCACCAGUGGUGGGGAUUGAAUGGGUGGUGUAGUACUCGUACCUGGGCAUCUUAAUAACCAGGUACUUUACUUUAAUAGAAAUGAUCACGCUGAA
.(((...(.((((((((((((..(((((((...)))))....))....))))))))((((...((((((((............))))))))..))))...........)))).).))).. ( -42.60)
>consensus
_CAGGUAGCGAUCGCACCACCA_____UCUAGUGGUGGGUAUCAAAUGGGCGGUG_________UACCUGGGCAUUUUAAUAACCAGGUACUUUACUUUAAUAGAAAUGAUCACGCUUAA
.........((((.((((((...........))))))...........................(((((((............)))))))..................))))........ (-12.76 = -14.32 +   1.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,914,442 – 18,914,541
Length 99
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.34
Mean single sequence MFE -31.60
Consensus MFE -19.06
Energy contribution -19.88
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.60
SVM decision value 0.06
SVM RNA-class probability 0.565337
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18914442 99 - 22224390
UAAACAAUAGCUGCCAGC------AACAUGAUCCAAUAAA-CAGGUAGCGAUCGCACCAUCA-----UCUAGUGGUGGAUAUCAAAUGGGCGGUG---------UACCUGGGCAUUUUAA
...........((((...------...((......))...-((((((.(.(((((.((((((-----(...)))))))...((....))))))))---------))))))))))...... ( -24.50)
>DroSec_CAF1 147858 99 - 1
UAAAAAAUAGCUGCCGGC------AGCAUGAUCCAAUAAA-AAGGUAGCGAUCGCACCACCA-----UCUAGUGGUGGGUAUCAAAUGGUCGGUG---------UACCUGGGCAUUUUAA
.........((((((...------................-..))))))((((.((((((..-----....)))))).).)))(((((.((((..---------...)))).)))))... ( -28.70)
>DroEre_CAF1 142014 98 - 1
UAAACAAUAGCUGCCAGC------AGCAUGAUCCAAUAAA-CAGGUAGCGAUCGCACCAC------CGCUAGUGGUGGCCAUUAAAUGGGUGGUG---------UACCUGGGCACUUUAA
.........((((....)------))).............-((((((.(.(((((.((((------((....))))))((((...))))))))))---------)))))).......... ( -30.60)
>DroYak_CAF1 142967 120 - 1
UAAACAAUAGCUGCCAGCAGCAGCAGCAUGAUCCAAUAAACCAGGUAGCGAUCGCACCACCAGCACCACCAGUGGUGGGGAUUGAAUGGGUGGUGUAGUACUCGUACCUGGGCAUCUUAA
.........(((((.....)))))................(((((((.(((.(((((((((..(((((((...)))))....))....)))))))).)...))))))))))......... ( -42.60)
>consensus
UAAACAAUAGCUGCCAGC______AGCAUGAUCCAAUAAA_CAGGUAGCGAUCGCACCACCA_____UCUAGUGGUGGGUAUCAAAUGGGCGGUG_________UACCUGGGCAUUUUAA
...........((((.((.......))..............((((((((....)).((((((..........))))))..........................))))))))))...... (-19.06 = -19.88 +   0.81)

alignment

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secondary structure

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Window 1

Location 18,914,473 – 18,914,581
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.26
Mean single sequence MFE -24.44
Consensus MFE -14.72
Energy contribution -15.80
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -1.76
Structure conservation index 0.60
SVM decision value 0.00
SVM RNA-class probability 0.534938
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18914473 108 - 22224390
UAUGCAAUUCAUCGAAAUCGACACAAAGUUGCAAAAAUAAUAAACAAUAGCUGCCAGC------AACAUGAUCCAAUAAA-CAGGUAGCGAUCGCACCAUCA-----UCUAGUGGUGGAU
..(((((((..(((....))).....)))))))................((((((...------................-..)))))).(((.((((((..-----....))))))))) ( -24.50)
>DroSec_CAF1 147889 108 - 1
UAUGCAAUUCAUCCAAAUCGACACAAAGUUGCAAAAAUAAUAAAAAAUAGCUGCCGGC------AGCAUGAUCCAAUAAA-AAGGUAGCGAUCGCACCACCA-----UCUAGUGGUGGGU
..(((...((........((((.....))))..................((((((...------................-..))))))))..)))((((((-----(...))))))).. ( -23.70)
>DroSim_CAF1 121351 91 - 1
U-UGC-AUUCAUCCA-AUCGACACAAAGUUGCAAAA-UAA--AAACAAAGCUGC-GGC------AGC-UGAUCA---AAA-AAGGUAGCG-UCG--CCCCCA-----UCAG--GGUGAG-
.-...-..((((((.-..((((.....)))).....-...--..........((-(((------.((-(.(((.---...-..)))))))-)))--).....-----...)--))))).- ( -21.00)
>DroEre_CAF1 142045 107 - 1
UAUGCAAUUCAUCCGAAUCGACACAAAGUUGCAAAAAUAAUAAACAAUAGCUGCCAGC------AGCAUGAUCCAAUAAA-CAGGUAGCGAUCGCACCAC------CGCUAGUGGUGGCC
..(((.((((....)))).........(((((.................((((....)------))).....((......-..))..))))).)))((((------((....)))))).. ( -23.40)
>DroYak_CAF1 143007 120 - 1
UAUGCAAUUCAUCCGAAUCGACACAAAGUUGCAAAAAUAAUAAACAAUAGCUGCCAGCAGCAGCAGCAUGAUCCAAUAAACCAGGUAGCGAUCGCACCACCAGCACCACCAGUGGUGGGG
(((((.............((((.....))))..................(((((.....))))).)))))..........((.(((.((....))))).....(((((....))))))). ( -29.60)
>consensus
UAUGCAAUUCAUCCAAAUCGACACAAAGUUGCAAAAAUAAUAAACAAUAGCUGCCAGC______AGCAUGAUCCAAUAAA_CAGGUAGCGAUCGCACCACCA_____UCUAGUGGUGGGU
..(((((((.................)))))))................((((((............................)))))).....((((((...........))))))... (-14.72 = -15.80 +   1.08)

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 12:42:48 2006