Locus 2356

Sequence ID X_DroMel_CAF1
Location 6,286,519 – 6,286,778
Length 259
Max. P 0.967438
window3835 window3836 window3837 window3838 window3839

overview

Window 5

Location 6,286,519 – 6,286,622
Length 103
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 81.09
Mean single sequence MFE -25.53
Consensus MFE -20.17
Energy contribution -20.40
Covariance contribution 0.23
Combinations/Pair 1.09
Mean z-score -1.98
Structure conservation index 0.79
SVM decision value 1.03
SVM RNA-class probability 0.903238
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6286519 103 + 22224390
UACAAACGUAACGCAACGAAAAGUAACCAAGCAACGGGGCGUAUACGCAAUGCGAAUGCUUGACAUUACGUAUACGUAAGUAGCUGGCAAUGCAAG--AGGCAAG
......(((......)))........(((.((.((...(((((((((.(((((((....))).)))).)))))))))..)).)))))...(((...--..))).. ( -27.10)
>DroSec_CAF1 23279 91 + 1
UACAAACGUAUCGAAACGAAAAGUAACCAAGCAACGGUGCGUAUACGCAAUGCGAAUGCUUGAUAUUACGUAUACGUAAGUAGCUGGC--------------AUG
......(((......)))........(((.((.((..((((((((((.(((((((....))).)))).)))))))))).)).))))).--------------... ( -23.80)
>DroYak_CAF1 20399 104 + 1
UACAAAUAUAGUGCAACAGAAAGUAACCUAGCAACGGGGCGUAUACGCAAUGCAAAUGCUUGAUAUUACGCAUACGUAAGAAGCUGGCA-UGCGAGUAUGGCAAG
...........(((............(((......))).(((((.((((.(((....((((....(((((....))))).))))..)))-)))).)))))))).. ( -25.70)
>consensus
UACAAACGUAACGCAACGAAAAGUAACCAAGCAACGGGGCGUAUACGCAAUGCGAAUGCUUGAUAUUACGUAUACGUAAGUAGCUGGCA_UGC_AG___GGCAAG
..........................((.(((.((...(((((((((.(((((((....))).)))).)))))))))..)).))))).................. (-20.17 = -20.40 +   0.23)

alignment

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secondary structure

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Window 6

Location 6,286,519 – 6,286,622
Length 103
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 81.09
Mean single sequence MFE -24.89
Consensus MFE -21.64
Energy contribution -20.75
Covariance contribution -0.88
Combinations/Pair 1.12
Mean z-score -2.02
Structure conservation index 0.87
SVM decision value 1.61
SVM RNA-class probability 0.967438
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6286519 103 - 22224390
CUUGCCU--CUUGCAUUGCCAGCUACUUACGUAUACGUAAUGUCAAGCAUUCGCAUUGCGUAUACGCCCCGUUGCUUGGUUACUUUUCGUUGCGUUACGUUUGUA
..(((..--...)))..((((((.((...((((((((((((((.........))))))))))))))....)).)).))))(((....(((......)))...))) ( -27.40)
>DroSec_CAF1 23279 91 - 1
CAU--------------GCCAGCUACUUACGUAUACGUAAUAUCAAGCAUUCGCAUUGCGUAUACGCACCGUUGCUUGGUUACUUUUCGUUUCGAUACGUUUGUA
...--------------......(((..(((((((((....((((((((..((...((((....)))).)).)))))))).......)))....))))))..))) ( -23.30)
>DroYak_CAF1 20399 104 - 1
CUUGCCAUACUCGCA-UGCCAGCUUCUUACGUAUGCGUAAUAUCAAGCAUUUGCAUUGCGUAUACGCCCCGUUGCUAGGUUACUUUCUGUUGCACUAUAUUUGUA
..(((.(((......-.((((((......((((((((((((.....((....)))))))))))))).......))).))).......))).)))........... ( -23.96)
>consensus
CUUGCC___CU_GCA_UGCCAGCUACUUACGUAUACGUAAUAUCAAGCAUUCGCAUUGCGUAUACGCCCCGUUGCUUGGUUACUUUUCGUUGCGAUACGUUUGUA
.................((((((......((((((((((((.....((....)))))))))))))).......))).)))(((....(((......)))...))) (-21.64 = -20.75 +  -0.88)

alignment

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secondary structure

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Window 7

Location 6,286,544 – 6,286,662
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.91
Mean single sequence MFE -32.93
Consensus MFE -21.63
Energy contribution -21.63
Covariance contribution 0.01
Combinations/Pair 1.13
Mean z-score -2.11
Structure conservation index 0.66
SVM decision value 0.37
SVM RNA-class probability 0.710819
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6286544 118 + 22224390
ACCAAGCAACGGGGCGUAUACGCAAUGCGAAUGCUUGACAUUACGUAUACGUAAGUAGCUGGCAAUGCAAG--AGGCAAGUACGAUGACGUAUAAGUGCCAAGUUACAUAACACAUGGCU
....(((......(((((((((.(((((((....))).)))).)))))))))..((((((((((.(((...--..))).(((((....)))))...)))).))))))..........))) ( -37.40)
>DroSec_CAF1 23304 106 + 1
ACCAAGCAACGGUGCGUAUACGCAAUGCGAAUGCUUGAUAUUACGUAUACGUAAGUAGCUGGC--------------AUGUAUGUUGAUGUAUAAGUGCGAAGUUACAUAACACAUGGCU
....(((.....((((((((((.(((((((....))).)))).)))))))))).((((((.((--------------((.((((......)))).))))..))))))..........))) ( -30.10)
>DroYak_CAF1 20424 116 + 1
ACCUAGCAACGGGGCGUAUACGCAAUGCAAAUGCUUGAUAUUACGCAUACGUAAGAAGCUGGCA-UGCGAGUAUGGCAAGUA---UGAUGUAUAAGUGCAAAGCUACAUAGCACAUGGCU
....(((.((..(.(((((.((((.(((....((((....(((((....))))).))))..)))-)))).))))).)..)).---..........((((...........))))...))) ( -31.30)
>consensus
ACCAAGCAACGGGGCGUAUACGCAAUGCGAAUGCUUGAUAUUACGUAUACGUAAGUAGCUGGCA_UGC_AG___GGCAAGUA_G_UGAUGUAUAAGUGCAAAGUUACAUAACACAUGGCU
.((.(((.((...(((((((((.(((((((....))).)))).)))))))))..)).))))).................((((............))))...(((....)))........ (-21.63 = -21.63 +   0.01)

alignment

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secondary structure

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Window 8

Location 6,286,544 – 6,286,662
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.91
Mean single sequence MFE -30.37
Consensus MFE -23.76
Energy contribution -23.65
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.31
Structure conservation index 0.78
SVM decision value 1.16
SVM RNA-class probability 0.923960
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6286544 118 - 22224390
AGCCAUGUGUUAUGUAACUUGGCACUUAUACGUCAUCGUACUUGCCU--CUUGCAUUGCCAGCUACUUACGUAUACGUAAUGUCAAGCAUUCGCAUUGCGUAUACGCCCCGUUGCUUGGU
.((((((.((.((((((...((((....((((....))))..)))).--.)))))).))))((.((...((((((((((((((.........))))))))))))))....)).)).)))) ( -37.80)
>DroSec_CAF1 23304 106 - 1
AGCCAUGUGUUAUGUAACUUCGCACUUAUACAUCAACAUACAU--------------GCCAGCUACUUACGUAUACGUAAUAUCAAGCAUUCGCAUUGCGUAUACGCACCGUUGCUUGGU
.....(((((((((((............))))).))))))...--------------((((((.((...((((((((((((.....((....))))))))))))))....)).)).)))) ( -26.60)
>DroYak_CAF1 20424 116 - 1
AGCCAUGUGCUAUGUAGCUUUGCACUUAUACAUCA---UACUUGCCAUACUCGCA-UGCCAGCUUCUUACGUAUGCGUAAUAUCAAGCAUUUGCAUUGCGUAUACGCCCCGUUGCUAGGU
...((((((....(((.....(((..(((.....)---))..)))..))).))))-))(((((......((((((((((((.....((....)))))))))))))).......))).)). ( -26.72)
>consensus
AGCCAUGUGUUAUGUAACUUCGCACUUAUACAUCA_C_UACUUGCC___CU_GCA_UGCCAGCUACUUACGUAUACGUAAUAUCAAGCAUUCGCAUUGCGUAUACGCCCCGUUGCUUGGU
....((((((..(((......)))...))))))........................((((((......((((((((((((.....((....)))))))))))))).......))).))) (-23.76 = -23.65 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,286,662 – 6,286,778
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.78
Mean single sequence MFE -32.27
Consensus MFE -20.15
Energy contribution -20.61
Covariance contribution 0.46
Combinations/Pair 1.19
Mean z-score -1.70
Structure conservation index 0.62
SVM decision value -0.03
SVM RNA-class probability 0.517211
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6286662 116 - 22224390
CUUUUGGGGACUGUGGUACCCAAUGUUUCGCAUUCGC-AUUGGGUGUCUUUGGUUUAUACUGAAUAUGUGACAUUUAUGCAUUAUUGCUUAACAUUCACAACCGU---UGUAAGUCCAUA
.......(((((..(..(((((((((.........))-)))))))..)((..((....))..))..(((((...(((.(((....))).)))...))))).....---....)))))... ( -31.90)
>DroSec_CAF1 23410 118 - 1
CUC-UGGGGGCUGCGGUACCCAAUGUUUCGCAUUGGC-GAUGGGUGUCUUUGGUUUCUGCUGAAUAUGUGACAUUUAUGCAUUAUUGCUUAACACUCACAGCCGUUGUUGUAAGUCCAUA
...-...(((((((((((((((.....((((....))-)))))))...((..((....))..))..(((((...(((.(((....))).)))...)))))))))).......)))))... ( -32.41)
>DroYak_CAF1 20540 108 - 1
CUU-UGGGGCCUGCGGUACCCAAUGU-GCGCAUUGGCUGCUGGGUGUCUUCGGUUUCUACUGAAUAUGUGACAUUUAUGCAUUAUUGCAUAACCUUUUAGAC--UU--------ACUGUA
((.-.((((((.((((...((((((.-...)))))))))).))(((((((((((....)))))).....)))))(((((((....)))))))))))..))..--..--------...... ( -32.50)
>consensus
CUU_UGGGGACUGCGGUACCCAAUGUUUCGCAUUGGC_GAUGGGUGUCUUUGGUUUCUACUGAAUAUGUGACAUUUAUGCAUUAUUGCUUAACAUUCACAACCGUU__UGUAAGUCCAUA
.......(((((..(..((((((((.....))).......)))))..)((((((....))))))..(((((...(((.(((....))).)))...)))))............)))))... (-20.15 = -20.61 +   0.46)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:38 2006