Locus 7073

Sequence ID 3L_DroMel_CAF1
Location 19,137,090 – 19,137,243
Length 153
Max. P 0.950866
window11463 window11464 window11465 window11466

overview

Window 3

Location 19,137,090 – 19,137,203
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.14
Mean single sequence MFE -27.40
Consensus MFE -26.75
Energy contribution -27.25
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.98
SVM decision value 0.18
SVM RNA-class probability 0.620524
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19137090 113 + 23771897
UUUUAUCUGCUAAGGGUCUUGUUAAAAGUAAUUCGUAACACGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUCUCUCUCGUGCGCUCUCUAGCCCUCU------CCCUCGCU-
........((..((((....((((................(((((((....)))))))..(..(((.((((((..........)))))).)))..))))).....------)))).)).- ( -23.60)
>DroSec_CAF1 111 114 + 1
UUUUAUCUGCUAAGGGUCUUGUUAAAAGUAAUUCGUAACACGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUCUCUCUCGUGCGCUCUCUAGCCCUUU------CCCUCGCUA
........((.((((((..(((((.((....))..)))))(((((((....)))))))..(..(((.((((((..........)))))).)))..)..)))))).------.....)).. ( -24.00)
>DroEre_CAF1 320 119 + 1
UUUUAUCUGCUAAGGGUCUUGUUAAAAGUAAUUCGUAACACGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUUUCUCUCGUGGGCUCUCUAGCCCUCUCCCUCUCCCUCGCU-
........((((..(((.(((((....(((((.((.....))..)))))..))))).)))(..((((((((((..........))))))))))..)))))...................- ( -30.30)
>DroYak_CAF1 321 113 + 1
UUUUAUCUGCUAAGGGUCUUGUUAAAAGUAAUUCGUAACACGUUGUUACCAGAUAACGCCGUCAGCCCACGAGUUCCGUCUCUCUCGUGGGCUCUCUAGCCCUCU------CCCUCGCU-
........((..((((....((((................(((((((....)))))))..(..((((((((((..........))))))))))..))))).....------)))).)).- ( -31.70)
>consensus
UUUUAUCUGCUAAGGGUCUUGUUAAAAGUAAUUCGUAACACGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUCUCUCUCGUGCGCUCUCUAGCCCUCU______CCCUCGCU_
........((((..(((.(((((....(((((.((.....))..)))))..))))).)))(..((((((((((..........))))))))))..))))).................... (-26.75 = -27.25 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,137,090 – 19,137,203
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.14
Mean single sequence MFE -35.58
Consensus MFE -33.73
Energy contribution -34.05
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.06
Structure conservation index 0.95
SVM decision value 1.41
SVM RNA-class probability 0.950866
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19137090 113 - 23771897
-AGCGAGGG------AGAGGGCUAGAGAGCGCACGAGAGAGACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACGUGUUACGAAUUACUUUUAACAAGACCCUUAGCAGAUAAAA
-.(((((((------.....((((((.(((((.(....)...((.((((....))))..))))))).)))))).......(((((.((.....)).)))))...))))).))........ ( -32.90)
>DroSec_CAF1 111 114 - 1
UAGCGAGGG------AAAGGGCUAGAGAGCGCACGAGAGAGACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACGUGUUACGAAUUACUUUUAACAAGACCCUUAGCAGAUAAAA
..(((((((------.....((((((.(((((.(....)...((.((((....))))..))))))).)))))).......(((((.((.....)).)))))...))))).))........ ( -32.90)
>DroEre_CAF1 320 119 - 1
-AGCGAGGGAGAGGGAGAGGGCUAGAGAGCCCACGAGAGAAACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACGUGUUACGAAUUACUUUUAACAAGACCCUUAGCAGAUAAAA
-.(((((((....(((.((.(((.(..((((((((((..........))))))))))..)))).)).))).(((((.....)))))..................))))).))........ ( -39.10)
>DroYak_CAF1 321 113 - 1
-AGCGAGGG------AGAGGGCUAGAGAGCCCACGAGAGAGACGGAACUCGUGGGCUGACGGCGUUAUCUGGUAACAACGUGUUACGAAUUACUUUUAACAAGACCCUUAGCAGAUAAAA
-.(((((((------.....(((.(..((((((((((..........))))))))))..))))((((...(((((...((.....))..)))))..))))....))))).))........ ( -37.40)
>consensus
_AGCGAGGG______AGAGGGCUAGAGAGCCCACGAGAGAGACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACGUGUUACGAAUUACUUUUAACAAGACCCUUAGCAGAUAAAA
..(((((((......((((((((.(..((((((((((..........))))))))))..))))........(((((.....)))))......))))).......))))).))........ (-33.73 = -34.05 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,137,130 – 19,137,243
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.20
Mean single sequence MFE -23.65
Consensus MFE -23.60
Energy contribution -24.10
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 1.00
SVM decision value 0.68
SVM RNA-class probability 0.821601
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19137130 113 + 23771897
CGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUCUCUCUCGUGCGCUCUCUAGCCCUCU------CCCUCGCU-CAGCGACUCUUCUGAAAACCCCUUUCGAUCAUGAUCAUUC
(((((((....)))))))..((((((.((((((..........)))))).)))..(((((.....------.....)))-.)).)))......((((.....))))(((....))).... ( -20.00)
>DroSec_CAF1 151 114 + 1
CGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUCUCUCUCGUGCGCUCUCUAGCCCUUU------CCCUCGCUACAGCGACUCUUCUGAAAACCCCUUUCGAUCAUGAUCAUUC
(((((((....)))))))..((((((.((((((..........)))))).)))((.((((.....------.....)))).)).)))......((((.....))))(((....))).... ( -22.10)
>DroEre_CAF1 360 113 + 1
CGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUUUCUCUCGUGGGCUCUCUAGCCCUCUCCCUCUCCCUCGCU-CAGCGACUCUUCUGAAAACCCCUCUCGAU------CAUUC
(((((((....)))))))..(((((((((((((..........)))))))))).....................((((.-..))))....................)))------..... ( -25.40)
>DroYak_CAF1 361 107 + 1
CGUUGUUACCAGAUAACGCCGUCAGCCCACGAGUUCCGUCUCUCUCGUGGGCUCUCUAGCCCUCU------CCCUCGCU-CAGCGACUCUUCUGAAAACCCCUUUCGAU------CAUUC
(((((((....)))))))..(((((((((((((..........))))))))))..(((((.....------.....)))-.)).))).....(((((.....)))))..------..... ( -27.10)
>consensus
CGUUGUUACCAGAUAACGCCGUCAGCCCACGAGCUCCGUCUCUCUCGUGCGCUCUCUAGCCCUCU______CCCUCGCU_CAGCGACUCUUCUGAAAACCCCUUUCGAU______CAUUC
(((((((....)))))))..(((((((((((((..........)))))))))).....................((((....))))....................)))........... (-23.60 = -24.10 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,137,130 – 19,137,243
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.20
Mean single sequence MFE -34.35
Consensus MFE -31.83
Energy contribution -32.33
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.93
SVM decision value 0.77
SVM RNA-class probability 0.846764
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19137130 113 - 23771897
GAAUGAUCAUGAUCGAAAGGGGUUUUCAGAAGAGUCGCUG-AGCGAGGG------AGAGGGCUAGAGAGCGCACGAGAGAGACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACG
...((((....))))...(..(((.(((((.....(((((-(((.....------.....)))....(((.((((((..........)))))).)))..)))))...))))).)))..). ( -32.10)
>DroSec_CAF1 151 114 - 1
GAAUGAUCAUGAUCGAAAGGGGUUUUCAGAAGAGUCGCUGUAGCGAGGG------AAAGGGCUAGAGAGCGCACGAGAGAGACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACG
...((((....))))...(..(((.(((((.((((((((.((((.....------.....)))).))(((.((((((..........)))))).)))..)))).)).))))).)))..). ( -34.20)
>DroEre_CAF1 360 113 - 1
GAAUG------AUCGAGAGGGGUUUUCAGAAGAGUCGCUG-AGCGAGGGAGAGGGAGAGGGCUAGAGAGCCCACGAGAGAAACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACG
.....------.......(..(((.(((((.....(((((-(((................)))....((((((((((..........))))))))))..)))))...))))).)))..). ( -35.39)
>DroYak_CAF1 361 107 - 1
GAAUG------AUCGAAAGGGGUUUUCAGAAGAGUCGCUG-AGCGAGGG------AGAGGGCUAGAGAGCCCACGAGAGAGACGGAACUCGUGGGCUGACGGCGUUAUCUGGUAACAACG
.....------.......(..(((.(((((.....(((((-(((.....------.....)))....((((((((((..........))))))))))..)))))...))))).)))..). ( -35.70)
>consensus
GAAUG______AUCGAAAGGGGUUUUCAGAAGAGUCGCUG_AGCGAGGG______AGAGGGCUAGAGAGCCCACGAGAGAGACGGAGCUCGUGGGCUGACGGCGUUAUCUGGUAACAACG
..................(..(((.(((((....((((....))))...........((.(((.(..((((((((((..........))))))))))..)))).)).))))).)))..). (-31.83 = -32.33 +   0.50)

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 12:36:59 2006