Locus 1929

Sequence ID X_DroMel_CAF1
Location 5,304,823 – 5,305,081
Length 258
Max. P 0.997991
window3134 window3135 window3136 window3137

overview

Window 4

Location 5,304,823 – 5,304,927
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.57
Mean single sequence MFE -34.84
Consensus MFE -23.32
Energy contribution -25.24
Covariance contribution 1.92
Combinations/Pair 1.10
Mean z-score -2.21
Structure conservation index 0.67
SVM decision value 0.79
SVM RNA-class probability 0.850169
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5304823 104 - 22224390
AGAAUCCUAGGAAAAUCGAAAG-AAAAUCGAAGGAAAAUCCGUGCGUGUCUGGGUGGACUAAUGUGCAGACACUGCGAUUUGAUCGGUCAGUCUGGGAAUCCU----------GG-----
.((.(((((((...(((((...-.(((((...((.....))..(((((((((.(..........).))))))).)))))))..)))))...))))))).))..----------..----- ( -32.30)
>DroSec_CAF1 41527 107 - 1
AGAAUCCUAGGAAA------------AUCGAAGGAAAAUCCGUGCGUGUCUGGGUAGACUAAUGUGCAGACACUGCGAUUUGAUCGGUCAGUCUGGGAAUGCUUGGGUAUCGUGGGAAU-
....(((((.((..------------.((....))..(((((.((((..(..((..(((..((.(((((...))))).....))..)))..))..)..)))).))))).)).)))))..- ( -34.30)
>DroSim_CAF1 32312 119 - 1
AGAAUCCUAGGAAAAUCGAAAGGAAAAUCGAAGGAAAAUCCGUGCGUGUCUGAGUAGACUAAUGUGCAGACACUGCGAUUUGAUCGGUCAGUCUGGGAAUGCCUGGGUAUCGUGGGAAU-
....(((((.((..(((((..(((...((....))...))).((((((((((..((......))..))))))).)))......)))))...((..((....))..))..)).)))))..- ( -36.10)
>DroEre_CAF1 42873 117 - 1
GGAAUCGUAGGAAAAUCGGAGA-AAAAUCGAAGGAAAAUCCGUGCGUGUCUGGG-AGACUAAUGUGCAGACACUGCGAUUUGAUCGGUCAGUCUGGGAAUCCA-GGGCAUCCAGGGAAUC
.(((((((((......((((..-....((....))...))))((((..(.(((.-...))))..))))....)))))))))....((....(((((....)))-))....))........ ( -34.10)
>DroYak_CAF1 43625 117 - 1
AGACUCGUAGGAAAAUCGGAGA-AAAAUCGAAGGAAAUUGUGUGCGUGUCUGGG-AGACUAAUGUGCAGACACUGCGAUUUGAUCGGUCAGUCUGGGAAUCCU-UAGAAUCCUGGGAAUC
.(((.((.....((((((.((.-....((....))...(((.((((..(.(((.-...))))..)))).))))).))))))...)))))..((..(((.((..-..)).)))..)).... ( -37.40)
>consensus
AGAAUCCUAGGAAAAUCGAAAA_AAAAUCGAAGGAAAAUCCGUGCGUGUCUGGGUAGACUAAUGUGCAGACACUGCGAUUUGAUCGGUCAGUCUGGGAAUCCU_GGGUAUCCUGGGAAU_
....(((((((...(((((.....(((((...((.....))..(((((((((.(((......))).))))))).)))))))..)))))...)))))))...................... (-23.32 = -25.24 +   1.92)

alignment

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secondary structure

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Window 5

Location 5,304,848 – 5,304,962
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.51
Mean single sequence MFE -20.23
Consensus MFE -12.94
Energy contribution -13.94
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.64
SVM decision value 2.20
SVM RNA-class probability 0.990201
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5304848 114 + 22224390
AAUCGCAGUGUCUGCACAUUAGUCCACCCAGACACGCACGGAUUUUCCUUCGAUUUU-CUUUCGAUUUUCCUAGGAUUCUCCAUUC-----CAACAUUCCCCCCUGAUGAACUGCGACUG
..((((((((((((..............)))))))....(((...((((..((...(-(....))...))..))))...)))....-----.....................)))))... ( -25.24)
>DroSec_CAF1 41566 99 + 1
AAUCGCAGUGUCUGCACAUUAGUCUACCCAGACACGCACGGAUUUUCCUUCGAU------------UUUCCUAGGAUUCUCCCUAC-----CAACUUACCCC----AUGAGCUGCGACUG
..((((((((((((..............)))))))((..(((...((....)).------------..)))((((......)))).-----...........----....)))))))... ( -23.24)
>DroSim_CAF1 32351 111 + 1
AAUCGCAGUGUCUGCACAUUAGUCUACUCAGACACGCACGGAUUUUCCUUCGAUUUUCCUUUCGAUUUUCCUAGGAUUCUCCCUAC-----CAACUUACCCC----AUCAACUGCGACUG
..((((((((((((..............)))))))....(((...((((((((........)))).......))))...)))....-----...........----......)))))... ( -24.05)
>DroEre_CAF1 42912 96 + 1
AAUCGCAGUGUCUGCACAUUAGUCU-CCCAGACACGCACGGAUUUUCCUUCGAUUUU-UCUCCGAUUUUCCUACGAUUCCCCUCCUCCCCCCGCACU----------------------G
((((((.(((((((.((....))..-..))))))))).((((...............-..))))..........))))...................----------------------. ( -15.53)
>DroYak_CAF1 43664 91 + 1
AAUCGCAGUGUCUGCACAUUAGUCU-CCCAGACACGCACACAAUUUCCUUCGAUUUU-UCUCCGAUUUUCCUACGAGUCUCCUUCC-----CAACUU----------------------A
....((.(((((((.((....))..-..)))))))))....................-.....(((((......))))).......-----......----------------------. ( -13.10)
>consensus
AAUCGCAGUGUCUGCACAUUAGUCUACCCAGACACGCACGGAUUUUCCUUCGAUUUU_CCUCCGAUUUUCCUAGGAUUCUCCCUAC_____CAACUU_CCCC____AU_A_CUGCGACUG
....((.(((((((..............)))))))))..(((...((((..((...............))..))))...)))...................................... (-12.94 = -13.94 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,304,848 – 5,304,962
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.51
Mean single sequence MFE -29.98
Consensus MFE -15.78
Energy contribution -15.90
Covariance contribution 0.12
Combinations/Pair 1.15
Mean z-score -2.61
Structure conservation index 0.53
SVM decision value 2.98
SVM RNA-class probability 0.997991
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5304848 114 - 22224390
CAGUCGCAGUUCAUCAGGGGGGAAUGUUG-----GAAUGGAGAAUCCUAGGAAAAUCGAAAG-AAAAUCGAAGGAAAAUCCGUGCGUGUCUGGGUGGACUAAUGUGCAGACACUGCGAUU
.(((((((((((.(((((.(.(.......-----..(((((...((((..((...((....)-)...))..))))...))))).).).))))).((.((....)).)))).))))))))) ( -33.80)
>DroSec_CAF1 41566 99 - 1
CAGUCGCAGCUCAU----GGGGUAAGUUG-----GUAGGGAGAAUCCUAGGAAA------------AUCGAAGGAAAAUCCGUGCGUGUCUGGGUAGACUAAUGUGCAGACACUGCGAUU
.((((((((((...----..)))......-----(((.(((...((((..(...------------..)..))))...))).)))(((((((.(((......))).)))))))))))))) ( -31.80)
>DroSim_CAF1 32351 111 - 1
CAGUCGCAGUUGAU----GGGGUAAGUUG-----GUAGGGAGAAUCCUAGGAAAAUCGAAAGGAAAAUCGAAGGAAAAUCCGUGCGUGUCUGAGUAGACUAAUGUGCAGACACUGCGAUU
.(((((((......----...........-----(((.(((...((((..((...((....))....))..))))...))).)))(((((((..((......))..)))))))))))))) ( -34.10)
>DroEre_CAF1 42912 96 - 1
C----------------------AGUGCGGGGGGAGGAGGGGAAUCGUAGGAAAAUCGGAGA-AAAAUCGAAGGAAAAUCCGUGCGUGUCUGGG-AGACUAAUGUGCAGACACUGCGAUU
.----------------------...................((((((((......((((..-....((....))...))))((((..(.(((.-...))))..))))....)))))))) ( -24.50)
>DroYak_CAF1 43664 91 - 1
U----------------------AAGUUG-----GGAAGGAGACUCGUAGGAAAAUCGGAGA-AAAAUCGAAGGAAAUUGUGUGCGUGUCUGGG-AGACUAAUGUGCAGACACUGCGAUU
.----------------------...(((-----.((.(....))).)))...(((((.((.-....((....))...(((.((((..(.(((.-...))))..)))).))))).))))) ( -25.70)
>consensus
CAGUCGCAG_U_AU____GGGG_AAGUUG_____GGAAGGAGAAUCCUAGGAAAAUCGAAAA_AAAAUCGAAGGAAAAUCCGUGCGUGUCUGGGUAGACUAAUGUGCAGACACUGCGAUU
......................................(((...((....))...............((....))...))).((((((((((.(((......))).))))))).)))... (-15.78 = -15.90 +   0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,304,962 – 5,305,081
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.32
Mean single sequence MFE -39.50
Consensus MFE -28.76
Energy contribution -29.84
Covariance contribution 1.08
Combinations/Pair 1.12
Mean z-score -2.96
Structure conservation index 0.73
SVM decision value 0.83
SVM RNA-class probability 0.862254
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5304962 119 + 22224390
CCACUGCCACUGGCACUUGCCUUGCGCUUUUCCCUGGCUCCUGUCUAAAUGUCCAUCUGCCAGUUUCAAUUUGAAACAAUGUCGCCCGGG-GCCAGAGAAGUGCAAUUACUUUCAUGUUU
...........(((....)))(((((((((((..(((((((.(.(.....).).........(((((.....)))))..........)))-))))))))))))))).............. ( -33.60)
>DroSec_CAF1 41665 119 + 1
CCACUGCCACUGGCACUUGCCUUGCGCUUUUCCUUGGCUCCUGUCCAGAUGUCCAUCUGCCAGUUUUAAUUUGAAACAAUGUCGCCGGGG-GCCAGAGAAGUGCAAUUACUUUCAUGUUU
...........(((....)))(((((((((((..(((((((((..(((((....)))))...(((((.....)))))........)))))-))))))))))))))).............. ( -40.20)
>DroSim_CAF1 32462 119 + 1
CCACUGCCACUGGCACUUGCCUUGCGCUUUUCCUUGGCUCCUGUCCAGAUGUCCAUCUGCCAGUUUCAAUUUGAAACAAUGUCGCCGGGG-GCCAGAGAAGUGCAAUUACUUUCAUGUUU
...........(((....)))(((((((((((..(((((((((..(((((....)))))...(((((.....)))))........)))))-))))))))))))))).............. ( -42.60)
>DroEre_CAF1 43008 120 + 1
CGACUGCCACUGGCACUCUCCUUGCGCUUUUCCUUGGCUCCCGUCUAGAUGUCCAUCUGCCAGUUUCCAUUUGAAACAAUGUCGCCCGGGGGCCAGAGAAGUGCAAUUACUUUCAUGUUU
.((.((((...)))).))...(((((((((((..(((((((((..(((((....)))))...(((((.....))))).........)))))))))))))))))))).............. ( -43.30)
>DroYak_CAF1 43755 120 + 1
CCACUGCCAGUGGCACUUGCCAUGCGCUUUUCCUCGGCUGCUGUCUGAAUGUCCAUCUGCCAGUUUCAAUUUGAAACAAUGUCGCCCGGGGCCGAGAGAAGUGCAAUUACUUUCAUGUUU
.........(((((....)))))(((((((((.((((((.(((..(((..((......))..(((((.....)))))....)))..))))))))))))))))))................ ( -37.80)
>consensus
CCACUGCCACUGGCACUUGCCUUGCGCUUUUCCUUGGCUCCUGUCUAGAUGUCCAUCUGCCAGUUUCAAUUUGAAACAAUGUCGCCCGGG_GCCAGAGAAGUGCAAUUACUUUCAUGUUU
....((((...))))......(((((((((((..((((.((((..(((((....)))))...(((((.....))))).........)))).))))))))))))))).............. (-28.76 = -29.84 +   1.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:06 2006