Locus 3127

Sequence ID X_DroMel_CAF1
Location 8,338,016 – 8,338,173
Length 157
Max. P 0.999428
window5111 window5112 window5113 window5114

overview

Window 1

Location 8,338,016 – 8,338,133
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.52
Mean single sequence MFE -28.72
Consensus MFE -15.88
Energy contribution -16.24
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -2.42
Structure conservation index 0.55
SVM decision value 0.66
SVM RNA-class probability 0.814322
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8338016 117 + 22224390
UAUUUUCUGUAAACACGCCAGCGU---CUAUUUGUUAGCUUGUUGUUAUUUGUUGUGUGGUUUUAUUUUUUGUUGCAAUCGGCUGCUCGGUUGCAAUAUUAUAAUGACACUUGCAGUUGC
......(((((((((.((.((((.---.....)))).)).))))..........((((.(((.((.....((((((((((((....)))))))))))).)).))).)))).))))).... ( -30.80)
>DroSec_CAF1 2891 117 + 1
UAUUUUCUGUAAACACGCCAGUGG---CUAUUUGUUAGUUCGUUGUUAUUUGUUGUAAUUUUUUUUUUGUUUUUGCAAUCGGCUGCUCGGUUGCAAUAUUGUAAUGGCACUUGCAGUUGC
......((((((.(((....)))(---(((((...((((.....(((((.....))))).............((((((((((....)))))))))).)))).))))))..)))))).... ( -24.60)
>DroSim_CAF1 2973 115 + 1
UAUUUUCUGUAAACACGCCAGUGG---CUAUUUGUUAGUUUGUUGUUAUUUGUUGUA--UUUUUUUUUGUUUUUGCAAUCGGCUUCUCGGUUGCAAUAUUGUAAUGGCACUUGCAGUUGC
......((((((.(((....)))(---(((.....)))).(((..((((........--.............((((((((((....))))))))))....))))..))).)))))).... ( -24.01)
>DroEre_CAF1 984 106 + 1
UAUUUUGUGUAAACACGACAGUGG---CUAUUUGUUA--UUAUUGUUGUU---------UUUGUGUGUGUUUUUGCAAUCGGCUGUUCGGUUGCAAUAUUGCAAUGGCACUUGCAGUUGC
......(..((((.((((((((((---.((.....))--)))))))))).---------))))..)......((((((((((....))))))))))....(((((.((....)).))))) ( -28.10)
>DroYak_CAF1 1617 103 + 1
UAUUUUGUGUAAACACGCCAGUGGCGGCUAUUUGUUG--------UUAUU---------UUUGUGUGUGCUUUUGCAAUCGGCUGUGCGGUUGCAAUAUUGCAAUGGCACUUGCAGUUGC
........(((.(((((..(((((((((.....))))--------)))))---------..))))).)))....(((((..((.((((.((((((....)))))).))))..)).))))) ( -36.10)
>consensus
UAUUUUCUGUAAACACGCCAGUGG___CUAUUUGUUAG_UUGUUGUUAUUUGUUGU___UUUUUGUUUGUUUUUGCAAUCGGCUGCUCGGUUGCAAUAUUGUAAUGGCACUUGCAGUUGC
.............(((....))).................................................(((((((((......)))))))))....(((((.((....)).))))) (-15.88 = -16.24 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 8,338,016 – 8,338,133
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.52
Mean single sequence MFE -18.23
Consensus MFE -10.42
Energy contribution -10.42
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.15
Structure conservation index 0.57
SVM decision value 0.34
SVM RNA-class probability 0.695321
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8338016 117 - 22224390
GCAACUGCAAGUGUCAUUAUAAUAUUGCAACCGAGCAGCCGAUUGCAACAAAAAAUAAAACCACACAACAAAUAACAACAAGCUAACAAAUAG---ACGCUGGCGUGUUUACAGAAAAUA
..((((((.((((((.........((((((.((......)).)))))).................................(....).....)---))))).))).)))........... ( -17.40)
>DroSec_CAF1 2891 117 - 1
GCAACUGCAAGUGCCAUUACAAUAUUGCAACCGAGCAGCCGAUUGCAAAAACAAAAAAAAAAUUACAACAAAUAACAACGAACUAACAAAUAG---CCACUGGCGUGUUUACAGAAAAUA
....(((.(((..(..........((((((.((......)).))))))............................................(---((...))))..))).)))...... ( -16.50)
>DroSim_CAF1 2973 115 - 1
GCAACUGCAAGUGCCAUUACAAUAUUGCAACCGAGAAGCCGAUUGCAAAAACAAAAAAAAA--UACAACAAAUAACAACAAACUAACAAAUAG---CCACUGGCGUGUUUACAGAAAAUA
....(((.(((..(..........((((((.((......)).)))))).............--.............................(---((...))))..))).)))...... ( -16.50)
>DroEre_CAF1 984 106 - 1
GCAACUGCAAGUGCCAUUGCAAUAUUGCAACCGAACAGCCGAUUGCAAAAACACACACAAA---------AACAACAAUAA--UAACAAAUAG---CCACUGUCGUGUUUACACAAAAUA
((((..((....))..))))....((((((.((......)).))))))(((((((((....---------...........--..........---....))).)))))).......... ( -17.25)
>DroYak_CAF1 1617 103 - 1
GCAACUGCAAGUGCCAUUGCAAUAUUGCAACCGCACAGCCGAUUGCAAAAGCACACACAAA---------AAUAA--------CAACAAAUAGCCGCCACUGGCGUGUUUACACAAAAUA
((....))..((((..(((((((..(((....)))......)))))))..)))).......---------.....--------.........((((....))))(((....)))...... ( -23.50)
>consensus
GCAACUGCAAGUGCCAUUACAAUAUUGCAACCGAGCAGCCGAUUGCAAAAACAAAAAAAAA___ACAACAAAUAACAACAA_CUAACAAAUAG___CCACUGGCGUGUUUACAGAAAAUA
((....))..(((...........((((((.((......)).))))))....................................((((..(((......)))...)))))))........ (-10.42 = -10.42 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 8,338,053 – 8,338,173
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.19
Mean single sequence MFE -33.34
Consensus MFE -26.84
Energy contribution -28.24
Covariance contribution 1.40
Combinations/Pair 1.06
Mean z-score -2.71
Structure conservation index 0.81
SVM decision value 2.38
SVM RNA-class probability 0.993125
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8338053 120 + 22224390
UGUUGUUAUUUGUUGUGUGGUUUUAUUUUUUGUUGCAAUCGGCUGCUCGGUUGCAAUAUUAUAAUGACACUUGCAGUUGCACUUUCAUUGCCAUUGCCAGAUGACGAGGCUUUAACGGUU
..((((((((((..((((.(((.((.....((((((((((((....)))))))))))).)).))).))))..(((((.(((.......))).)))))))))))))))............. ( -35.50)
>DroSec_CAF1 2928 120 + 1
CGUUGUUAUUUGUUGUAAUUUUUUUUUUGUUUUUGCAAUCGGCUGCUCGGUUGCAAUAUUGUAAUGGCACUUGCAGUUGCACUUUCAUUGCCAUUGCCAGAUGACGAGGCUUUAACGGUU
(.((((((((((....................((((((((((....))))))))))....(((((((((..(((....))).......))))))))))))))))))).)........... ( -33.70)
>DroSim_CAF1 3010 118 + 1
UGUUGUUAUUUGUUGUA--UUUUUUUUUGUUUUUGCAAUCGGCUUCUCGGUUGCAAUAUUGUAAUGGCACUUGCAGUUGCACUUUCAUUGCCAUUGCCAGAUGACGAGGCUUUAACGGUU
..((((((((((.....--.............((((((((((....))))))))))....(((((((((..(((....))).......)))))))))))))))))))............. ( -32.80)
>DroEre_CAF1 1019 111 + 1
UAUUGUUGUU---------UUUGUGUGUGUUUUUGCAAUCGGCUGUUCGGUUGCAAUAUUGCAAUGGCACUUGCAGUUGCACUUUCAUUGCCAUUGCCAGAUGACGAGGCUUUAACGGUU
.(((((((.(---------(((((((.((...((((((((((....))))))))))....(((((((((..(((....))).......))))))))))).)).))))))...))))))). ( -32.90)
>DroYak_CAF1 1654 106 + 1
-----UUAUU---------UUUGUGUGUGCUUUUGCAAUCGGCUGUGCGGUUGCAAUAUUGCAAUGGCACUUGCAGUUGCACUUUCAUUGCCAUUGCCAGAUGACGAGGCUUUAACGGUU
-----.....---------...(((.((((..((((((......((((.((((((....)))))).))))))))))..))))...))).(((.(((.(....).)))))).......... ( -31.80)
>consensus
UGUUGUUAUUUGUUGU___UUUUUGUUUGUUUUUGCAAUCGGCUGCUCGGUUGCAAUAUUGUAAUGGCACUUGCAGUUGCACUUUCAUUGCCAUUGCCAGAUGACGAGGCUUUAACGGUU
..((((((((((....................(((((((((......)))))))))....(((((((((..(((....))).......)))))))))))))))))))............. (-26.84 = -28.24 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 8,338,053 – 8,338,173
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.19
Mean single sequence MFE -25.00
Consensus MFE -22.18
Energy contribution -22.42
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.89
Structure conservation index 0.89
SVM decision value 3.59
SVM RNA-class probability 0.999428
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8338053 120 - 22224390
AACCGUUAAAGCCUCGUCAUCUGGCAAUGGCAAUGAAAGUGCAACUGCAAGUGUCAUUAUAAUAUUGCAACCGAGCAGCCGAUUGCAACAAAAAAUAAAACCACACAACAAAUAACAACA
....((((..(((..(((....)))...)))(((((...(((....)))....)))))......((((((.((......)).))))))........................)))).... ( -23.10)
>DroSec_CAF1 2928 120 - 1
AACCGUUAAAGCCUCGUCAUCUGGCAAUGGCAAUGAAAGUGCAACUGCAAGUGCCAUUACAAUAUUGCAACCGAGCAGCCGAUUGCAAAAACAAAAAAAAAAUUACAACAAAUAACAACG
....((((..(((.........)))(((((((.......(((....)))..)))))))......((((((.((......)).))))))........................)))).... ( -24.60)
>DroSim_CAF1 3010 118 - 1
AACCGUUAAAGCCUCGUCAUCUGGCAAUGGCAAUGAAAGUGCAACUGCAAGUGCCAUUACAAUAUUGCAACCGAGAAGCCGAUUGCAAAAACAAAAAAAAA--UACAACAAAUAACAACA
....((((..(((.........)))(((((((.......(((....)))..)))))))......((((((.((......)).)))))).............--.........)))).... ( -24.60)
>DroEre_CAF1 1019 111 - 1
AACCGUUAAAGCCUCGUCAUCUGGCAAUGGCAAUGAAAGUGCAACUGCAAGUGCCAUUGCAAUAUUGCAACCGAACAGCCGAUUGCAAAAACACACACAAA---------AACAACAAUA
....(((................(((((((((.......(((....)))..)))))))))....((((((.((......)).)))))).))).........---------.......... ( -26.10)
>DroYak_CAF1 1654 106 - 1
AACCGUUAAAGCCUCGUCAUCUGGCAAUGGCAAUGAAAGUGCAACUGCAAGUGCCAUUGCAAUAUUGCAACCGCACAGCCGAUUGCAAAAGCACACACAAA---------AAUAA-----
..........(((..(((....)))...))).......((((...(((((((((..(((((....)))))..))))......)))))...)))).......---------.....----- ( -26.60)
>consensus
AACCGUUAAAGCCUCGUCAUCUGGCAAUGGCAAUGAAAGUGCAACUGCAAGUGCCAUUACAAUAUUGCAACCGAGCAGCCGAUUGCAAAAACAAAAAAAAA___ACAACAAAUAACAACA
....((((..(((.........)))(((((((.......(((....)))..)))))))......((((((.((......)).))))))........................)))).... (-22.18 = -22.42 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:36 2006