Locus 4371

Sequence ID 3L_DroMel_CAF1
Location 12,824,183 – 12,824,311
Length 128
Max. P 0.894472
window6763 window6764 window6765

overview

Window 3

Location 12,824,183 – 12,824,282
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 75.87
Mean single sequence MFE -24.60
Consensus MFE -14.28
Energy contribution -14.83
Covariance contribution 0.56
Combinations/Pair 1.20
Mean z-score -1.60
Structure conservation index 0.58
SVM decision value 0.39
SVM RNA-class probability 0.718153
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12824183 99 + 23771897
AUUUUUGUGGACUCAAAACAGUUGGAAAAUUAAAGAGACAUGUCGGUUAAUACGGCUCACGCCAACAAUGGCGUGCUCAUCCAUGCUGGAGAGUAGUAA
..........((((....((((((((...............((((.......)))).(((((((....)))))))....)))).))))..))))..... ( -27.50)
>DroVir_CAF1 81923 94 + 1
AUCUUUGUGUUACC-----UAUUGAAAAAUCUAUUCGGCAUGUCGGUCAACACGGCACACGCAAAUAAUGGUGUGCUCAUACAUGCGGGCGAGUAGUAA
..............-----...........(((((((((((((((.......))((((((.((.....))))))))....))))))...)))))))... ( -23.60)
>DroSec_CAF1 65361 84 + 1
AUUUUUGUG---------------GAAAAUUAAAGAGACAUGUCGGUUAAUACGGCUCACGCCAACAACGGCGUGCUCAUCCAUGCUGGAGAGUAGUAA
.........---------------..........(((.(((((((((....))(((....))).....)))))))))).(((.....)))......... ( -20.60)
>DroYak_CAF1 69059 99 + 1
AUUUUUGUGGAUUCAAAACAGUUAAAAAAAUAAAGAGACAUGUCGGUUAAUACGGCUCACGCCAACAAUGGCGUGCUCAUCCACGCUGGAGAGUAGUAA
......((((((........(((.....)))...(((....((((.......)))).(((((((....))))))))))))))))((((.....)))).. ( -24.50)
>DroMoj_CAF1 74766 94 + 1
AUCUUUGAGAAAAU-----UAUUUAAAAAACUAUCCAACAUGUCGAUCAAUACGGCACACGCAAAUAAUGGUGUGCUCAUACAUGCAGGAGAGUAGUAA
..............-----..........(((.(((..(((((((.......))((((((.((.....))))))))....)))))..))).)))..... ( -18.90)
>DroAna_CAF1 60039 94 + 1
AUUUUGGUGGAC-----AUAGUUGGAUAAUCCGUUCAGCAUGUCGGUUAACACGGCUCACGCCAACAAUGGCGUGCUUAUCCACGCCGGAGAGUAGUAA
.(((((((((((-----((.(((((((.....)))))))))))).........((..(((((((....))))))).....)).))))))))........ ( -32.50)
>consensus
AUUUUUGUGGAA_C_____AGUUGAAAAAUCAAAGAGACAUGUCGGUUAAUACGGCUCACGCCAACAAUGGCGUGCUCAUCCAUGCUGGAGAGUAGUAA
......(((((..............................((((.......)))).((((((......))))))....)))))............... (-14.28 = -14.83 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,824,218 – 12,824,311
Length 93
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 74.38
Mean single sequence MFE -24.10
Consensus MFE -16.41
Energy contribution -16.55
Covariance contribution 0.14
Combinations/Pair 1.12
Mean z-score -1.42
Structure conservation index 0.68
SVM decision value 0.98
SVM RNA-class probability 0.894472
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12824218 93 + 23771897
AGACAUGUCGGUUAAUACGGCUCACGCCAACAAUGGCGUGCUCAUCCAUGCUGGAGAGUAGUAAGUUAACGGAA-AAG------UCCUUUAAUUAACACU
.(((...((.((((((...(((.((((((....))))))((((.(((.....))))))))))..)))))).)).-..)------)).............. ( -27.90)
>DroGri_CAF1 78481 95 + 1
CGGCAUGUCGGUGAAUACGGCACACGCCAAUAAUGGUGUGCUCAUCCAUGCGGGCGAGUAGUAAGUA----CAA-AACACAUACACAUACAAUUUGAACU
..((((((((.......)))).(((((((....))))))).......))))(..(((((.(((.((.----...-.........)).))).)))))..). ( -23.12)
>DroEre_CAF1 69798 92 + 1
AGACAUGUCGGUUAAUACGGCUCACGCCAAUAAUGGCGUGCUCAUCCAUGCUGGAGAGUAGUAAGUUGCCGGAA--AC------UCCUUAAAUUGCCACU
.((....))((......((((..((((((....))))))((((.(((.....)))))))........))))...--..------.))............. ( -26.00)
>DroYak_CAF1 69094 94 + 1
AGACAUGUCGGUUAAUACGGCUCACGCCAACAAUGGCGUGCUCAUCCACGCUGGAGAGUAGUAAGUUGCCGGAAAAAG------UCCUUAAAUUGAAACG
.(((...(((((...(((.((((((((((....)))))).....(((.....))))))).)))....))))).....)------)).............. ( -26.80)
>DroMoj_CAF1 74796 78 + 1
CAACAUGUCGAUCAAUACGGCACACGCAAAUAAUGGUGUGCUCAUACAUGCAGGAGAGUAGUAAGUA----U------------------AAUUAGAACU
.......((.....(((((((((((.((.....)))))))))..(((.(((......)))))).)))----)------------------.....))... ( -15.00)
>DroAna_CAF1 60069 82 + 1
CAGCAUGUCGGUUAACACGGCUCACGCCAACAAUGGCGUGCUUAUCCACGCCGGAGAGUAGUAAGUAG----------------UCCGUGAA--AAUGCA
..((((..((((((..((.((((((((((....)))))).....(((.....))))))).))...)))----------------.)))....--.)))). ( -25.80)
>consensus
AGACAUGUCGGUUAAUACGGCUCACGCCAACAAUGGCGUGCUCAUCCAUGCUGGAGAGUAGUAAGUAG___GAA__A_______UCCUUAAAUUAAAACU
......((((.......)))).(((((((....)))))))(((.(((.....)))))).......................................... (-16.41 = -16.55 +   0.14)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,824,218 – 12,824,311
Length 93
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 74.38
Mean single sequence MFE -24.85
Consensus MFE -13.58
Energy contribution -13.63
Covariance contribution 0.06
Combinations/Pair 1.14
Mean z-score -1.54
Structure conservation index 0.55
SVM decision value 0.12
SVM RNA-class probability 0.591123
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12824218 93 - 23771897
AGUGUUAAUUAAAGGA------CUU-UUCCGUUAACUUACUACUCUCCAGCAUGGAUGAGCACGCCAUUGUUGGCGUGAGCCGUAUUAACCGACAUGUCU
.(((((.......(((------...-.)))(((((..(((..((((((.....))).)))(((((((....)))))))....)))))))).))))).... ( -26.50)
>DroGri_CAF1 78481 95 - 1
AGUUCAAAUUGUAUGUGUAUGUGUU-UUG----UACUUACUACUCGCCCGCAUGGAUGAGCACACCAUUAUUGGCGUGUGCCGUAUUCACCGACAUGCCG
.(((((...(.((((((..((.((.-..(----(....)).)).))..)))))).))))))...........(((((((.(.((....)).)))))))). ( -22.80)
>DroEre_CAF1 69798 92 - 1
AGUGGCAAUUUAAGGA------GU--UUCCGGCAACUUACUACUCUCCAGCAUGGAUGAGCACGCCAUUAUUGGCGUGAGCCGUAUUAACCGACAUGUCU
...((((......((.------..--...((((.........((((((.....))).)))(((((((....))))))).))))......))....)))). ( -29.10)
>DroYak_CAF1 69094 94 - 1
CGUUUCAAUUUAAGGA------CUUUUUCCGGCAACUUACUACUCUCCAGCGUGGAUGAGCACGCCAUUGUUGGCGUGAGCCGUAUUAACCGACAUGUCU
(((.((.......(((------.....)))(((.........((((((.....))).)))(((((((....))))))).))).........)).)))... ( -27.60)
>DroMoj_CAF1 74796 78 - 1
AGUUCUAAUU------------------A----UACUUACUACUCUCCUGCAUGUAUGAGCACACCAUUAUUUGCGUGUGCCGUAUUGAUCGACAUGUUG
..........------------------.----................(((((((((.((((((((.....)).)))))))))........)))))).. ( -15.50)
>DroAna_CAF1 60069 82 - 1
UGCAUU--UUCACGGA----------------CUACUUACUACUCUCCGGCGUGGAUAAGCACGCCAUUGUUGGCGUGAGCCGUGUUAACCGACAUGCUG
.((((.--(((((((.----------------((.((((((((.(....).)))).))))(((((((....))))))))))))))......)).)))).. ( -27.60)
>consensus
AGUUUUAAUUUAAGGA_______U__UUC___CAACUUACUACUCUCCAGCAUGGAUGAGCACGCCAUUAUUGGCGUGAGCCGUAUUAACCGACAUGUCG
.................................................(((((......(((((((....)))))))...((.......)).))))).. (-13.58 = -13.63 +   0.06)

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 11:20:48 2006