Locus 4834

Sequence ID 3L_DroMel_CAF1
Location 13,563,438 – 13,563,637
Length 199
Max. P 0.997072
window7622 window7623 window7624

overview

Window 2

Location 13,563,438 – 13,563,532
Length 94
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 78.79
Mean single sequence MFE -21.01
Consensus MFE -9.67
Energy contribution -9.39
Covariance contribution -0.28
Combinations/Pair 1.19
Mean z-score -2.35
Structure conservation index 0.46
SVM decision value 1.14
SVM RNA-class probability 0.921363
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13563438 94 + 23771897
UGCGAGUGUAUGUGUGCGUGUGCGUUUGACACACAAUAAACACCAAUUAAGAAAAUAAUAUUUUGUGUACACACAC------AAGCAAACA-AAUGUCU-------CU
(((...(((.((((((((((((.......)))))....................((((....))))))))))).))------).)))....-.......-------.. ( -21.50)
>DroSec_CAF1 45069 86 + 1
UG--------------CGUGUGCGUUUGACACACAAUAAACACCAAUUAAGAAAAUAAUAUUUUGUGUACACACACACACAGAAGCAAACA-AAUGUCU-------CU
..--------------.(((((.((.(((((((.((((....................)))).))))).)).)).)))))(((..((....-..))..)-------)) ( -17.95)
>DroSim_CAF1 31166 98 + 1
UGCG--UGUGGGUGUGCGUGUGCGUUUGACACACAAUAAACACCAAUUAAGAAAAUAAUAUUUUGUGUACACACAUACACAGAAGCAAACA-AAUGUCU-------CU
(((.--....(((((...((((.(.....).))))....)))))................(((((((((......))))))))))))....-.......-------.. ( -23.80)
>DroYak_CAF1 47459 89 + 1
---G--UGUGUGUGUGGGUGUGCGUUUGACACACAAUAAACACCAAUUAAGAAAAUAAUAUUUUGUGUACACACAC------AGGCAAACA-AAUGUCU-------CU
---.--(((((((((((((((....(((.....)))...)))))..........((((....)))).)))))))))------)((((....-..)))).-------.. ( -24.00)
>DroMoj_CAF1 62522 86 + 1
U------------GUGUGUGUGUGUGUGACACACAAUAAACACCAAUUAAGAAUAUAAUAUUUUGUGUAUACAGGC------A----AACAAAAUGUCUCCCCUGGCU
.------------((((.((((((.....))))))....)))).........((((((....))))))...((((.------.----.((.....))....))))... ( -17.80)
>consensus
UG_G__UGU__GUGUGCGUGUGCGUUUGACACACAAUAAACACCAAUUAAGAAAAUAAUAUUUUGUGUACACACAC______AAGCAAACA_AAUGUCU_______CU
.................(((((.((...(((((.((((....................)))).))))))).)))))................................ ( -9.67 =  -9.39 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,563,438 – 13,563,532
Length 94
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 78.79
Mean single sequence MFE -24.36
Consensus MFE -14.16
Energy contribution -15.00
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.98
Structure conservation index 0.58
SVM decision value 2.79
SVM RNA-class probability 0.997072
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13563438 94 - 23771897
AG-------AGACAUU-UGUUUGCUU------GUGUGUGUACACAAAAUAUUAUUUUCUUAAUUGGUGUUUAUUGUGUGUCAAACGCACACGCACACAUACACUCGCA
.(-------((.....-(((.(((.(------((((((.((((((((((((((.((....)).)))))))..)))))))....))))))).))).)))....)))... ( -27.20)
>DroSec_CAF1 45069 86 - 1
AG-------AGACAUU-UGUUUGCUUCUGUGUGUGUGUGUACACAAAAUAUUAUUUUCUUAAUUGGUGUUUAUUGUGUGUCAAACGCACACG--------------CA
((-------(..((..-....))..)))((((((((((.((((((((((((((.((....)).)))))))..)))))))....)))))))))--------------). ( -26.60)
>DroSim_CAF1 31166 98 - 1
AG-------AGACAUU-UGUUUGCUUCUGUGUAUGUGUGUACACAAAAUAUUAUUUUCUUAAUUGGUGUUUAUUGUGUGUCAAACGCACACGCACACCCACA--CGCA
..-------((((...-.))))((...((((..(((((((((((.....((((......))))..)))).....(((((.....))))))))))))..))))--.)). ( -25.70)
>DroYak_CAF1 47459 89 - 1
AG-------AGACAUU-UGUUUGCCU------GUGUGUGUACACAAAAUAUUAUUUUCUUAAUUGGUGUUUAUUGUGUGUCAAACGCACACCCACACACACA--C---
..-------((((...-.))))...(------((((((((((((.....((((......))))..))))....((((((.....))))))...)))))))))--.--- ( -23.60)
>DroMoj_CAF1 62522 86 - 1
AGCCAGGGGAGACAUUUUGUU----U------GCCUGUAUACACAAAAUAUUAUAUUCUUAAUUGGUGUUUAUUGUGUGUCACACACACACACAC------------A
.....(((.((((.....)))----)------.)))(((.((((.....((((......))))..)))).)))(((((((.....)))))))...------------. ( -18.70)
>consensus
AG_______AGACAUU_UGUUUGCUU______GUGUGUGUACACAAAAUAUUAUUUUCUUAAUUGGUGUUUAUUGUGUGUCAAACGCACACGCACAC__ACA__C_CA
.........((((.....))))..........(((((((((((((((((((((..........))))))))....)))))...))))))))................. (-14.16 = -15.00 +   0.84)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,563,532 – 13,563,637
Length 105
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 77.68
Mean single sequence MFE -23.43
Consensus MFE -12.04
Energy contribution -12.15
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.51
SVM decision value 1.02
SVM RNA-class probability 0.901167
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13563532 105 + 23771897
GGCAAUUUGAAAAGCCAGCGCCA------AAGCGUU--CGUCUCUAG---UUU-UGUACAAGUGCUGUGCAAAUAAUGCACAAAAGUAUUCUACAAA-AUGCGAACAACAAACAACCG
(((..........))).((....------..))(((--(((.....(---(((-((((..(((((((((((.....)))))...)))))).))))))-))))))))............ ( -27.30)
>DroVir_CAF1 66186 94 + 1
GGCAAAUUGAAAAGCCAAGUC-------------UU--UCGCUCUGGACUUUU-CCUGCAAGUGCUGUGCAAAUAAUGCACAAAAGUAUGCUACAAAAAUACAAACAA-------AC-
((((.(((((((((((((((.-------------..--..))).))).)))))-)..((....))((((((.....))))))..))).))))................-------..- ( -20.60)
>DroPse_CAF1 52394 99 + 1
GGCAAAUUGAAAAGCCAAAGCCAAG--CGACGCCUU--CGUCUCUAG---UUC-CGUACAAGUGCUGUGCAAAUAAUGCACAAAAGUAUGCUACAAA-AUACGAACAA----------
(((...(((......))).))).((--.((((....--)))).)).(---(((-.(((....)))((((((.....))))))...((((........-))))))))..---------- ( -22.30)
>DroGri_CAF1 63264 103 + 1
GGCAAAUUGAAAAGCCAAGUC-A------AGAC-UUGCUCUCACUGGACUUUUCUCUGCAAGUGCUGUGCAAAUAAUGCACAAAAGUAUGCUACAAAAAUACAAACAA--A----AC-
.(((....(((((((((.((.-.------(((.-....))).))))).))))))..)))......((((((.....))))))...((((.........))))......--.----..- ( -20.80)
>DroYak_CAF1 47548 111 + 1
GGCAAUUUGAAAAGCCAACGCCAAAGCCAAAGCGUU--CGUCUCUAG---UUU-UGUACAAGUGCUGUGCAAAUAGUGCACAAAAGUAUGCUACAAA-AUGCGAACAACAAACAACCG
((...((((....((....((....))....))(((--(((.....(---(((-((((...((((((((((.....)))))...)))))..))))))-))))))))..))))...)). ( -27.30)
>DroPer_CAF1 52244 99 + 1
GGCAAAUUGAAAAGCCAAAGCCAAG--CGACGCCUU--CGUCUCUAG---UUC-CGUACAAGUGCUGUGCAAAUAAUGCACAAAAGUAUGCUACAAA-AUACGAACAA----------
(((...(((......))).))).((--.((((....--)))).)).(---(((-.(((....)))((((((.....))))))...((((........-))))))))..---------- ( -22.30)
>consensus
GGCAAAUUGAAAAGCCAAAGCCA______AAGC_UU__CGUCUCUAG___UUU_CGUACAAGUGCUGUGCAAAUAAUGCACAAAAGUAUGCUACAAA_AUACGAACAA________C_
(((..........))).......................................(((...((((((((((.....)))))...)))))..)))........................ (-12.04 = -12.15 +   0.11)

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 11:34:43 2006