Locus 3603

Sequence ID 2R_DroMel_CAF1
Location 11,984,691 – 11,984,799
Length 108
Max. P 0.997238
window5870 window5871

overview

Window 0

Location 11,984,691 – 11,984,799
Length 108
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 71.10
Mean single sequence MFE -22.13
Consensus MFE -10.10
Energy contribution -10.70
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.46
SVM decision value 2.82
SVM RNA-class probability 0.997238
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11984691 108 + 20766785
AAUACUUAGCAUUAAUCUGCCGAAGUUGCGGUGUGUUUCAUUUAGCUUGGCAUA---AAAGCACUAUGCAUUUCUUGCAGUGCACCCAUAUGCACACAUAUGCACAAUAGC
........((.......((((.((((((.((((.....))))))))))))))..---...(((...((((.....))))(((((......))))).....)))......)) ( -25.10)
>DroSec_CAF1 35906 108 + 1
AAUACCUAGUAUUAAAGUGCCCAAA-UGCAGCGUGUUUUAUUGAUUUUGCCAUGCACAAUGCACAAUGCAUUGCUUGCAGUGCACCCA--UGCACACAUAUGCACAAUAGC
................((((.....-(((((((((...............))))).((((((.....))))))..))))(((((....--)))))......))))...... ( -27.06)
>DroSim_CAF1 39464 96 + 1
AAUACUUAGCAUUAAUGUGCCAAA----------GUUAAAUUUAGCUUUCCAUA---AAAGCACUAUGCAUUUCUUGCAGUGCACCCA--UGCACACAUAUGCACAAUAGC
........((((...(((((.(((----------((((....))))))).....---...(((((..(((.....)))))))).....--.)))))...))))........ ( -24.10)
>DroEre_CAF1 36123 83 + 1
AAUACUUGCUAUUAG--------------------U----UUUAUUUUGUCAUGC--CAAACCCAAUGCAUUUCUCGCAGUGCACCCG--UGCACACAUAUGCACAAUAGC
.......((((((..--------------------.----...............--.........((((((......))))))...(--((((......))))))))))) ( -15.80)
>DroYak_CAF1 36673 83 + 1
UAAACUUAAUAGUAG--------------------C----UCUAUUUUGGCAUGA--AAAGCACAAUGCAUUUCUUGCAGUGCACCCA--UGCACACAAAUGCACAAUAGC
...........((.(--------------------(----.....(((((((.((--((.((.....)).)))).))).(((((....--))))).)))).))))...... ( -18.60)
>consensus
AAUACUUAGUAUUAA__UGCC_AA__________GUU__AUUUAUUUUGCCAUG___AAAGCACAAUGCAUUUCUUGCAGUGCACCCA__UGCACACAUAUGCACAAUAGC
............................................................(((...((((.....))))(((((......))))).....)))........ (-10.10 = -10.70 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,984,691 – 11,984,799
Length 108
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 71.10
Mean single sequence MFE -25.14
Consensus MFE -14.08
Energy contribution -13.76
Covariance contribution -0.32
Combinations/Pair 1.12
Mean z-score -1.70
Structure conservation index 0.56
SVM decision value 0.63
SVM RNA-class probability 0.805914
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11984691 108 - 20766785
GCUAUUGUGCAUAUGUGUGCAUAUGGGUGCACUGCAAGAAAUGCAUAGUGCUUU---UAUGCCAAGCUAAAUGAAACACACCGCAACUUCGGCAGAUUAAUGCUAAGUAUU
((...(((((((.(((((((((....)))))).)))....)))))))(((.(((---(((..........)))))))))...)).((((.((((......))))))))... ( -28.20)
>DroSec_CAF1 35906 108 - 1
GCUAUUGUGCAUAUGUGUGCA--UGGGUGCACUGCAAGCAAUGCAUUGUGCAUUGUGCAUGGCAAAAUCAAUAAAACACGCUGCA-UUUGGGCACUUUAAUACUAGGUAUU
(((...(((((..(((((...--(((.(((..(((..(((((((.....))))))))))..)))...))).....))))).))))-)...)))((((.......))))... ( -31.20)
>DroSim_CAF1 39464 96 - 1
GCUAUUGUGCAUAUGUGUGCA--UGGGUGCACUGCAAGAAAUGCAUAGUGCUUU---UAUGGAAAGCUAAAUUUAAC----------UUUGGCACAUUAAUGCUAAGUAUU
...(((((((((.((((((((--....))))).)))....)))))))))(((((---(...))))))........((----------((.((((......))))))))... ( -24.60)
>DroEre_CAF1 36123 83 - 1
GCUAUUGUGCAUAUGUGUGCA--CGGGUGCACUGCGAGAAAUGCAUUGGGUUUG--GCAUGACAAAAUAAA----A--------------------CUAAUAGCAAGUAUU
((((((((((((.((((((((--....))))).)))....)))))(((..((((--......)))).))).----.--------------------.)))))))....... ( -20.10)
>DroYak_CAF1 36673 83 - 1
GCUAUUGUGCAUUUGUGUGCA--UGGGUGCACUGCAAGAAAUGCAUUGUGCUUU--UCAUGCCAAAAUAGA----G--------------------CUACUAUUAAGUUUA
(((...(((((((..(....)--..))))))).(((.((((.((.....)).))--)).)))........)----)--------------------).............. ( -21.60)
>consensus
GCUAUUGUGCAUAUGUGUGCA__UGGGUGCACUGCAAGAAAUGCAUUGUGCUUU___CAUGCCAAAAUAAAU__AAC__________UU_GGCA__UUAAUACUAAGUAUU
((....((((((.((((((((......))))).)))....))))))...))............................................................ (-14.08 = -13.76 +  -0.32)

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 10:59:41 2006