Locus 7933

Sequence ID X_DroMel_CAF1
Location 19,803,514 – 19,803,640
Length 126
Max. P 0.999292
window13016 window13017 window13018 window13019

overview

Window 6

Location 19,803,514 – 19,803,610
Length 96
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 72.86
Mean single sequence MFE -25.67
Consensus MFE -16.96
Energy contribution -17.88
Covariance contribution 0.92
Combinations/Pair 1.10
Mean z-score -2.03
Structure conservation index 0.66
SVM decision value 2.04
SVM RNA-class probability 0.986454
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19803514 96 + 22224390
----GAAAAAACAGAUAUGCAGACCGAAAAGUGC--AUAGACGAAAAGCAAAGCACAAGCGUUUGCAUUUUCUGCUUUUGCGCGUCUGCUUUUGCUUUUGGC---
----..((((.((((...((((((......((((--(.((..((((((((((((....)).))))).)))))..))..))))))))))).)))).))))...--- ( -28.50)
>DroSec_CAF1 2225 88 + 1
CAGCGGAAAAGCAGAUAUGAAA--------------AUCAGCCAAAAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUACUUUUGCUUUUUGCU--
.((((.(((((((((...((..--------------....(((((((((...((....))...-((.....))))))))).)).))....)))))))))))))-- ( -24.10)
>DroSim_CAF1 2294 102 + 1
CAGCGGAAAAGCAGAUAUGCAGACCCAAAAGUGCACAUAGGCCAAAAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUACUUUUGCUUUUUGCU--
.((((((((.(((((...(((((.((((..((((......((.....))...)))).....))-))....))))).)))))(((........)))))))))))-- ( -27.90)
>DroEre_CAF1 2028 79 + 1
----------------------AUGGAAAAGUAU--AAAAGCCAAAAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUGUUUUUGCUUUU-GCUUU
----------------------............--.(((((.((((((((((.(((..(((.-((.....))((....)))))..)))))))))))))-))))) ( -21.80)
>DroYak_CAF1 2269 90 + 1
------------AUGCAUGCAGAUGGAAAAGUGC--AUAAGCCAACAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUGCUUUUGCUUUUCGCUUU
------------..(((.((((((((((((((..--.....(((((.((.........)))))-)).......)))))).).)))))))...))).......... ( -26.04)
>consensus
____G_AAAA_CAGAUAUGCAGACCGAAAAGUGC__AUAAGCCAAAAGCAAAGCACAAGCGUU_GGAUUUUCUGCUUUUGCGCGUCUGCUUUUGCUUUUUGCU__
.......................................(((.((((((((((((...((((..((........))...))))...))).))))))))).))).. (-16.96 = -17.88 +   0.92)

alignment

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secondary structure

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Window 7

Location 19,803,514 – 19,803,610
Length 96
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 72.86
Mean single sequence MFE -24.74
Consensus MFE -16.78
Energy contribution -17.38
Covariance contribution 0.60
Combinations/Pair 1.10
Mean z-score -2.31
Structure conservation index 0.68
SVM decision value 2.74
SVM RNA-class probability 0.996720
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19803514 96 - 22224390
---GCCAAAAGCAAAAGCAGACGCGCAAAAGCAGAAAAUGCAAACGCUUGUGCUUUGCUUUUCGUCUAU--GCACUUUUCGGUCUGCAUAUCUGUUUUUUC----
---...(((((((...((((((.((.(((((..(((((.(((((.((....))))))))))))((....--)).))))))))))))).....)))))))..---- ( -27.20)
>DroSec_CAF1 2225 88 - 1
--AGCAAAAAGCAAAAGUAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUUUUGGCUGAU--------------UUUCAUAUCUGCUUUUCCGCUG
--(((......((((((((((.(((((..(((.........-...))))))))))))))))))((.(((--------------......))).))......))). ( -24.20)
>DroSim_CAF1 2294 102 - 1
--AGCAAAAAGCAAAAGUAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUUUUGGCCUAUGUGCACUUUUGGGUCUGCAUAUCUGCUUUUCCGCUG
--(((.(((((((((((((((.(((((..(((.........-...)))))))))))))))))((((((..........)))))).........))))))..))). ( -29.60)
>DroEre_CAF1 2028 79 - 1
AAAGC-AAAAGCAAAAACAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUUUUGGCUUUU--AUACUUUUCCAU----------------------
(((((-(((((((((.......(((((..(((.........-...))))))))))))))))).))))).--............---------------------- ( -18.11)
>DroYak_CAF1 2269 90 - 1
AAAGCGAAAAGCAAAAGCAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUGUUGGCUUAU--GCACUUUUCCAUCUGCAUGCAU------------
...((...((((...((((((.(((((..(((.........-...))))))))))))))....))))((--(((..........)))))))..------------ ( -24.60)
>consensus
__AGCAAAAAGCAAAAGCAGACGCGCAAAAGCAGAAAAUCC_AACGCUUGUGCUUUGCUUUUGGCUUAU__GCACUUUUCCAUCUGCAUAUCUG_UUUU_C____
........(((((((((((((.(((((..(((.............))))))))))))))))).))))...................................... (-16.78 = -17.38 +   0.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,803,535 – 19,803,640
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.98
Mean single sequence MFE -38.84
Consensus MFE -25.28
Energy contribution -26.20
Covariance contribution 0.92
Combinations/Pair 1.07
Mean z-score -4.26
Structure conservation index 0.65
SVM decision value 2.71
SVM RNA-class probability 0.996523
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19803535 105 + 22224390
GAAAAGUGC--AUAGACGAAAAGCAAAGCACAAGCGUUUGCAUUUUCUGCUUUUGCGCGUCUGCUUUUGCUUUUGGC-------------UUUUGCGCUGUUGCGCUUUUGCUUUCGCAC
.....((((--.......((((((((((((...((((..(((.....)))....))))...))).)))))))))(((-------------....((((....))))....)))...)))) ( -36.40)
>DroSec_CAF1 2247 101 + 1
-----------AUCAGCCAAAAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUACUUUUGCUUUUUGCU-------UUUGCUUUUGCGCUGUUGCGCUUUUGCUUCCGCAC
-----------..(((((((((((((((((.(((((.(-((((....(((....))).)))))....)))))..))).-------)))))))))).)))).((((..........)))). ( -31.60)
>DroSim_CAF1 2319 112 + 1
CAAAAGUGCACAUAGGCCAAAAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUACUUUUGCUUUUUGCU-------UUUGCUUUUGCGCUGUUGCGCUUUUGCUUCCGCAU
((((((((((....((((((((((((((((.(((((.(-((((....(((....))).)))))....)))))..))).-------)))))))))).)))..))))))))))......... ( -39.90)
>DroEre_CAF1 2031 116 + 1
GAAAAGUAU--AAAAGCCAAAAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUGUUUUUGCUUUU-GCUUUUGGCUUUGGCUUUUGCGCUGUUGCGCUUUUGCUUCCGCAC
.((((((..--.((((((((((((((((((.(((((..-........))))).)))(((........))).)))-)))))))))))).))))))((((....))))...(((....))). ( -44.10)
>DroYak_CAF1 2282 117 + 1
GAAAAGUGC--AUAAGCCAACAGCAAAGCACAAGCGUU-GGAUUUUCUGCUUUUGCGCGUCUGCUUUUGCUUUUCGCUUUUGCUUUUGGCUUUUGCGCUGUUGCGCUUUUGCUUCCGCAC
....(((((--(.(((((((.(((((((((.(((((..-........))))).)))(((...((....))....))).)))))).))))))).))))))..((((..........)))). ( -42.20)
>consensus
GAAAAGUGC__AUAAGCCAAAAGCAAAGCACAAGCGUU_GGAUUUUCUGCUUUUGCGCGUCUGCUUUUGCUUUUUGCU_______UUGGCUUUUGCGCUGUUGCGCUUUUGCUUCCGCAC
..............(((.((((((((((((...((((..((........))...))))...))).))))))))).)))................((((....))))...(((....))). (-25.28 = -26.20 +   0.92)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,803,535 – 19,803,640
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.98
Mean single sequence MFE -37.08
Consensus MFE -29.40
Energy contribution -30.00
Covariance contribution 0.60
Combinations/Pair 1.07
Mean z-score -4.70
Structure conservation index 0.79
SVM decision value 3.49
SVM RNA-class probability 0.999292
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19803535 105 - 22224390
GUGCGAAAGCAAAAGCGCAACAGCGCAAAA-------------GCCAAAAGCAAAAGCAGACGCGCAAAAGCAGAAAAUGCAAACGCUUGUGCUUUGCUUUUCGUCUAU--GCACUUUUC
(((((...((....((((....))))....-------------((.....))....))((((((......)).(((((.(((((.((....)))))))))))))))).)--))))..... ( -34.10)
>DroSec_CAF1 2247 101 - 1
GUGCGGAAGCAAAAGCGCAACAGCGCAAAAGCAAA-------AGCAAAAAGCAAAAGUAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUUUUGGCUGAU-----------
.(((....))).........((((.((((((((((-------.(((..((((....(....)((......)).........-...)))).)))))))))))))))))..----------- ( -33.30)
>DroSim_CAF1 2319 112 - 1
AUGCGGAAGCAAAAGCGCAACAGCGCAAAAGCAAA-------AGCAAAAAGCAAAAGUAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUUUUGGCCUAUGUGCACUUUUG
.(((....)))...(((((...((.((((((((((-------.(((..((((....(....)((......)).........-...)))).)))))))))))))))...)))))....... ( -36.20)
>DroEre_CAF1 2031 116 - 1
GUGCGGAAGCAAAAGCGCAACAGCGCAAAAGCCAAAGCCAAAAGC-AAAAGCAAAAACAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUUUUGGCUUUU--AUACUUUUC
.(((....)))...((((....))))(((((..((((((((((((-(((.((..........))(((.((((.........-...)))).)))))))))))))))))).--...))))). ( -41.00)
>DroYak_CAF1 2282 117 - 1
GUGCGGAAGCAAAAGCGCAACAGCGCAAAAGCCAAAAGCAAAAGCGAAAAGCAAAAGCAGACGCGCAAAAGCAGAAAAUCC-AACGCUUGUGCUUUGCUGUUGGCUUAU--GCACUUUUC
(((((.........((((....))))..(((((((.((((((.(((....((....))...)))(((.((((.........-...)))).))))))))).))))))).)--))))..... ( -40.80)
>consensus
GUGCGGAAGCAAAAGCGCAACAGCGCAAAAGCAAA_______AGCAAAAAGCAAAAGCAGACGCGCAAAAGCAGAAAAUCC_AACGCUUGUGCUUUGCUUUUGGCUUAU__GCACUUUUC
.(((....)))...((((....))))......................(((((((((((((.(((((..(((.............))))))))))))))))).))))............. (-29.40 = -30.00 +   0.60)

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 12:51:10 2006