Locus 2367

Sequence ID 2R_DroMel_CAF1
Location 8,596,822 – 8,596,953
Length 131
Max. P 0.995360
window3907 window3908 window3909

overview

Window 7

Location 8,596,822 – 8,596,927
Length 105
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 72.55
Mean single sequence MFE -35.58
Consensus MFE -12.81
Energy contribution -14.40
Covariance contribution 1.59
Combinations/Pair 1.11
Mean z-score -2.26
Structure conservation index 0.36
SVM decision value 0.98
SVM RNA-class probability 0.894491
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8596822 105 + 20766785
CUCUGUCAGCUUGAUUCAUUGUGGAAGUGAAAAUG-AGCCAGCAGGGCGAAAGAAACUGGACGAGGUAAUAGGUC-----CUGGGACAGGUCCUGUCCAACUGACAGAUGG
.((((((((.(((.((((((.....))))))....-.....(((((((....)...(((..(.(((........)-----)).)..))).)))))).)))))))))))... ( -36.40)
>DroPse_CAF1 30733 92 + 1
CUCUGUCAGCUUGAUUCAUU--CGCAACGAAAGUUUGGGCAGUUG-----------CCGG------AGAUGGCUACGGGGAUGCGACAGGUCCUGCCCUGCUGACAGAUGG
.(((((((((..........--...(((....))).((((.((.(-----------(((.------...)))).)).(((((.......))))))))).)))))))))... ( -37.10)
>DroSec_CAF1 81158 91 + 1
CUCUGUCAGCUUGAUUCAUUGUGGAAGUGAAAAUG-AGCCAGCCGGGCGAAAGAAACUGGACGAGGUAAUAGGUC-----CUGGGACAGGUCCUGUC--------------
(((.(((.((((..((((((.....))))))...)-)))....(((.(....)...)))))))))...(((((.(-----(((...)))).))))).-------------- ( -27.80)
>DroSim_CAF1 73087 105 + 1
CUCUGUCAGCUUGAUUCAUUGUGGAAGUGAAAAUG-AGCCAGCCGGGCGAAAGAAACUGGACGAGGUAAUAGGUC-----CUGGGACAGGUCCUGUCCAACUGACAGAUGG
.((((((((.(((.((((((.....))))))....-.(((.(((((.(....)...)))).)..))).(((((.(-----(((...)))).))))).)))))))))))... ( -38.20)
>DroYak_CAF1 76099 105 + 1
CUCUGUCAGCUUGAUUCAUUGUGGAAGUGAAAAUG-AGCCAGCAGGGCGAAAGAAACAGGACGAGGUAAUAGGUC-----CUGGGACAGGUCCUGUCCAACUGACAGAUGG
.(((((((((((..((((((.....))))))....-.(((.....)))..)))...((((((..........)))-----)))((((((...))))))..))))))))... ( -37.00)
>DroPer_CAF1 31012 92 + 1
CUCUGUCAGCUUGAUUCAUU--CGCAACGAAAGUUUGGGCAGUUG-----------CCGG------AGAUGGCUACGGGGAUGCGACAGGUCCUGCCCCGCUGACAGAUGG
.(((((((((..........--...(((....))).((((.((.(-----------(((.------...)))).)).(((((.......))))))))).)))))))))... ( -37.00)
>consensus
CUCUGUCAGCUUGAUUCAUUGUGGAAGUGAAAAUG_AGCCAGCAGGGCGAAAGAAACUGGACGAGGUAAUAGGUC_____CUGGGACAGGUCCUGUCCAACUGACAGAUGG
.((((((((.....((((((.....)))))).......((((.....(....)...(((..........)))........))))(((((...)))))...))))))))... (-12.81 = -14.40 +   1.59)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,596,822 – 8,596,927
Length 105
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 72.55
Mean single sequence MFE -30.82
Consensus MFE -14.82
Energy contribution -16.60
Covariance contribution 1.78
Combinations/Pair 1.16
Mean z-score -2.66
Structure conservation index 0.48
SVM decision value 2.57
SVM RNA-class probability 0.995360
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8596822 105 - 20766785
CCAUCUGUCAGUUGGACAGGACCUGUCCCAG-----GACCUAUUACCUCGUCCAGUUUCUUUCGCCCUGCUGGCU-CAUUUUCACUUCCACAAUGAAUCAAGCUGACAGAG
...(((((((((((((((((....(((....-----)))......))).))))..........(((.....))).-........................)))))))))). ( -30.10)
>DroPse_CAF1 30733 92 - 1
CCAUCUGUCAGCAGGGCAGGACCUGUCGCAUCCCCGUAGCCAUCU------CCGG-----------CAACUGCCCAAACUUUCGUUGCG--AAUGAAUCAAGCUGACAGAG
...(((((((((.((((((((....))...........(((....------..))-----------)..)))))).....(((((....--.)))))....))))))))). ( -35.80)
>DroSec_CAF1 81158 91 - 1
--------------GACAGGACCUGUCCCAG-----GACCUAUUACCUCGUCCAGUUUCUUUCGCCCGGCUGGCU-CAUUUUCACUUCCACAAUGAAUCAAGCUGACAGAG
--------------((.((((.(((..(.((-----(........))).)..))).)))).))...((((((..(-((((...........)))))..).)))))...... ( -20.70)
>DroSim_CAF1 73087 105 - 1
CCAUCUGUCAGUUGGACAGGACCUGUCCCAG-----GACCUAUUACCUCGUCCAGUUUCUUUCGCCCGGCUGGCU-CAUUUUCACUUCCACAAUGAAUCAAGCUGACAGAG
...(((((((((((((((((....(((....-----)))......))).))))..........(((.....))).-........................)))))))))). ( -30.10)
>DroYak_CAF1 76099 105 - 1
CCAUCUGUCAGUUGGACAGGACCUGUCCCAG-----GACCUAUUACCUCGUCCUGUUUCUUUCGCCCUGCUGGCU-CAUUUUCACUUCCACAAUGAAUCAAGCUGACAGAG
...((((((((((((((((...))))))(((-----(((..........))))))........(((.....))).-........................)))))))))). ( -32.60)
>DroPer_CAF1 31012 92 - 1
CCAUCUGUCAGCGGGGCAGGACCUGUCGCAUCCCCGUAGCCAUCU------CCGG-----------CAACUGCCCAAACUUUCGUUGCG--AAUGAAUCAAGCUGACAGAG
...(((((((((.((((((((....))...........(((....------..))-----------)..)))))).....(((((....--.)))))....))))))))). ( -35.60)
>consensus
CCAUCUGUCAGUUGGACAGGACCUGUCCCAG_____GACCUAUUACCUCGUCCAGUUUCUUUCGCCCAGCUGGCU_CAUUUUCACUUCCACAAUGAAUCAAGCUGACAGAG
...(((((((((..(((((...)))))........................(((((............)))))............................))))))))). (-14.82 = -16.60 +   1.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,596,859 – 8,596,953
Length 94
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 98.58
Mean single sequence MFE -38.97
Consensus MFE -37.50
Energy contribution -37.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.97
Structure conservation index 0.96
SVM decision value 1.85
SVM RNA-class probability 0.979955
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8596859 94 + 20766785
CCAGCAGGGCGAAAGAAACUGGACGAGGUAAUAGGUCCUGGGACAGGUCCUGUCCAACUGACAGAUGGCCUGGCCGGACCGAAACUUCUAGCUG
.((((((..(....)...))....(((((....(((((.((..(((((((((((.....)))))..)))))).)))))))...)))))..)))) ( -38.80)
>DroSim_CAF1 73124 94 + 1
CCAGCCGGGCGAAAGAAACUGGACGAGGUAAUAGGUCCUGGGACAGGUCCUGUCCAACUGACAGAUGGCCUGGCCGGACCGAAACUUCUAGCUG
.(((((((.(....)...)))...(((((....(((((.((..(((((((((((.....)))))..)))))).)))))))...)))))..)))) ( -40.00)
>DroYak_CAF1 76136 94 + 1
CCAGCAGGGCGAAAGAAACAGGACGAGGUAAUAGGUCCUGGGACAGGUCCUGUCCAACUGACAGAUGGCCUGGCCGGACCGAAACUUCUAGCUG
.((((.(..(....)...).....(((((....(((((.((..(((((((((((.....)))))..)))))).)))))))...)))))..)))) ( -38.10)
>consensus
CCAGCAGGGCGAAAGAAACUGGACGAGGUAAUAGGUCCUGGGACAGGUCCUGUCCAACUGACAGAUGGCCUGGCCGGACCGAAACUUCUAGCUG
.((((.(..(....)...).....(((((....(((((.((..(((((((((((.....)))))..)))))).)))))))...)))))..)))) (-37.50 = -37.50 +   0.00)

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 10:28:09 2006