Locus 4975

Sequence ID 3L_DroMel_CAF1
Location 13,735,237 – 13,735,429
Length 192
Max. P 0.999693
window7853 window7854 window7855

overview

Window 3

Location 13,735,237 – 13,735,349
Length 112
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 94.77
Mean single sequence MFE -16.40
Consensus MFE -13.54
Energy contribution -13.74
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.83
SVM decision value 0.15
SVM RNA-class probability 0.609109
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13735237 112 + 23771897
AAGUUAUGAAUCAAAAAUAAUAUAGAAAAA-AA---GAUGAGGCGUAGAAAA-GAGGCCAGAUAGAACGG-GGGAAACUUUUUAUGAUUUCAAUAAAGUUGUUAACUUUAUUAAAAUU
((((((((((....................-..---.....(((.(......-.).)))..........(-((....))))))))))))).((((((((.....))))))))...... ( -16.10)
>DroSec_CAF1 142107 112 + 1
AAGUUAUGAAUCAAAAAUAAUAUAGAAAAA-AA---GAUGAGGCGUAGAAAA-GAGACCAGAUAGAACGG-GGGAAACUUUUUAUGAUUUCAAUAAAGUUGUUAACUUUAUUAAAAUU
..(((((.........))))).........-..---...((((((((((((.-....((.(......).)-)(....))))))))).))))((((((((.....))))))))...... ( -13.70)
>DroSim_CAF1 152852 111 + 1
AAGUUAUGAAUCAAAAAUAAUAUA-AAAAA-AA---GAUGAGGCGUAGAAAA-GAGGCCAGAUAGAACGG-GGGAAACUUUUUAUGAUUUCAAUAAAGUUGUUAACUUUAUUAAAAUU
((((((((((..............-.....-..---.....(((.(......-.).)))..........(-((....))))))))))))).((((((((.....))))))))...... ( -16.10)
>DroEre_CAF1 148694 113 + 1
AAGUUAUGAAUCAAAAAUAAUGUAGAAAAAAAA---AAUGAGGCGAAGAAAA-GAGGCCAGAUAGAACGG-GGGAAACUUUUUAUGAUUUCAAUAAAGUUGUUAACUUUAUUAAAAUU
((((((((((.......................---.....(((........-...)))..........(-((....))))))))))))).((((((((.....))))))))...... ( -15.40)
>DroYak_CAF1 152767 118 + 1
AAGUUAUGAAUCAAAAAUAAUAUAGAAAAAAAAGAAGAUGAGGCCAAGAAAACGGGGCCAGAUAGAAGGGGGGGAAACUUUUUAUGAUUUCAAUAAAGUUGUUAACUUUAUUAAAAUU
.......((((((............................((((..(....)..))))........((((((....)))))).)))))).((((((((.....))))))))...... ( -20.70)
>consensus
AAGUUAUGAAUCAAAAAUAAUAUAGAAAAA_AA___GAUGAGGCGUAGAAAA_GAGGCCAGAUAGAACGG_GGGAAACUUUUUAUGAUUUCAAUAAAGUUGUUAACUUUAUUAAAAUU
((((((((((...............................(((............)))............((....)).)))))))))).((((((((.....))))))))...... (-13.54 = -13.74 +   0.20)

alignment

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secondary structure

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Window 4

Location 13,735,237 – 13,735,349
Length 112
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 94.77
Mean single sequence MFE -12.04
Consensus MFE -11.52
Energy contribution -11.36
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -2.17
Structure conservation index 0.96
SVM decision value 3.90
SVM RNA-class probability 0.999693
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13735237 112 - 23771897
AAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAAAAAGUUUCCC-CCGUUCUAUCUGGCCUC-UUUUCUACGCCUCAUC---UU-UUUUUCUAUAUUAUUUUUGAUUCAUAACUU
.(((((((((((((.....)))))))))))))...............-...........(((...-........))).....---..-.............................. ( -11.40)
>DroSec_CAF1 142107 112 - 1
AAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAAAAAGUUUCCC-CCGUUCUAUCUGGUCUC-UUUUCUACGCCUCAUC---UU-UUUUUCUAUAUUAUUUUUGAUUCAUAACUU
.(((((((((((((.....)))))))))))))....(((((...((.-...........))...)-))))............---..-.............................. ( -10.70)
>DroSim_CAF1 152852 111 - 1
AAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAAAAAGUUUCCC-CCGUUCUAUCUGGCCUC-UUUUCUACGCCUCAUC---UU-UUUUU-UAUAUUAUUUUUGAUUCAUAACUU
.(((((((((((((.....))))))))))))).((((((((......-..(......).(((...-........))).....---..-)))))-)))..................... ( -11.80)
>DroEre_CAF1 148694 113 - 1
AAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAAAAAGUUUCCC-CCGUUCUAUCUGGCCUC-UUUUCUUCGCCUCAUU---UUUUUUUUCUACAUUAUUUUUGAUUCAUAACUU
.(((((((((((((.....)))))))))))))...............-...........(((...-........))).....---................................. ( -11.40)
>DroYak_CAF1 152767 118 - 1
AAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAAAAAGUUUCCCCCCCUUCUAUCUGGCCCCGUUUUCUUGGCCUCAUCUUCUUUUUUUUCUAUAUUAUUUUUGAUUCAUAACUU
.(((((((((((((.....)))))))))))))...........................((((..(....)..))))......................................... ( -14.90)
>consensus
AAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAAAAAGUUUCCC_CCGUUCUAUCUGGCCUC_UUUUCUACGCCUCAUC___UU_UUUUUCUAUAUUAUUUUUGAUUCAUAACUU
.(((((((((((((.....)))))))))))))...........................(((............)))......................................... (-11.52 = -11.36 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,735,311 – 13,735,429
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.43
Mean single sequence MFE -26.62
Consensus MFE -22.25
Energy contribution -22.92
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.84
SVM decision value 0.79
SVM RNA-class probability 0.851733
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13735311 118 - 23771897
GUCGUAGUCGGCGAAAGUAUUUUCUCAUAGUAAUUCUAUGCUCGGCUGGCUUUUAGACAACUUUUCUUGAGCUGAGCAAAAAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAA--A
((((....))))..........................(((((((((.(.....((....)).....).)))))))))...(((((((((((((.....))))))))))))).....--. ( -27.60)
>DroPse_CAF1 136265 112 - 1
GUCGU------CGAAAGUAUUUUCUCAUAGUAAUUCUCUGCUCGGCUGGCUUUUGCACAACUUUUCUU--GCUGAGCAAAAAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCGUAAAAA
.....------(((........................((((((((((((....)).)).........--))))))))....((((((((((((.....)))))))))))))))...... ( -23.50)
>DroSim_CAF1 152925 118 - 1
GUCGUAGUCGGCGAAAGUAUUUUCUCAUAGUAAUUCUAUGCUCGGCUGGCUUUUAGACAACUUUUCUUGAGCUGAGCAAAAAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAA--A
((((....))))..........................(((((((((.(.....((....)).....).)))))))))...(((((((((((((.....))))))))))))).....--. ( -27.60)
>DroEre_CAF1 148769 118 - 1
GUCGUAGUCGGCGAAAGUAUUUUCUCAUAGUAAUUCUAUGCUCGGCUGGCUUUUAGACAACUUUUCUUGAGCUGAGCAAAAAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAA--A
((((....))))..........................(((((((((.(.....((....)).....).)))))))))...(((((((((((((.....))))))))))))).....--. ( -27.60)
>DroYak_CAF1 152847 118 - 1
GUCGUAGUCGGCGAAAGUAUUUUUUCAUAGUAAUUCUAUGCUCGGCUGGCUUUUAGACAACUUUUCUUGAGCUGAGCAAAAAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAA--A
((((....))))(((((....)))))............(((((((((.(.....((....)).....).)))))))))...(((((((((((((.....))))))))))))).....--. ( -29.90)
>DroPer_CAF1 137592 112 - 1
GUCGU------CGAAAGUAUUUUCUCAUAGUAAUUCUCUGCUCGGCUGGCUUUUGCACAACUUUUCUU--GCUGAGCAAAAAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCGUAAAAA
.....------(((........................((((((((((((....)).)).........--))))))))....((((((((((((.....)))))))))))))))...... ( -23.50)
>consensus
GUCGUAGUCGGCGAAAGUAUUUUCUCAUAGUAAUUCUAUGCUCGGCUGGCUUUUAGACAACUUUUCUUGAGCUGAGCAAAAAUUUUAAUAAAGUUAACAACUUUAUUGAAAUCAUAA__A
.((((.....))))........................(((((((((......................)))))))))...(((((((((((((.....)))))))))))))........ (-22.25 = -22.92 +   0.67)

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 11:38:24 2006