Locus 2961

Sequence ID 2R_DroMel_CAF1
Location 10,212,330 – 10,212,449
Length 119
Max. P 0.974405
window4895 window4896 window4897 window4898

overview

Window 5

Location 10,212,330 – 10,212,424
Length 94
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 77.79
Mean single sequence MFE -25.30
Consensus MFE -15.37
Energy contribution -15.15
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -2.51
Structure conservation index 0.61
SVM decision value 1.73
SVM RNA-class probability 0.974405
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10212330 94 + 20766785
G-GAAACGGAGAA-AACCCAGAAAGAGAUGGC--GGCUGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACG
(-....)((....-...))...........((--((((......((((((((((((.....))))))))))))((((......))))))).))).... ( -24.60)
>DroGri_CAF1 47054 90 + 1
--------AGUUUAGGCCGAGUUAGGGAUAGCUAGACCGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACA
--------.(((((((.(.(((((....))))).).))((....((((((((((((.....))))))))))))...)).......)))))........ ( -24.50)
>DroEre_CAF1 45080 89 + 1
------CGGGGAA-AACCCAGAAAGAGAUGGC--GGCUGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACG
------.(((...-..)))...........((--((((......((((((((((((.....))))))))))))((((......))))))).))).... ( -27.60)
>DroYak_CAF1 41515 95 + 1
GGAAA-CGGGGAAAAGCCCAGAAAGAGAUGGC--GGCUGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACG
(....-)(((......)))...........((--((((......((((((((((((.....))))))))))))((((......))))))).))).... ( -28.30)
>DroAna_CAF1 45567 71 + 1
-------------------------AACUGGC--GGCUGGAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACG
-------------------------.....((--((((.((...((((((((((((.....))))))))))))...)).........))).))).... ( -22.90)
>DroPer_CAF1 23820 89 + 1
GGAGGCAGGA----GGCACUGGCA---AAGGA--GAAUGGAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACG
...(.(((..----....))).).---.....--((((((....((((((((((((.....))))))))))))...))))))................ ( -23.90)
>consensus
______CGGGGAA_AGCCCAGAAAGAGAUGGC__GGCUGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACG
......................................((....((((((((((((.....))))))))))))...)).................... (-15.37 = -15.15 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,212,330 – 10,212,424
Length 94
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 77.79
Mean single sequence MFE -16.71
Consensus MFE -13.98
Energy contribution -13.98
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.29
Structure conservation index 0.84
SVM decision value 0.80
SVM RNA-class probability 0.853336
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10212330 94 - 20766785
CGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCAGCC--GCCAUCUCUUUCUGGGUU-UUCUCCGUUUC-C
.(((((((((......(((((.....))))))))))))))........................--.(((........)))...-...........-. ( -15.60)
>DroGri_CAF1 47054 90 - 1
UGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCGGUCUAGCUAUCCCUAACUCGGCCUAAACU--------
.(((((((((......(((((.....))))))))))))))....................((((.((.((....)).)).))))......-------- ( -18.60)
>DroEre_CAF1 45080 89 - 1
CGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCAGCC--GCCAUCUCUUUCUGGGUU-UUCCCCG------
.(((((((((......(((((.....))))))))))))))........................--.............(((..-...))).------ ( -17.70)
>DroYak_CAF1 41515 95 - 1
CGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCAGCC--GCCAUCUCUUUCUGGGCUUUUCCCCG-UUUCC
.(((((((((......(((((.....))))))))))))))........................--.............(((......))).-..... ( -17.60)
>DroAna_CAF1 45567 71 - 1
CGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUCCAGCC--GCCAGUU-------------------------
.(((((((((......(((((.....))))))))))))))........................--.......------------------------- ( -14.00)
>DroPer_CAF1 23820 89 - 1
CGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUCCAUUC--UCCUU---UGCCAGUGCC----UCCUGCCUCC
.(((((((((......(((((.....))))))))))))))....((((................--.....---.....)))).----.......... ( -16.77)
>consensus
CGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCAGCC__GCCAUCUCUUUCUGGGCU_UUCCCCG______
.(((((((((......(((((.....)))))))))))))).......................................................... (-13.98 = -13.98 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,212,354 – 10,212,449
Length 95
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 76.30
Mean single sequence MFE -28.45
Consensus MFE -16.08
Energy contribution -15.67
Covariance contribution -0.42
Combinations/Pair 1.21
Mean z-score -2.11
Structure conservation index 0.57
SVM decision value 1.28
SVM RNA-class probability 0.940160
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10212354 95 + 20766785
GAUGGC--GGCUGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACGAAGAGCA--CAACU-AGUCGGGGG------UU---UU-
....((--((((......((((((((((((.....))))))))))))((((......))))))).)))..(((..((..--...))-..)))....------..---..- ( -25.90)
>DroVir_CAF1 53581 95 + 1
GAUAGCUAGACCGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACGGCGCACA----AGCCAGAAACAGGACA-----------
..........((.........(((((((((((.(((((.(((((((.....)))))......)).))))))))))))))----)).........))...----------- ( -27.87)
>DroGri_CAF1 47072 95 + 1
GAUAGCUAGACCGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACAGCGAACA----GGCAGGCAGGCGGCCA-----------
....(((.(...((....((((((((((((.....))))))))))))...)).............(((....)))..).----))).(((.....))).----------- ( -26.70)
>DroEre_CAF1 45099 90 + 1
GAUGGC--GGCUGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACGAAGAGCA--CAACU-AGUAGGGG---------------
....((--((((......((((((((((((.....))))))))))))((((......))))))).)))...........--.....-........--------------- ( -22.20)
>DroAna_CAF1 45568 104 + 1
ACUGGC--GGCUGGAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACGGCGAGCA--GAAG--AGCUGGGAGCCUGGGUUCGGUUU
.(..((--..((.((...((((((((((((.....))))))))))))...))..........((.(((....))).)).--..))--.))..)((((....))))..... ( -34.10)
>DroPer_CAF1 23840 96 + 1
-AAGGA--GAAUGGAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACGGCGAAUCCGGAAAC-GGUAGCUGG------AC---CU-
-.(((.--((((((....((((((((((((.....))))))))))))...))))))..............((((....(((....)-))..)))).------.)---))- ( -33.90)
>consensus
GAUGGC__GACUGAAAAUUUAUUUGUGCGUUGAUUGCGCGCAAAUGAUGAUCAUUUAAUUAAGCACGCAACGGCGAACA___AAGC_AGUAGGGGG______________
........................((.(((((.(((((.(((((((.....)))))......)).)))))))))).))................................ (-16.08 = -15.67 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,212,354 – 10,212,449
Length 95
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 76.30
Mean single sequence MFE -22.82
Consensus MFE -14.27
Energy contribution -14.35
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.03
Structure conservation index 0.63
SVM decision value 1.46
SVM RNA-class probability 0.955900
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10212354 95 - 20766785
-AA---AA------CCCCCGACU-AGUUG--UGCUCUUCGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCAGCC--GCCAUC
-..---..------.........-..(((--(((..((.(((((((((......(((((.....)))))))))))))).)).))))))..............--...... ( -21.80)
>DroVir_CAF1 53581 95 - 1
-----------UGUCCUGUUUCUGGCU----UGUGCGCCGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCGGUCUAGCUAUC
-----------......(((...((((----((((((..(((((((((......(((((.....))))))))))))))...))))))...........)))).))).... ( -25.70)
>DroGri_CAF1 47072 95 - 1
-----------UGGCCGCCUGCCUGCC----UGUUCGCUGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCGGUCUAGCUAUC
-----------.(((((..........----(((.((.((((((((((......(((((.....))))))))))))).)).)).)))..........)))))........ ( -24.65)
>DroEre_CAF1 45099 90 - 1
---------------CCCCUACU-AGUUG--UGCUCUUCGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCAGCC--GCCAUC
---------------........-..(((--(((..((.(((((((((......(((((.....)))))))))))))).)).))))))..............--...... ( -21.80)
>DroAna_CAF1 45568 104 - 1
AAACCGAACCCAGGCUCCCAGCU--CUUC--UGCUCGCCGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUCCAGCC--GCCAGU
............((((...(((.--....--.))).((.(((((((((......(((((.....))))))))))))))....))..............))))--...... ( -23.50)
>DroPer_CAF1 23840 96 - 1
-AG---GU------CCAGCUACC-GUUUCCGGAUUCGCCGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUCCAUUC--UCCUU-
-.(---(.------.......((-(....)))....((.(((((((((......(((((.....))))))))))))))....))............))....--.....- ( -19.50)
>consensus
______________CCCCCUACU_GCUU___UGCUCGCCGUUGCGUGCUUAAUUAAAUGAUCAUCAUUUGCGCGCAAUCAACGCACAAAUAAAUUUUCAGCC__GCCAUC
...............................(((.....(((((((((......(((((.....))))))))))))))....)))......................... (-14.27 = -14.35 +   0.08)

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 10:44:04 2006