Locus 387

Sequence ID 2L_DroMel_CAF1
Location 1,205,002 – 1,205,178
Length 176
Max. P 0.999806
window611 window612 window613

overview

Window 1

Location 1,205,002 – 1,205,113
Length 111
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 83.77
Mean single sequence MFE -27.95
Consensus MFE -18.35
Energy contribution -18.24
Covariance contribution -0.11
Combinations/Pair 1.11
Mean z-score -2.87
Structure conservation index 0.66
SVM decision value 1.14
SVM RNA-class probability 0.920802
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1205002 111 + 22407834
UCAGGCUCA------GAUUCAGAUUCCGAGCCUUACUCAUCCCCGGCACAUCAACAUCAUCAUCAUCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUC
..((((((.------((.......)).)))))).(((.((((..((((.........................))))..(((((((((.....))))))))).))))...))).... ( -26.61)
>DroSim_CAF1 721 108 + 1
UCAGGCUCG------GAUUCAGAUUCCGAGCCUUACUCAUCCCCGGCACAUCAC---CAUCAUCAUCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUC
..(((((((------((.......))))))))).(((.((((..((((......---................))))..(((((((((.....))))))))).))))...))).... ( -32.85)
>DroEre_CAF1 672 113 + 1
-CGGAUUCAGAUUCAGAUACAGAUUCCGAGCCUUGCUCAUCCCCUACACAUCCUCAGCAU---CACCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAUUCUCU
-.((((...((.((.......)).)).((((...))))...........)))).((((..---........))))(((.(((((((((.....))))))))))))............ ( -24.40)
>consensus
UCAGGCUCA______GAUUCAGAUUCCGAGCCUUACUCAUCCCCGGCACAUCAACA_CAUCAUCAUCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUC
..((((((...................))))))..........................................(((.(((((((((.....))))))))))))............ (-18.35 = -18.24 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,205,036 – 1,205,138
Length 102
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 68.73
Mean single sequence MFE -25.86
Consensus MFE -13.30
Energy contribution -13.30
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.26
Structure conservation index 0.51
SVM decision value 4.12
SVM RNA-class probability 0.999806
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1205036 102 + 22407834
CCCCGGCACAUCAACAUCAUCAUCAUCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUCCAGGGAGCCUGAUUU----------UC-----CUUCCCCG
...........................(((((((.((..(((((((((.....)))))))))((((.........)))))).)).)))))..----------..-----........ ( -23.60)
>DroPse_CAF1 741 106 + 1
----------CCUCCAUCGUCGUCAUCAUCAUCUGCCAUGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCACUUUGCCUGGCCGUCUCCCUCCACAGCCCUCUCCAGCCCGUC-CCC
----------........((.((.........(.((((.(((.(((((((.((((.......)))).))))))).))))))).).........)).))...............-... ( -26.27)
>DroSim_CAF1 755 90 + 1
CCCCGGCACAUCAC---CAUCAUCAUCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUCCAGGGAGCCUGAUUU----------U--------------
....((.......)---).........(((((((.((..(((((((((.....)))))))))((((.........)))))).)).)))))..----------.-------------- ( -24.10)
>DroEre_CAF1 711 99 + 1
CCCCUACACAUCCUCAGCAU---CACCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAUUCUCUCAGGCAGCCUGAUUU----------UC-----CUUCACCG
....................---....((((((((((..(((((((((.....))))))))).(((......)))....))))).)))))..----------..-----........ ( -25.10)
>DroPer_CAF1 735 101 + 1
----------CCUCCAUCGACGUCAUCAUCAUCUGCCAUGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCACUUUGCCUGGGCGUCUCCCUCCACAGCCCUCUC-----CGUC-CCC
----------........((((.................(((.(((((((.((((.......)))).))))))).))).((((.............))))....-----))))-... ( -30.22)
>consensus
CCCC__CACAUCACCAUCAUCAUCAUCAUCAGCUGCCACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCACUCUGCCAGGGAGCCUGAUUU__________UC_____CGUC_CCC
...................................(((.(((((((((.....)))))))))))).................................................... (-13.30 = -13.30 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,205,073 – 1,205,178
Length 105
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 76.57
Mean single sequence MFE -20.99
Consensus MFE -11.88
Energy contribution -12.02
Covariance contribution 0.14
Combinations/Pair 1.18
Mean z-score -1.90
Structure conservation index 0.57
SVM decision value 0.84
SVM RNA-class probability 0.863256
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1205073 105 + 22407834
ACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUCCAGGGAGCCUGAUUU----------UCCUUCCCCGACUUCGUCUUUUUUUACUUUUCCAUCGCUUUGUUCUUGGA
..(((((((((.....))))))))).(((..((((.(((.....))).))))...----------)))......(((...)))............((((............)))) ( -22.30)
>DroSec_CAF1 799 89 + 1
ACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUCCAGGGAGCCUGAUUU----------U----------------CUUUUUUCACUUUUCCUUCGCUUUGUUCUUGAA
..((..(((((((.((((.......))))..((((.(((.....))).))))...----------.----------------.....)))))))..))................. ( -19.30)
>DroSim_CAF1 789 89 + 1
ACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUCCAGGGAGCCUGAUUU----------U----------------CUUUUUUCACUUUUCCUUCGCUUUGUUCUUGAA
..((..(((((((.((((.......))))..((((.(((.....))).))))...----------.----------------.....)))))))..))................. ( -19.30)
>DroEre_CAF1 745 102 + 1
ACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAUUCUCUCAGGCAGCCUGAUUU----------UCCUUCACCGACUUCG---UUUUUUACAUUUCCUUCGCUCUGUUCUUGAA
.(((...((((((.((((.......)))).))))))...(((((...)))))...----------.......)))......---............................... ( -17.10)
>DroYak_CAF1 811 102 + 1
ACGGCUAAGUGAAUUUCAUUUAGCUUGGAUUUCAUUCUUGCAGGGAGCCUGAUUU----------CCCUUCGCCGACUUUG---UUUUUUACUUAUCCUUCGUUUUGUUCUUGAA
.((((..((((((.((((.......)))).))))))...(.((((((......))----------)))).)))))......---............................... ( -20.90)
>DroPer_CAF1 762 109 + 1
AUGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCACUUUGCCUGGGCGUCUCCCUCCACAGCCCUCUCCGUC-CCCACUUUA---UAUUUCACUUUUC--UGGUCUUGUUCUUGGC
..(((.(((((((.((((.......)))).))))))).))).((((.............))))........-.(((....(---((..(((......--)))...)))...))). ( -27.02)
>consensus
ACGGCUAAGUGAAUUCCAUUUAGCUUGGAUUUCAGUCUUCCAGGGAGCCUGAUUU__________UCCUUC_CCGACUU_G___UUUUUCACUUUUCCUUCGCUUUGUUCUUGAA
..((..(((((((.((((.......))))...........((((...))))....................................)))))))..))................. (-11.88 = -12.02 +   0.14)

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 09:34:40 2006