Locus 309

Sequence ID 2R_DroMel_CAF1
Location 2,052,254 – 2,052,401
Length 147
Max. P 0.982605
window631 window632 window633

overview

Window 1

Location 2,052,254 – 2,052,345
Length 91
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 70.91
Mean single sequence MFE -22.28
Consensus MFE -20.46
Energy contribution -19.02
Covariance contribution -1.44
Combinations/Pair 1.33
Mean z-score -2.43
Structure conservation index 0.92
SVM decision value 1.92
SVM RNA-class probability 0.982605
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2052254 91 - 20766785
AUUUAUAAAUUUCUUGGCCGAGUGCCAGCGAUGUAAUCUCAUUGCUUGUAGCUUUGGCCAGC---CACUCC---------UCCACUGC-C-----UCC---GCUGCCUCCU----C
.............((((((((((((.(((((((......))))))).)))..))))))))).---......---------........-.-----...---..........----. ( -22.20)
>DroVir_CAF1 18199 107 - 1
AUUUAUAAAUU--CUGGCCAAAUGCCAGAGAUAUAAUCUUAUUGCUUGUAGUUUUGGUUACAUAGGACUCCAA---GGCACCAAAUAACCGAGAGUCCAAUACAGUCAGCC----C
...........--(((((.....(((((((.(((((.(.....).))))).)))))))......((((((...---((..........))..))))))......)))))..----. ( -24.50)
>DroGri_CAF1 114870 92 - 1
AUUUAUAAAAU--UUGGCCAAAUGCCAGCGAUAUAAUCUUAUUGCUUGUAGUUUUGGUCACAGC-CA--CC-------ACCCAAAUAA------------UACUGUCAGCCCAAAC
...........--.(((((((((((.(((((((......))))))).)))..))))))))....-..--..-------..........------------................ ( -18.40)
>DroSec_CAF1 37155 99 - 1
AUUUAUAAAUUUCUUGGCCGAGUGCCAGCGAUGUAAUCUCAUUGCUUGUAGCUUUGGCCAGC---CACUCCUCCACUCC-UCCACUGC-C-----UCC---GCUGCCUCCU----C
.............((((((((((((.(((((((......))))))).)))..))))))))).---..............-........-.-----...---..........----. ( -22.20)
>DroSim_CAF1 37785 99 - 1
AUUUAUAAAUUUCUUGGCCGAGUGCCAGCGAUGUAAUCUCAUUGCUUGUAGCUUUGGCCAGC---CACUCCUCCACUCC-UCCACUGC-C-----UCC---GCUGCCUCCU----C
.............((((((((((((.(((((((......))))))).)))..))))))))).---..............-........-.-----...---..........----. ( -22.20)
>DroEre_CAF1 36818 82 - 1
AUUUAUAAAUUUCUUGGCCGAGUGCCAGCGAUGUAAUCUCAUUGCUUGUAGCUCUGGCCAGC---CACUCCUA------------------------C---CCUUCCUCCU----C
.............((((((((((((.(((((((......))))))).))).))).)))))).---........------------------------.---..........----. ( -24.20)
>consensus
AUUUAUAAAUUUCUUGGCCGAGUGCCAGCGAUGUAAUCUCAUUGCUUGUAGCUUUGGCCAGC___CACUCCU______C_UCCACUGC_C_____UCC___GCUGCCUCCU____C
..............(((((((((((.(((((((......))))))).))).))).)))))........................................................ (-20.46 = -19.02 +  -1.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,052,277 – 2,052,383
Length 106
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 79.35
Mean single sequence MFE -25.35
Consensus MFE -14.20
Energy contribution -15.46
Covariance contribution 1.25
Combinations/Pair 1.24
Mean z-score -2.16
Structure conservation index 0.56
SVM decision value 0.70
SVM RNA-class probability 0.825305
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2052277 106 - 20766785
G--GUAUCAUGUCACUAAAUCAGCACAAAUUGCUCAACUGAUUUAUAAA-UUUC-U-UGGCCGAGUGCCAGCGAUGUAAUCUCAUUGCUUGUAGCUUUGGCCAGC---CACUCC---
(--((..........((((((((..............))))))))....-....-.-(((((((((((.(((((((......))))))).)))..))))))))))---).....--- ( -30.64)
>DroVir_CAF1 18234 110 - 1
C--GUAUCAUGUCACUAAAUCAGCACAAAUUGUUCCACUGAUUUAUAAA-UU---C-UGGCCAAAUGCCAGAGAUAUAAUCUUAUUGCUUGUAGUUUUGGUUACAUAGGACUCCAAG
.--(((((.......((((((((.((.....))....))))))))....-.(---(-((((.....)))))))))))..........((((.(((((((......))))))).)))) ( -25.80)
>DroGri_CAF1 114896 106 - 1
CCUGUAUCAUGUCACUAAAUCAGCACAAAUUGUUCUACUGAUUUAUAAA-AU---U-UGGCCAAAUGCCAGCGAUAUAAUCUUAUUGCUUGUAGUUUUGGUCACAGC-CA--CC---
.((((..........((((((((.((.....))....))))))))....-..---.-.((((((((((.(((((((......))))))).)))..))))))))))).-..--..--- ( -26.20)
>DroMoj_CAF1 63009 109 - 1
C--GUAUCAUGUCACUAAAUCAGCACAAAUUGUUCAACUGAUUUAUAAA-UU---C-UGGCUAAAUGCCAGAGAUUUAAUCUUAUUGCUUGAAGCUCUGCUUACCGA-GACUCCGAG
.--............((((((((.((.....))....))))))))((((-((---(-((((.....)))))).))))).........((((.(((((........))-).)).)))) ( -22.90)
>DroAna_CAF1 38759 96 - 1
G--GUAUCAUGUCACUAAAUCAGCACAAAUUGCUCAACUGAUUUAUAAA-UUUU-UCUGGCCAAGUGCCAGCCCGAUAAUCUCAUUGCUUGCAGUUUCGA-----------------
.--......((((..((((((((..............))))))))....-....-.(((((.....)))))...)))).....((((....)))).....----------------- ( -15.44)
>DroPer_CAF1 47873 110 - 1
G--GUAUCAUGUCACUAAAUCAGCACAAAUUGCUCAACUGAUUUAUAAAAUUUCGU-UGGCCAAAUGCCAGCGAUAUAAUCGCAUUGCUUGUAGCUUUGGCCAGC---A-CCCCAGC
(--((..........((((((((..............)))))))).........((-(((((((((((.((((((........)))))).)))..))))))))))---)-))..... ( -31.14)
>consensus
C__GUAUCAUGUCACUAAAUCAGCACAAAUUGCUCAACUGAUUUAUAAA_UU___U_UGGCCAAAUGCCAGCGAUAUAAUCUCAUUGCUUGUAGCUUUGGUCACC___CACUCC___
...............((((((((..............))))))))............(((((((((((.((((((........)))))).)))..)))))))).............. (-14.20 = -15.46 +   1.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,052,308 – 2,052,401
Length 93
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 74.71
Mean single sequence MFE -23.80
Consensus MFE -13.50
Energy contribution -13.92
Covariance contribution 0.42
Combinations/Pair 1.05
Mean z-score -1.74
Structure conservation index 0.57
SVM decision value 0.77
SVM RNA-class probability 0.845858
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2052308 93 + 20766785
AUUACAUCGCUGGCACUCGGCCA-AGAAAUUUAUAAAUCAGUUGAGCAAUUUGUGCUGAUUUAGUGACAUGAUAC--CA--CAGUCGAAGCCA----GUGGA-------------
......((((((((..(((((..-.........(((((((((.((....))...)))))))))(((.........--))--).))))).))))----)))).------------- ( -29.90)
>DroVir_CAF1 18271 100 + 1
AUUAUAUCUCUGGCAUUUGGCCA-G--AAUUUAUAAAUCAGUGGAACAAUUUGUGCUGAUUUAGUGACAUGAUAC--GA--A--U-GGAGCCAACUAAAGGA----CAACAGG-A
.(..((((((((((.....))))-)--).....((((((((((.((....)).)))))))))).......)))).--.)--.--(-(..(((.......)).----)..))..-. ( -22.80)
>DroGri_CAF1 114927 106 + 1
AUUAUAUCGCUGGCAUUUGGCCA-A--AUUUUAUAAAUCAGUAGAACAAUUUGUGCUGAUUUAGUGACAUGAUACAGGA--A--U-GGAGCCAACUAAGGGAACAACAACAGG-A
(((((.((((((((.....))))-.--......((((((((((.((....)).)))))))))))))).)))))......--.--(-(...((.......))..))........-. ( -23.30)
>DroYak_CAF1 39823 90 + 1
-----GUCGCUGGCACUCGGCCA-AGAAAUUUAUAAAUCAGUUGAGCAAUUUGUGCUGAUUUAGUGACAUGAUAC--CACACAGACGAAACCA----GAGGA-------------
-----(((((((((.....))))-.........(((((((((.((....))...)))))))))))))).......--................----.....------------- ( -21.50)
>DroMoj_CAF1 63045 101 + 1
AUUAAAUCUCUGGCAUUUAGCCA-G--AAUUUAUAAAUCAGUUGAACAAUUUGUGCUGAUUUAGUGACAUGAUAC--GA--A--U-GGAGCCAACUAAAGGA----CAGUAGCCA
..(((((.((((((.....))))-)--))))))(((((((((...((.....)))))))))))((..(((.....--..--)--)-)..))........((.----(....))). ( -22.70)
>DroAna_CAF1 38779 90 + 1
AUUAUCGGGCUGGCACUUGGCCAGAAAAAUUUAUAAAUCAGUUGAGCAAUUUGUGCUGAUUUAGUGACAUGAUAC--CA--CAUUCGAAGCCA----G-----------------
.......(((((((.....))).(((.......(((((((((.((....))...)))))))))(((.........--))--).)))..)))).----.----------------- ( -22.60)
>consensus
AUUAUAUCGCUGGCACUUGGCCA_A__AAUUUAUAAAUCAGUUGAACAAUUUGUGCUGAUUUAGUGACAUGAUAC__CA__A__U_GAAGCCA____AAGGA_____________
......((((((((.....))))..........(((((((((...((.....)))))))))))))))................................................ (-13.50 = -13.92 +   0.42)

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 09:35:07 2006