Locus 983

Sequence ID X_DroMel_CAF1
Location 2,849,903 – 2,850,033
Length 130
Max. P 0.968685
window1588 window1589 window1590 window1591

overview

Window 8

Location 2,849,903 – 2,849,999
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.47
Mean single sequence MFE -25.28
Consensus MFE -15.96
Energy contribution -16.52
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -1.89
Structure conservation index 0.63
SVM decision value 0.90
SVM RNA-class probability 0.878608
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2849903 96 + 22224390
----AGAAAUAAAAUCAAAGUGUUACACGACAAUCCGUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCCAGUUGAUGGCGCCA-----ACAUAUAG-------ACAG
----.......((((((.........(((......)))((((((.((...)).))))))...))))))(((((((.....))))))).-----........-------.... ( -29.40)
>DroGri_CAF1 351500 98 + 1
----AAAAAUAAAUUCAAAGUGUUACACGAUAAUUCGUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCCAGUUUACGGAAUAA-----UAUGAUAGU---CAAAG--
----........((((..........((((....))))((((((.((...)).))))))))))..((((((..((..(((.....)))-----..))...))---)))).-- ( -18.40)
>DroEre_CAF1 258390 103 + 1
----AGAAAUAAAAUCAAAGUGUUACACGACAAUCCGUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCCAGUUGAUGGCGCCA-----ACAUAUAGAGAAUAGAGAG
----.......((((((.........(((......)))((((((.((...)).))))))...))))))(((((((.....))))))).-----................... ( -29.40)
>DroMoj_CAF1 424860 102 + 1
----AAAAAUAAAUUCAAAGCGUUACACGACAAUUCGUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCCAGUUUAUGGCAUUAUACUAUAUGACAGA---CUUA---
----..........(((((.((((.(((((....))))((((((.((...)).))))))))))).))))).((((.....))))..................---....--- ( -21.80)
>DroAna_CAF1 383793 90 + 1
AAUAAGAAAUAAAAUCAAAGUGUUACACGACAAUUCGUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCCAGUUAAUGGCGCUA-----AG-----------------
...........((((((.........((((....))))((((((.((...)).))))))...))))))(((((((.....))))))).-----..----------------- ( -27.80)
>DroPer_CAF1 349134 102 + 1
AAGAAGAAAUAAAACCAAAGUGUUACACGACAAUUC--GCAGGUGUCAUUGAGAGUUGCAAAUGAUUUGGCGCCAGUUUAUGGCCUCA-----ACUGACAGU---UGGAGGG
..............((....((((....))))..((--.(((.((((((((((....((.((....)).))((((.....))))))))-----).))))).)---)))))). ( -24.90)
>consensus
____AGAAAUAAAAUCAAAGUGUUACACGACAAUUCGUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCCAGUUUAUGGCGCCA_____ACUGAUAG_______AG__
..............(((((.((((..(((......)))((((((.((...)).)))))).)))).))))).((((.....))))............................ (-15.96 = -16.52 +   0.56) 

alignment

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secondary structure

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Window 9

Location 2,849,903 – 2,849,999
Length 96
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.47
Mean single sequence MFE -21.87
Consensus MFE -14.72
Energy contribution -15.22
Covariance contribution 0.50
Combinations/Pair 1.19
Mean z-score -2.02
Structure conservation index 0.67
SVM decision value 1.23
SVM RNA-class probability 0.933821
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2849903 96 - 22224390
CUGU-------CUAUAUGU-----UGGCGCCAUCAACUGGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCACGGAUUGUCGUGUAACACUUUGAUUUUAUUUCU----
.(((-------..((...(-----((((((((.....)))))))))...))..))).(((.....)))...(((((((....)))))))...................---- ( -27.20)
>DroGri_CAF1 351500 98 - 1
--CUUUG---ACUAUCAUA-----UUAUUCCGUAAACUGGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCACGAAUUAUCGUGUAACACUUUGAAUUUAUUUUU----
--.....---.........-----......(((......))).......((((....(((.....)))...(((((((....))))))).......))))........---- ( -12.80)
>DroEre_CAF1 258390 103 - 1
CUCUCUAUUCUCUAUAUGU-----UGGCGCCAUCAACUGGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCACGGAUUGUCGUGUAACACUUUGAUUUUAUUUCU----
..................(-----((((((((.....)))))))))((((.......(((.....)))...(((((((....)))))))......)))).........---- ( -27.00)
>DroMoj_CAF1 424860 102 - 1
---UAAG---UCUGUCAUAUAGUAUAAUGCCAUAAACUGGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCACGAAUUGUCGUGUAACGCUUUGAAUUUAUUUUU----
---.(((---(.((((((..........((((.....))))...........(....).....))))))..(((((((....)))))))..)))).............---- ( -19.70)
>DroAna_CAF1 383793 90 - 1
-----------------CU-----UAGCGCCAUUAACUGGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCACGAAUUGUCGUGUAACACUUUGAUUUUAUUUCUUAUU
-----------------..-----..((((((.....)))))).((((((.......(((.....)))...(((((((....)))))))......))))))........... ( -23.90)
>DroPer_CAF1 349134 102 - 1
CCCUCCA---ACUGUCAGU-----UGAGGCCAUAAACUGGCGCCAAAUCAUUUGCAACUCUCAAUGACACCUGC--GAAUUGUCGUGUAACACUUUGGUUUUAUUUCUUCUU
....(((---(.(((((.(-----((((((((.....))))((.((....)).))....))))))))))...((--((....))))........)))).............. ( -20.60)
>consensus
__CU_______CUAUCAGU_____UGACGCCAUAAACUGGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCACGAAUUGUCGUGUAACACUUUGAUUUUAUUUCU____
...........................(((((.....)))))..((((((.......(((.....)))...(((((((....)))))))......))))))........... (-14.72 = -15.22 +   0.50) 

alignment

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secondary structure

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dotplot

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Window 0

Location 2,849,935 – 2,850,033
Length 98
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 80.78
Mean single sequence MFE -29.35
Consensus MFE -22.45
Energy contribution -22.45
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.76
SVM decision value 0.02
SVM RNA-class probability 0.546166
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2849935 98 + 22224390
GUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCC----AGUUGAUGGCGCCAACAUAUAG-------ACAGAUUCCAAGUGUCCCCCAGUCU-CCGAAAACCAAAA
.....(((......((((((.....(((..((((((((----(.....))))))))))))...(-------(((.........))))....)))))-).....))).... ( -29.50)
>DroSec_CAF1 237627 98 + 1
GUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCC----AAUUGAUGGCGCCAACAUAUAG-------AGAGAUUCCAAGUGUCCCCCAGUCAGUCGAAAACCGAA-
..((((((.((...)).))))))((.((((((((((((----(.....))))))))........-------.((.((.....)).))....))))).))..........- ( -29.10)
>DroEre_CAF1 258422 98 + 1
GUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCC----AGUUGAUGGCGCCAACAUAUAGAGAAUAGAGAGAAUCCAAG--UCGCCAAGUCU-CC-AAAGCU----
.....(((......(((((((((((..(((((((((((----(.....)))))))....(((.....)))....)))))....--))).)))))))-).-...)))---- ( -31.90)
>DroYak_CAF1 245484 90 + 1
GUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCCAGCCAGUUGAUGGCGCCAACAUAUAGC-----GAGAGAAUCCAAG--UCCCCAAGUCG-A------------
.(((((((.((...)).)))))))..(((((((((((((..(....).))))))).........(-----....)........--.....))))))-.------------ ( -26.90)
>consensus
GUGCAGGUGUCAUUGAGACUUGCGAAUGAUUUGGCGCC____AGUUGAUGGCGCCAACAUAUAG_______AGAGAAUCCAAG__UCCCCAAGUCU_CC_AAAACC____
.(((((((.((...)).))))))).(((..((((((((...........))))))))))).................................................. (-22.45 = -22.45 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 1

Location 2,849,935 – 2,850,033
Length 98
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -30.88
Consensus MFE -20.27
Energy contribution -20.77
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.66
SVM decision value 1.63
SVM RNA-class probability 0.968685
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2849935 98 - 22224390
UUUUGGUUUUCGG-AGACUGGGGGACACUUGGAAUCUGU-------CUAUAUGUUGGCGCCAUCAACU----GGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCAC
....(((.((..(-(((((.(.(((((..((((.....)-------)))..))(((((((((.....)----))))))))....))).).))))))...)).)))..... ( -32.80)
>DroSec_CAF1 237627 98 - 1
-UUCGGUUUUCGACUGACUGGGGGACACUUGGAAUCUCU-------CUAUAUGUUGGCGCCAUCAAUU----GGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCAC
-.((((((...)))))).((.((((((..((((.....)-------)))..)))((((((((.....)----)))))))............(((.....))).))).)). ( -30.80)
>DroEre_CAF1 258422 98 - 1
----AGCUUU-GG-AGACUUGGCGA--CUUGGAUUCUCUCUAUUCUCUAUAUGUUGGCGCCAUCAACU----GGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCAC
----......-.(-(((((((.(((--..((((.....))))...........(((((((((.....)----)))))))).....))))))))))).............. ( -32.50)
>DroYak_CAF1 245484 90 - 1
------------U-CGACUUGGGGA--CUUGGAUUCUCUC-----GCUAUAUGUUGGCGCCAUCAACUGGCUGGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCAC
------------.-.......((((--((((((.....))-----........(((((((((((....)).)))))))))........)))))))).............. ( -27.40)
>consensus
____GGUUUU_GG_AGACUGGGGGA__CUUGGAAUCUCU_______CUAUAUGUUGGCGCCAUCAACU____GGCGCCAAAUCAUUCGCAAGUCUCAAUGACACCUGCAC
.................(((((.....))))).....................((((((((...........)))))))).......(((.(((.....)))...))).. (-20.27 = -20.77 +   0.50) 

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 09:58:39 2006