Locus 4945

Sequence ID 3R_DroMel_CAF1
Location 13,015,847 – 13,015,973
Length 126
Max. P 0.805660
window8092 window8093

overview

Window 2

Location 13,015,847 – 13,015,937
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.96
Mean single sequence MFE -25.77
Consensus MFE -15.07
Energy contribution -14.77
Covariance contribution -0.30
Combinations/Pair 1.30
Mean z-score -2.12
Structure conservation index 0.58
SVM decision value 0.39
SVM RNA-class probability 0.716110
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13015847 90 - 27905053
----CCAGAAGCG--GUCGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGUAAUUCCACAAAUGGC-CCGGCAGAAACUUU----
----......(((--(((((((((((-....)))))))).(((..((((((.....))))))..))).............)))-)..)).........---- ( -23.70)
>DroSec_CAF1 35914 92 - 1
----CCAGAAGCGGGGUCGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCAAUUCCACAAAUGGC-CCGGCAGAAACUCU----
----......((.(((((((((((((-....))))))))...((((....((((.....))))..))))...........)))-)).)).........---- ( -31.90)
>DroSim_CAF1 28363 92 - 1
----CCAAAAGCGGGGUCGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCAAUUCCACAAAUGGC-CUGGCAGAAACUCU----
----......((.(((((((((((((-....))))))))...((((....((((.....))))..))))...........)))-)).)).........---- ( -30.30)
>DroEre_CAF1 36437 82 - 1
------------C--GAAGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCAAUUCCACAAAUGGC-CCGGCAGAAGCUCA----
------------.--((.((((((((-....))))))))))..((((((((.....))))))...(((....(((....))).-...)))...))...---- ( -23.00)
>DroYak_CAF1 37110 95 - 1
----CCAGGAGCG--GUCGUGUCCCCUCGGUCGUGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCAAUUCCACAAAUGGC-CCGGUAGAACCUCUCUCU
----...((((.(--((....((..((.((((((((....(((..((((((.....))))))..))).....))))....)))-).))..))))).)))).. ( -20.40)
>DroAna_CAF1 36731 92 - 1
CCUUCCAUGAAAA--UGCGUGUCCCU-CGAUGGGGGCACUCAUGCAAAAAUAAAAGAUUUUUAAAUGCAAUUUUAUAAAUGGCUCCGGCCAACAC-------
......((((((.--(((((((((((-....))))))))......((((((.....))))))....))).))))))...((((....))))....------- ( -25.30)
>consensus
____CCAGAAGCG__GUCGUGUCCCC_CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCAAUUCCACAAAUGGC_CCGGCAGAAACUCU____
..................((((((((.....))))))))......((((((.....))))))...(((....(((....))).....)))............ (-15.07 = -14.77 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,015,875 – 13,015,973
Length 98
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 76.41
Mean single sequence MFE -22.67
Consensus MFE -13.88
Energy contribution -13.97
Covariance contribution 0.08
Combinations/Pair 1.12
Mean z-score -1.61
Structure conservation index 0.61
SVM decision value 0.63
SVM RNA-class probability 0.805660
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13015875 98 - 27905053
CAGAACUCCCCCACUCAUCAGCCACC--CUCUGACCCC----CCAGAAGCG--GUCGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGUA
....................(((.(.--.((((.....----.)))).).)--)).((((((((-....)))))))).(((..((((((.....))))))..))).. ( -23.10)
>DroSec_CAF1 35942 100 - 1
CAGAACUCCCCCACUCAUCUGCCACC--CUCUGACCCC----CCAGAAGCGGGGUCGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCA
.((((.((....(((....(((....--....((((((----.(....).))))))((((((((-....))))))))....)))..)))....)).))))....... ( -29.10)
>DroSim_CAF1 28391 100 - 1
CAGAACUCCCCCACUCAUCUGCCACC--CUCUGACCCC----CCAAAAGCGGGGUCGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCA
.((((.((....(((....(((....--....((((((----.(....).))))))((((((((-....))))))))....)))..)))....)).))))....... ( -29.10)
>DroEre_CAF1 36465 77 - 1
CAGAACUCCCCCUCUCAGCUACC---------------------------C--GAAGUGUCCCC-CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCA
.................((....---------------------------.--((.((((((((-....))))))))))....((((((.....))))))....)). ( -18.20)
>DroYak_CAF1 37142 98 - 1
CAGAACUUCCCCUCCCAUCUACCGCC--CCCUCACCC-----CCAGGAGCG--GUCGUGUCCCCUCGGUCGUGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCA
.......................(((--.(((.....-----..))).(((--..((........))..)))))).....((((....((((.....))))..)))) ( -15.50)
>DroAna_CAF1 36757 100 - 1
CAGAGCACCUCU----AUCUGCCCCAAUUUUCGUCCCCCCUUCCAUGAAAA--UGCGUGUCCCU-CGAUGGGGGCACUCAUGCAAAAAUAAAAGAUUUUUAAAUGCA
....(((.....----((((((....((((((((..........)))))))--)))((((((((-....))))))))...............)))).......))). ( -21.00)
>consensus
CAGAACUCCCCCACUCAUCUGCCACC__CUCUGACCCC____CCAGAAGCG__GUCGUGUCCCC_CAAUGGGGGCACUCAUGCAAAAGUAAACGAUUUUUAAAUGCA
........................................................((((((((.....)))))))).(((..((((((.....))))))..))).. (-13.88 = -13.97 +   0.08)

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 11:42:41 2006