Locus 4643

Sequence ID X_DroMel_CAF1
Location 12,139,003 – 12,139,143
Length 140
Max. P 0.973112
window7627 window7628

overview

Window 7

Location 12,139,003 – 12,139,116
Length 113
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 82.39
Mean single sequence MFE -31.48
Consensus MFE -22.94
Energy contribution -22.87
Covariance contribution -0.06
Combinations/Pair 1.26
Mean z-score -2.44
Structure conservation index 0.73
SVM decision value 1.71
SVM RNA-class probability 0.973112
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12139003 113 + 22224390
ACUCCCGUUUUUUUCUCUCGCGCGAUUUCUGUUCAUUUUUUCUC-CUCCUCUUCUUUUUUUGGCAUCCAGUGAAAAAGGGAAAAUGUUGGAAAAAAGCGACGAGAAAUUCGCGG
....((((...((((((((((..((.......)).((((((((.-......((((((((((.((.....)).))))))))))......)))))))))))).))))))...)))) ( -31.72)
>DroSec_CAF1 12187 111 + 1
AUG-CCGU-UUUUUCUCUCGCGCGAUUUCUGUUCAUUUUUUCCU-CCUCUUUCUUUUUUUUGGCAUCCAGUGAAAAAGGGAAAAUGUUGGAAAAAAGCGACGAGAAAUUCGCGG
...-((((-..((((((((((..((.......)).((((((((.-.(..(((((((((((((........)))))))))))))..)..)))))))))))).))))))...)))) ( -33.90)
>DroEre_CAF1 11839 98 + 1
AUC-CUGU-UUUUUCUCUCGCGCGAUUUGUA----UUUUUUCCC--CU-U-------UUUUGGCAUCCAGUGAAAAAGGGAGAAUGUGGGAAAAAAGCGACGAGAAAUUCGCGG
...-((((-..((((((((((....(((.((----(.(((((((--..-(-------((((.((.....)).)))))))))))).))).)))....)))).))))))...)))) ( -30.80)
>DroYak_CAF1 8684 107 + 1
AUU-CGGU-UUUUUCUCUCGAGCGAUUUGUA----CUUUUUUCCGCCU-UUUUUUGUUUUUGGCAUCCAGCGAGAAAGGGAAAAUGUUGGGAAAAAGCGACGAGAAAUUCGCGG
...-(((.-..(((((((((.((.....)).----((((((((((.(.-((((((.(((((.((.....)).))))).)))))).).))))))))))))).)))))).)))... ( -29.50)
>consensus
AUU_CCGU_UUUUUCUCUCGCGCGAUUUCUA____UUUUUUCCC_CCU_UUUUUUUUUUUUGGCAUCCAGUGAAAAAGGGAAAAUGUUGGAAAAAAGCGACGAGAAAUUCGCGG
....((((...((((((((((....((((((......(((((((............(((((.((.....)).))))))))))))...))))))...)))).))))))...)))) (-22.94 = -22.87 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,139,043 – 12,139,143
Length 100
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 86.68
Mean single sequence MFE -26.35
Consensus MFE -19.19
Energy contribution -20.00
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.94
Structure conservation index 0.73
SVM decision value 0.61
SVM RNA-class probability 0.799637
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12139043 100 + 22224390
UCUC-CUCCUCUUCUUUUUUUGGCAUCCAGUGAAAAAGGGAAAAUGUUGGAAAAAAGCGACGAGAAAUUCGCGGAAUUUUCGCUGCAGUCGCACAAAAAAA---
..((-(..(..((((((((((.((.....)).))))))))))...)..))).....((((((((...)))((((........)))).))))).........--- ( -25.60)
>DroSec_CAF1 12225 99 + 1
UCCU-CCUCUUUCUUUUUUUUGGCAUCCAGUGAAAAAGGGAAAAUGUUGGAAAAAAGCGACGAGAAAUUCGCGGAAUUUUCGCUGCAGUCGCACAAA-AAA---
....-........(((((((..((((((..(....)..)))...)))..)))))))((((((((...)))((((........)))).))))).....-...--- ( -25.70)
>DroEre_CAF1 11873 90 + 1
UCCC--CU-U-------UUUUGGCAUCCAGUGAAAAAGGGAGAAUGUGGGAAAAAAGCGACGAGAAAUUCGCGGAAUUUUCGCUGCAGUCGCACAAA-AAA---
((.(--((-(-------((((.((.....)).)))))))).)).((((.((....(((((....((((((...)))))))))))....)).))))..-...--- ( -26.60)
>DroYak_CAF1 8718 102 + 1
UUCCGCCU-UUUUUUGUUUUUGGCAUCCAGCGAGAAAGGGAAAAUGUUGGGAAAAAGCGACGAGAAAUUCGCGGAAUUUUCGCUGCAGUCGCACAAA-AAAAUG
(((((.(.-((((((.(((((.((.....)).))))).)))))).).)))))....((((((((...)))((((........)))).))))).....-...... ( -27.50)
>consensus
UCCC_CCU_UUUUUUUUUUUUGGCAUCCAGUGAAAAAGGGAAAAUGUUGGAAAAAAGCGACGAGAAAUUCGCGGAAUUUUCGCUGCAGUCGCACAAA_AAA___
..............((((((..((((((..........)))...)))..)))))).((((((((...)))((((........)))).)))))............ (-19.19 = -20.00 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:03 2006