Locus 6672

Sequence ID	3L_DroMel_CAF1
Location	17,745,271 – 17,745,423
Length	152
Max. P	0.988290

overview

Window 9

Location	17,745,271 – 17,745,383
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	77.67
Mean single sequence MFE	-40.91
Consensus MFE	-21.92
Energy contribution	-24.30
Covariance contribution	2.38
Combinations/Pair	1.22
Mean z-score	-2.89
Structure conservation index	0.54
SVM decision value	2.11
SVM RNA-class probability	0.988290
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17745271 112 + 23771897
-AUCUCGUGUACGAGUGUGUGCUUAACCGCGAGUGCAAUUAUUACUUGCAAGUUGCAACAAACGGCAGCAGCCUGGGCAAACUUUCAAG-------AAUGCCCUAAUGGCUGCUGUUGAG
-..((((((...((((....))))...))))))(((((((..........))))))).....(((((((((((.(((((..((....))-------..)))))....))))))))))).. ( -44.20)
>DroPse_CAF1 24338 111 + 1
AGUCCCGAGCUC-UGAGUCUGCUCAACCGCCAGUGCAAUUAUUACUUGCAACUUGCAGCA----GCA-CAGUCGGGGCAAG-UUUCAAGCAGAAACAACGCUUUAAGGGCUCCGGCUG--
........((((-((((....)))....((.(((((((.......)))).))).)))).)----)).-((((((((((..(-((((.....)))))....((....))))))))))))-- ( -35.80)
>DroPer_CAF1 24102 111 + 1
AGUCCCGAGCUC-UGAGUCUGCUCAACCGCCAGUGCAAUUAUUACUUGCAAGUUGCAGCA----GCA-CAGGCGGGGCAAG-UUUCAAGCAGAAACAACGCUUUAAGGGCUCCGGCUG--
((.((.((((((-(((((.((((...(((((.((((.......(((....))).......----)))-).))))))))).(-((((.....)))))...))))..))))))).)))).-- ( -39.44)
>DroYak_CAF1 9487 112 + 1
-AUCUCGUGUACGAGUGUGUGCUUAACCGCGAGUGCAAUUAUUACUUGCAAGUUGCAACAAACGGCAGCAGCCUGGGCAAACUUUCAAG-------AAUGCCCUAAUGGCUGCUGUUGAA
-..((((((...((((....))))...))))))(((((((..........))))))).....(((((((((((.(((((..((....))-------..)))))....))))))))))).. ( -44.20)
>consensus
_AUCCCGAGCAC_AGAGUCUGCUCAACCGCCAGUGCAAUUAUUACUUGCAAGUUGCAACA____GCA_CAGCCGGGGCAAA_UUUCAAG_______AACGCCCUAAGGGCUCCGGCUG__
......((((((......))))))....(((..(((((.......)))))...)))........(((((((((.((((.....................))))....))))))))).... (-21.92 = -24.30 +   2.38)

alignment

secondary structure

dotplot

Window 0

Location	17,745,310 – 17,745,423
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	72.61
Mean single sequence MFE	-39.25
Consensus MFE	-20.67
Energy contribution	-20.30
Covariance contribution	-0.37
Combinations/Pair	1.27
Mean z-score	-2.36
Structure conservation index	0.53
SVM decision value	1.88
SVM RNA-class probability	0.981014
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17745310 113 + 23771897
AUUACUUGCAAGUUGCAACAAACGGCAGCAGCCUGGGCAAACUUUCAAG-------AAUGCCCUAAUGGCUGCUGUUGAGAGCAAGGAUUUGUGGUCCGAGUAGCCGGAAACCUGUAAUG
(((((((((.....))))....(((((((((((.(((((..((....))-------..)))))....)))))))))))......(((.(((.((((.......)))).))))))))))). ( -42.00)
>DroPse_CAF1 24377 108 + 1
AUUACUUGCAACUUGCAGCA----GCA-CAGUCGGGGCAAG-UUUCAAGCAGAAACAACGCUUUAAGGGCUCCGGCUG---GCCAAGUCUGGUUGUUACAUCAGC---GACCCCGUGAUG
(((((.....(((((.....----((.-((((((((((..(-((((.....)))))....((....))))))))))))---)))))))..(((((((.....)))---))))..))))). ( -36.40)
>DroPer_CAF1 24141 108 + 1
AUUACUUGCAAGUUGCAGCA----GCA-CAGGCGGGGCAAG-UUUCAAGCAGAAACAACGCUUUAAGGGCUCCGGCUG---GCCGAGUCUGGUUGUUACAUCAGC---GACCUCGUGAUG
.......((.....))((((----((.-((((((((((..(-((((.....)))))....((....)))))))((...---.))..))))))))))).(((((.(---(....))))))) ( -34.90)
>DroYak_CAF1 9526 113 + 1
AUUACUUGCAAGUUGCAACAAACGGCAGCAGCCUGGGCAAACUUUCAAG-------AAUGCCCUAAUGGCUGCUGUUGAAAGCAAGGAUUUGUGGCCCCAGCAGCCGGAAACCUGUAAUG
(((((((((.....))))....(((((((((((.(((((..((....))-------..)))))....)))))))))))......(((.(((.((((.......)))).))))))))))). ( -43.70)
>consensus
AUUACUUGCAAGUUGCAACA____GCA_CAGCCGGGGCAAA_UUUCAAG_______AACGCCCUAAGGGCUCCGGCUG___GCAAAGACUGGUGGUCACAGCAGC___AAACCCGUAAUG
(((((((((.....))))....((((.((((((.((((.....................))))....))))))(((.....)))...................)))).......))))). (-20.67 = -20.30 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:14 2006