Locus 2704

Sequence ID	2L_DroMel_CAF1
Location	7,580,777 – 7,580,918
Length	141
Max. P	0.886990

overview

Window 8

Location	7,580,777 – 7,580,883
Length	106
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	80.61
Mean single sequence MFE	-25.77
Consensus MFE	-18.91
Energy contribution	-18.94
Covariance contribution	0.03
Combinations/Pair	1.14
Mean z-score	-2.04
Structure conservation index	0.73
SVM decision value	0.94
SVM RNA-class probability	0.886990
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7580777 106 + 22407834
CAGUGCCAAUCGAAAGAAGACAGCAAACUGACCGCAG----AGUAGAA----AAAA---AAACUAAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGGAAA-AAACUCUUG-GCU
....(((((((....))...(((....))).((((((----.((((..----....---.........)))).))))..(((((........)))))...))...-......)))-)). ( -26.46)
>DroSec_CAF1 80183 106 + 1
CAGUGCCAAUCGAAAGAAGACAGCAAACUGACCGCAG----AGUAGAA----A--A---AAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGGAAAAAAACUCUUGGGUU
((((((...((....))...(((....))).(((..(----(((....----.--.---..))))..(((((.......)))))..)))......))))))......((((....)))) ( -26.00)
>DroSim_CAF1 85217 104 + 1
CAGUGCCAAUCGAAAGAAGACAGCAAACUGACCGCAG----AGUAGAA----A--A---AAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGGAAA-AAACUCUUG-GUU
((((((...((....))...(((....))).(((..(----(((....----.--.---..))))..(((((.......)))))..)))......))))))....-.........-... ( -24.90)
>DroEre_CAF1 79894 103 + 1
CAGUGCCAAUCGAAAGAAGACAGCAAACUGACCGCGG----AGUAGAA----AAAACU------CGAGCUGCACUGCCCGCAGUCUCGGAUAACUGCACUGAGCA-AAACUCCAU-GCU
((((((...((....))...(((....))).((...(----(((....----...)))------)(((((((.......)))).)))))......))))))((((-........)-))) ( -29.50)
>DroYak_CAF1 82098 109 + 1
CAGUGCCAAUCGAAAGAAGACAGCAAACUGACCGCAG----AGCAGAA----AAAACUCAAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGAACG-AAACUCUUU-GCU
((((((...((....)).........((((...((((----.((((..----................)))).))))...))))...........))))))....-.........-... ( -25.97)
>DroAna_CAF1 76482 101 + 1
CAGUGCCAAUCGACAGAAGACAGCAGACUGACCGCAGUUGUAGUGAAAAAUAAAAACAAAAGUUAAAACUGCAC--------GUCUCAGAUGACUGCACUGAGGA-AAAU---------
((((((..(((....((.(((....(((((....)))))(((((.......................)))))..--------))))).)))....))))))....-....--------- ( -21.80)
>consensus
CAGUGCCAAUCGAAAGAAGACAGCAAACUGACCGCAG____AGUAGAA____AAAA___AAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGAAAA_AAACUCUUG_GCU
((((((...((....))..........((((..((((....((...................))....))))((((....)))).))))......)))))).................. (-18.91 = -18.94 +   0.03)

alignment

secondary structure

dotplot

Window 9

Location	7,580,814 – 7,580,918
Length	104
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	82.88
Mean single sequence MFE	-23.18
Consensus MFE	-17.14
Energy contribution	-16.90
Covariance contribution	-0.24
Combinations/Pair	1.24
Mean z-score	-1.58
Structure conservation index	0.74
SVM decision value	0.09
SVM RNA-class probability	0.576788
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7580814 104 + 22407834
AGUAGAAAAAA---AAACUAAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGGAAA-AAACUCUUG-GCUUUUCUAUGUGUUCUUAAAAAUCUGCUCAAG----UAACA
((((((.....---...(..(.(((((.......))))).)..).(((..((((((((((-(..(....)-..))))))).))))..)))....))))))....----..... ( -23.00)
>DroSec_CAF1 80220 104 + 1
AGUAGAAA--A---AAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGGAAAAAAACUCUUGGGUUUUUCUAUGUGUUUUUAAGAUUCUGCUCAAG----UUAAA
(((((((.--.---.........((((.......))))(((..((.....((((((((((((..(....)..)))))))).)))).))..))))))))))....----..... ( -25.20)
>DroSim_CAF1 85254 102 + 1
AGUAGAAA--A---AAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGGAAA-AAACUCUUG-GUUUUUCUGUGUGUUCUUAAAAUUCUGCUCAAG----UAAAA
(((((((.--.---...((.(.(((((.......))))).).)).(((..((((((((((-((.(....)-.)))))))).))))..)))...)))))))....----..... ( -21.70)
>DroEre_CAF1 79931 104 + 1
AGUAGAAAAAACU------CGAGCUGCACUGCCCGCAGUCUCGGAUAACUGCACUGAGCA-AAACUCCAU-GCUUGUCUAGGUGUUCUUAAAAUUCUGCUCA-GUUUUUUAUU
(((((((.....(------((((((((.......)))).))))).(((..((((((((((-........)-)))).....)))))..)))...)))))))..-.......... ( -26.90)
>DroYak_CAF1 82135 111 + 1
AGCAGAAAAAACUCAAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGAACG-AAACUCUUU-GCUUUUCUAUGUGUUCUUAAAAUUCUGCUCAAGAUGUUUAUG
(((((((..........((.(.(((((.......))))).).)).(((..((((.(((((-((....)))-)...)))...))))..)))...)))))))............. ( -19.10)
>consensus
AGUAGAAAAAA___AAACUCAAACUGCACUGCCCGCAGUCUCGGAUAACUGCACUGGAAA_AAACUCUUG_GCUUUUCUAUGUGUUCUUAAAAUUCUGCUCAAG____UUAAA
(((((((...............(((((.......)))))......(((..((((((((((..............)))))).))))..)))...)))))))............. (-17.14 = -16.90 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:06 2006