Locus 5857

Sequence ID	3R_DroMel_CAF1
Location	15,350,136 – 15,350,262
Length	126
Max. P	0.867646

overview

Window 2

Location	15,350,136 – 15,350,229
Length	93
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	77.92
Mean single sequence MFE	-18.18
Consensus MFE	-11.74
Energy contribution	-11.85
Covariance contribution	0.11
Combinations/Pair	1.21
Mean z-score	-1.74
Structure conservation index	0.65
SVM decision value	0.86
SVM RNA-class probability	0.867646
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15350136 93 - 27905053
AUUUAAUUGCACUACAAGGUGCAAUUAGUGAAUAUUCACUUUAAAUAU--ACUGGACACGGACGGAAAAUGUAUUAUUAACACAUUGCAUUCAAA--------
...((((((((((....))))))))))((((....)))).........--.(((....)))..(((.(((((.........)))))...)))...-------- ( -18.20)
>DroVir_CAF1 126307 84 - 1
AAUUAAUUGCACUUCGCGGUGCAAUUAAUGAAAUUUG----------U--AUUCGACGCUGGUUGAAUGAAUGCAAGUGGC-------AUUUAAAUUUAUGGC
.((((((((((((....)))))))))))).(((((((----------(--(((((((....))))))))(((((.....))-------))))))))))..... ( -25.20)
>DroSec_CAF1 102976 93 - 1
AUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAGUCACUUUAAAUAU--ACUGGACACGGACGGAAAAUUUAUUAUUAACACAUAGCAUUCAAA--------
...((((((((((....))))))))))((((....))))..(((((..--.(((........)))...)))))......................-------- ( -16.40)
>DroSim_CAF1 106547 93 - 1
AUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAUUCACUUUAAAUAU--ACUGGACACGGACGGAAAAUUUAUUAUUAACACAUUGCAUUCAAA--------
...((((((((((....))))))))))((((....))))..(((((..--.(((........)))...)))))......................-------- ( -16.40)
>DroEre_CAF1 98938 93 - 1
GUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAUUAACUUUAAAAGU--ACUGGACACGGACGGAAAAUGUAUUAUUAACACAUUGCAUUCAAA--------
..(((((((((((....)))))))))))(((((.....)))))...((--.(((....)))))(((.(((((.........)))))...)))...-------- ( -18.20)
>DroYak_CAF1 129820 95 - 1
AUUUAAUUGCACUACAAGGUACAAUUAGUGAAGAUUCACUUUAAAUAUAGACUGGACACGGACAGAAAAUUUAUUAUUAACACCUUGCACUCAAA--------
..............((((((.....(((((((..(((.((........)).(((....)))...)))..))))))).....))))))........-------- ( -14.70)
>consensus
AUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAUUCACUUUAAAUAU__ACUGGACACGGACGGAAAAUUUAUUAUUAACACAUUGCAUUCAAA________
..(((((((((((....))))))))))).......................(((........)))...................................... (-11.74 = -11.85 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	15,350,162 – 15,350,262
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.87
Mean single sequence MFE	-23.67
Consensus MFE	-14.48
Energy contribution	-15.52
Covariance contribution	1.03
Combinations/Pair	1.19
Mean z-score	-1.80
Structure conservation index	0.61
SVM decision value	0.40
SVM RNA-class probability	0.721958
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15350162 100 - 27905053
---CGGCUGUAUU--UAUAUUCGCUUUUUUGAC-AUUCAAUUUAAUUGCACUACAAGGUGCAAUUAGUGAAUAUUCACUUUAAAUAU--ACUGGACACGGACGGAAAA
---...((((...--.((((((((....(((..-...)))..((((((((((....)))))))))))))))))).............--.(((....))))))).... ( -23.50)
>DroVir_CAF1 126334 94 - 1
CAGCGCCUUCACUUUAGUCAU--CGUCUUUAGCUUGUCAAAUUAAUUGCACUUCGCGGUGCAAUUAAUGAAAUUUG----------U--AUUCGACGCUGGUUGAAUG
............((((..((.--((((....((..((...((((((((((((....))))))))))))...))..)----------)--....)))).))..)))).. ( -24.40)
>DroSec_CAF1 103002 100 - 1
---CGGCUGUAUU--UGUAUUCGCUUUUUUGAC-AUUCAAUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAGUCACUUUAAAUAU--ACUGGACACGGACGGAAAA
---((.((((.((--(((((.........((((-.((((...((((((((((....)))))))))).))))..))))........))--)).))).)))).))..... ( -25.33)
>DroSim_CAF1 106573 100 - 1
---CGGCUGUAUU--UGUGUUCGCUUUUUUGAC-AUUCAAUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAUUCACUUUAAAUAU--ACUGGACACGGACGGAAAA
---...((((...--((((((((....(((((.-........((((((((((....))))))))))((((....)))).)))))...--..)))))))).)))).... ( -26.50)
>DroEre_CAF1 98964 100 - 1
---UGGCUGUAUU--UGUAUUCGCUUUUUUGAC-AUUCAGUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAUUAACUUUAAAAGU--ACUGGACACGGACGGAAAA
---...((((...--(((....((((((((((.-.((((..(((((((((((....)))))))))))))))..))))....))))))--.....)))...)))).... ( -23.60)
>DroYak_CAF1 129846 102 - 1
---UGGCUUUGUU--UGUAUUCGCUUUUUUGAC-AUUCAAUUUAAUUGCACUACAAGGUACAAUUAGUGAAGAUUCACUUUAAAUAUAGACUGGACACGGACAGAAAA
---....((((((--(((.(((.((..(((((.-........((((((.(((....))).))))))((((....)))).)))))...))...))).)))))))))... ( -18.70)
>consensus
___CGGCUGUAUU__UGUAUUCGCUUUUUUGAC_AUUCAAUUUAAUUGCACUACAAGGUGCAAUUAGUGAAGAUUCACUUUAAAUAU__ACUGGACACGGACGGAAAA
......((((.........(((((....((((....))))..((((((((((....)))))))))))))))...................(((....))))))).... (-14.48 = -15.52 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:22 2006