Locus 4035

Sequence ID	2R_DroMel_CAF1
Location	13,325,132 – 13,325,227
Length	95
Max. P	0.981394

overview

Window 3

Location	13,325,132 – 13,325,227
Length	95
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	89.24
Mean single sequence MFE	-26.91
Consensus MFE	-23.21
Energy contribution	-22.97
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-2.00
Structure conservation index	0.86
SVM decision value	1.89
SVM RNA-class probability	0.981394
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13325132 95 + 20766785
UUUGUCAUUUGCAUUUCUCAUGCAUUUGAAUUAACCGCUCUUGCCG--CGCGCAUUUUACUGUUAAUUAUUGCGAUAGGCCAA---------CCGGCAACGGCAGC--------
....(((..(((((.....)))))..))).......(((.(((((.--..((((................))))...((....---------))))))).)))...-------- ( -24.49)
>DroPse_CAF1 22661 106 + 1
UUUGUCAUUUGCAUUUCUCAUGCAUUUGAAUUAACCGCUUUUGCCGGGCGCGCAUUUUACUGUUAAUUAUUGCGAUAGGCCAACAUCGUCAACCGGCAACAGCAGC--------
....(((..(((((.....)))))..))).......(((.(((((((...((((................))))...(((.......)))..))))))).)))...-------- ( -30.19)
>DroSim_CAF1 25850 95 + 1
UUUGUCAUUUGCAUUUCUCAUGCAUUUGAAUUAACCGCUCUUGCCG--CGCGCAUUUUACUGUUAAUUAUUGCGAUAGGCCAA---------CCGGCAACGGCAGC--------
....(((..(((((.....)))))..))).......(((.(((((.--..((((................))))...((....---------))))))).)))...-------- ( -24.49)
>DroEre_CAF1 25251 103 + 1
UUUGUCAUUUGCAUUUCUCAUGCAUUUGAAUUAACCGCUCUUGCCG--CGCGCAUUUUACUGUUAAUUAUUGCGAUAGGCCAA---------CCGGCAACGGCUGCAACAUUGC
....(((..(((((.....)))))..))).......((....(((.--..((((................))))...)))...---------(((....)))..))........ ( -25.19)
>DroPer_CAF1 22793 106 + 1
UUUGUCAUUUGCAUUUCUCAUGCAUUUGAAUUAACCGCUUUUGCCGGGCGCGCAUUUUACUGUUAAUUAUUGCGAUAGGCCAACAUCGUCAACCGGCAACAGCAGC--------
....(((..(((((.....)))))..))).......(((.(((((((...((((................))))...(((.......)))..))))))).)))...-------- ( -30.19)
>consensus
UUUGUCAUUUGCAUUUCUCAUGCAUUUGAAUUAACCGCUCUUGCCG__CGCGCAUUUUACUGUUAAUUAUUGCGAUAGGCCAA_________CCGGCAACGGCAGC________
....(((..(((((.....)))))..))).......(((.(((((.....((((................))))...((.............))))))).)))........... (-23.21 = -22.97 +  -0.24)

alignment

secondary structure

dotplot

Window 4

Location	13,325,132 – 13,325,227
Length	95
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	89.24
Mean single sequence MFE	-27.39
Consensus MFE	-21.64
Energy contribution	-21.84
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.79
SVM decision value	0.46
SVM RNA-class probability	0.745293
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13325132 95 - 20766785
--------GCUGCCGUUGCCGG---------UUGGCCUAUCGCAAUAAUUAACAGUAAAAUGCGCG--CGGCAAGAGCGGUUAAUUCAAAUGCAUGAGAAAUGCAAAUGACAAA
--------(((((..(((((((---------....))...((((................))))..--.)))))..)))))....(((..(((((.....)))))..))).... ( -24.39)
>DroPse_CAF1 22661 106 - 1
--------GCUGCUGUUGCCGGUUGACGAUGUUGGCCUAUCGCAAUAAUUAACAGUAAAAUGCGCGCCCGGCAAAAGCGGUUAAUUCAAAUGCAUGAGAAAUGCAAAUGACAAA
--------((((((.((((((((((.(((((......)))))))).........((.....))....))))))).))))))....(((..(((((.....)))))..))).... ( -31.50)
>DroSim_CAF1 25850 95 - 1
--------GCUGCCGUUGCCGG---------UUGGCCUAUCGCAAUAAUUAACAGUAAAAUGCGCG--CGGCAAGAGCGGUUAAUUCAAAUGCAUGAGAAAUGCAAAUGACAAA
--------(((((..(((((((---------....))...((((................))))..--.)))))..)))))....(((..(((((.....)))))..))).... ( -24.39)
>DroEre_CAF1 25251 103 - 1
GCAAUGUUGCAGCCGUUGCCGG---------UUGGCCUAUCGCAAUAAUUAACAGUAAAAUGCGCG--CGGCAAGAGCGGUUAAUUCAAAUGCAUGAGAAAUGCAAAUGACAAA
(((....)))((((((((((((---------....))...((((................))))..--.))))...))))))...(((..(((((.....)))))..))).... ( -25.19)
>DroPer_CAF1 22793 106 - 1
--------GCUGCUGUUGCCGGUUGACGAUGUUGGCCUAUCGCAAUAAUUAACAGUAAAAUGCGCGCCCGGCAAAAGCGGUUAAUUCAAAUGCAUGAGAAAUGCAAAUGACAAA
--------((((((.((((((((((.(((((......)))))))).........((.....))....))))))).))))))....(((..(((((.....)))))..))).... ( -31.50)
>consensus
________GCUGCCGUUGCCGG_________UUGGCCUAUCGCAAUAAUUAACAGUAAAAUGCGCG__CGGCAAGAGCGGUUAAUUCAAAUGCAUGAGAAAUGCAAAUGACAAA
........(((((..((((((.............((.....))...........((.....)).....))))))..)))))....(((..(((((.....)))))..))).... (-21.64 = -21.84 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:08 2006