Locus 408

Sequence ID	X_DroMel_CAF1
Location	1,186,961 – 1,187,222
Length	261
Max. P	0.876027

overview

Window 7

Location	1,186,961 – 1,187,071
Length	110
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	89.09
Mean single sequence MFE	-38.43
Consensus MFE	-33.17
Energy contribution	-32.73
Covariance contribution	-0.43
Combinations/Pair	1.17
Mean z-score	-2.35
Structure conservation index	0.86
SVM decision value	0.89
SVM RNA-class probability	0.876027
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1186961 110 + 22224390
CAUCGCCAUCUUUCUGCUUGCCACUCUCGGUGGUGACAUUUUCCACGCUCUGACGCCUUUCUUUCAGAGUCUCAUCUUGGCCACUCUGAAGGGACUGCAGAUAGGCGGCG
...((((..((.((((((..((((.....))))..)..........((......))..((((((((((((..(......)..))))))))))))..))))).))..)))) ( -38.90)
>DroSec_CAF1 22841 110 + 1
CAUCGCCAUCUUUCUGCUUACCACUCUCGGUGGUGACAUUUUCCACGCUUUGACGCCUUGCUUUCAGAGUCUCAUCUUGGCCACUCUGAAGGGACUGCAGAUAGGCGGCG
...((((..((.((((((((((((.....)))))))....((((..((......))......((((((((..(......)..))))))))))))..))))).))..)))) ( -38.30)
>DroEre_CAF1 22188 110 + 1
CCUCACCAUCCCUCUGCUUGCCACUCUCCGUGGUGACAUUUGCCACGCUCUGCCGCCUCGCCUUCAGGGUCUCGUCUUGCCCAUUCUGAAGGGACUGCAGGUAGGCGGCA
..................((((.......((((..(...)..))))((.(((((((.((.((((((((((........))))....))))))))..)).))))))))))) ( -38.10)
>consensus
CAUCGCCAUCUUUCUGCUUGCCACUCUCGGUGGUGACAUUUUCCACGCUCUGACGCCUUGCUUUCAGAGUCUCAUCUUGGCCACUCUGAAGGGACUGCAGAUAGGCGGCG
....(((..((.((((((((((((.....)))))))..........((......))....((((((((((............))))))))))....))))).))..))). (-33.17 = -32.73 +  -0.43)

alignment

secondary structure

dotplot

Window 8

Location	1,187,071 – 1,187,185
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.20
Mean single sequence MFE	-42.98
Consensus MFE	-31.61
Energy contribution	-30.92
Covariance contribution	-0.69
Combinations/Pair	1.27
Mean z-score	-1.60
Structure conservation index	0.74
SVM decision value	0.20
SVM RNA-class probability	0.628825
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1187071 114 + 22224390
UCUGGAUUGGGCCUUGGACUUGAUGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU------
....((((.(((....(((.....)))((((..((..(((((((..(((((.....)))))...((((((......)))))).))))))).))..))))..)))..))))....------ ( -39.90)
>DroSec_CAF1 22951 114 + 1
UCUGGAUUGGGCCUCGGACUCGACGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUUAGGCGCUGCAGCUCGCUGAGAUUGCUU------
(((((........)))))((((.((..((((..((..(((((((..(((((.....)))))...((((((......)))))).))))))).))..)))).)).)))).......------ ( -39.00)
>DroEre_CAF1 22298 114 + 1
UCUGGAUUGGGUAUCGCAGUUGACGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGAAGCUCGCUAAGAUUGCUU------
..(((((..(((((((((((.......))))))).))))..)))))(((((.....)))))...(((((.(((((.((..(((..((((...))))))))).))))))))))..------ ( -45.70)
>DroAna_CAF1 7583 114 + 1
UCCGGACUGGGCGUGGGAGU-GACCACCU-----UGACCUUGUCCAGGCUCACGUUGAGCUGCUGCAGCUCCUGGAGGUUACUGAUCAGACGCUGCAGUUCGCUCAGGUUGCCGCCACUG
...((((.((((((((....-..))))..-----.).))).)))).(((..((.((((((.((((((((..((((((....))..))))..))))))))..)))))))).)))....... ( -47.30)
>consensus
UCUGGAUUGGGCCUCGGACUUGACGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU______
...((((..((.........((....)).........))..)))).(((((.....)))))((((((((.(((((((....))..))))).))))))))..((.......))........ (-31.61 = -30.92 +  -0.69)

alignment

secondary structure

dotplot

Window 9

Location	1,187,111 – 1,187,222
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.10
Mean single sequence MFE	-41.12
Consensus MFE	-27.99
Energy contribution	-29.43
Covariance contribution	1.44
Combinations/Pair	1.20
Mean z-score	-1.60
Structure conservation index	0.68
SVM decision value	0.06
SVM RNA-class probability	0.562185
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1187111 111 + 22224390
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU---------UUGGAGUCAUCCCUUUUUUCCUUGGGUGCCUCGGGCU
(((((.(((((.....)))))((((((((.(((((((....))..))))).))))))))..((.......))..---------...(((.((.(((..........))))).)))))))) ( -37.30)
>DroSec_CAF1 22991 111 + 1
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUUAGGCGCUGCAGCUCGCUGAGAUUGCUU---------UUGGAGUCAUCCCUUUUUUCCUUGGGUGCCUCGGGCU
(((((((((((.((.((((((((.((...((.....))..(((.....))))).)))))))).)).))..))))---------...(((.((.(((..........))))).)))))))) ( -37.00)
>DroEre_CAF1 22338 111 + 1
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGAAGCUCGCUAAGAUUGCUU---------GUGGAGUCAUCCCGUUUUUUCUUGGCUGUCUCGGGCU
((((..(((((.....)))))...((((((......)))))).)))).(((.((((..(..(((((((..(..(---------(.(((....)))))..)..))))))).)..))))))) ( -36.70)
>DroAna_CAF1 7617 114 + 1
UGUCCAGGCUCACGUUGAGCUGCUGCAGCUCCUGGAGGUUACUGAUCAGACGCUGCAGUUCGCUCAGGUUGCCGCCACUGGCGGGGGAGUUCUCCCGCUUCUCCUUGGGCGUC------U
.((((((((..((.((((((.((((((((..((((((....))..))))..))))))))..)))))))).)))......((((((((....))))))))......)))))...------. ( -53.50)
>consensus
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU_________GUGGAGUCAUCCCGUUUUUCCUUGGGUGCCUCGGGCU
(((((.(((((.....)))))((((((((.(((((((....))..))))).))))))))..((.......))..............(((.(((((...........))))).)))))))) (-27.99 = -29.43 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:54 2006