Locus 6225

Sequence ID	3L_DroMel_CAF1
Location	16,536,020 – 16,536,227
Length	207
Max. P	0.995911

overview

Window 7

Location	16,536,020 – 16,536,127
Length	107
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	82.82
Mean single sequence MFE	-28.16
Consensus MFE	-18.38
Energy contribution	-18.22
Covariance contribution	-0.16
Combinations/Pair	1.15
Mean z-score	-1.78
Structure conservation index	0.65
SVM decision value	0.14
SVM RNA-class probability	0.602303
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16536020 107 + 23771897
CCAUCUCUACUGGCCAAAUGCUUACAUAUUUGUUUGUUUGCUUUUCCCUAGGUAGUUAGUUGGCCCACAUAAUGGGCCGAAA-----CUCACCCACGCCCCUCAGGUAGCAA-
......((((((((.....((..(((........)))..)).........(((((((..((((((((.....))))))))))-----)).)))...))).....)))))...- ( -29.00)
>DroSec_CAF1 148988 108 + 1
CCAUCUCUUCUGGCCAAAUGCUUACAUAUUGGUUUGUUUGUUUUUACCUAGGUA----GUUGGCCCACAUAAUGGGCCGAGACUCGACUCACCCACGCUCCUCAUGUAGCAA-
(((.......))).....((((.((((...(((..(......)..))).(((.(----((.((((((.....))))))(((......)))......)))))).)))))))).- ( -26.00)
>DroSim_CAF1 152400 108 + 1
CCAUCUCUUCUGGCCAAAUGCUUACAUAUUGGUUUGUUUGUUUUUACCUAGGUA----GUUGGCCCAGAUAAUGGGCCGAGACUCGACUCACCCACGCUCCUCAUGUAGCAA-
........(((((((((.((((((......(((..(......)..)))))))))----.)))).)))))...((((..(((......))).)))).(((.(....).)))..- ( -27.40)
>DroEre_CAF1 146994 96 + 1
GCCUCUCUUUUGGCCAAAUGC--------UUGUUUGUUUGUUUUUUCCUAGGUA----GUUGGCCCACAUAAUGGGCCGACA-----CUCGCCCACGCCCCUCAGGUAGCAAA
(((........)))(((((..--------..)))))((((((....((((((..----(((((((((.....))))))))).-----...((....)).))).))).)))))) ( -30.40)
>DroYak_CAF1 150118 95 + 1
GCCUCUCUUUUGGCCAAAUAU--------UUGUUUGUUUGUUUUUUCAUAGGUA----GUUGGCCCACAUAAUGGGCCGGGA-----CUCACCCACGCCGCUCAGGUAGCAA-
(((........)))((((((.--------.....))))))..........(((.----...((((((.....))))))(((.-----....)))..)))(((.....)))..- ( -28.00)
>consensus
CCAUCUCUUCUGGCCAAAUGCUUACAUAUUUGUUUGUUUGUUUUUACCUAGGUA____GUUGGCCCACAUAAUGGGCCGAGA_____CUCACCCACGCCCCUCAGGUAGCAA_
...........((((((((............)))))..............(((........((((((.....))))))(((......))))))...))).............. (-18.38 = -18.22 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	16,536,127 – 16,536,227
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	89.29
Mean single sequence MFE	-28.26
Consensus MFE	-23.70
Energy contribution	-22.86
Covariance contribution	-0.84
Combinations/Pair	1.26
Mean z-score	-2.50
Structure conservation index	0.84
SVM decision value	2.63
SVM RNA-class probability	0.995911
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16536127 100 - 23771897
AAUAUUUGGAUUUUUUUGUGGUGUUUAGCCCUAGGAAAUAUUCGGAAUUCCCGCGAGUUUUUGCCGCUCGAAUAUGUCGACGGCUUCAAUACUUGUCAUU
....((((((((((((((.(((.....))).))))))).)))))))......((((((....((((.((((.....))))))))......)))))).... ( -25.90)
>DroSec_CAF1 149096 99 - 1
AAAAUCUGAAUU-UUCCGUGGGUUUCAGCCCUAGAAAAUAUUUGGAAUUCCCUCGAGUUUUUGCCGCUCGAAUGUGUCGACGGCUUCAAUACUUGUCAUU
....((..((((-(((...((((....))))..))))..)))..)).......(((((....((((.((((.....))))))))......)))))..... ( -25.70)
>DroSim_CAF1 152508 99 - 1
AAAAUCUGAAUU-UUCCGUGGGUUUCAGCCCUAGAAAAUAUUUGGAAUUCCCUCGAGUUCUUGCCGCUCGAAUGUGUCGACGGCUUCAAUACUUGUCAUU
....((..((((-(((...((((....))))..))))..)))..)).......(((((....((((.((((.....))))))))......)))))..... ( -25.70)
>DroEre_CAF1 147090 95 - 1
--AAUCUGGAUU-UUC--UGGGGCUCAGCCCUAGAAAAUAUUCGGAAUUCCCGCGAGUUUUUGCUGCUUGAAUAUGUCGACGGCUUCAAUACUUGUCAUU
--..((((((((-(((--((((((...))))))))))..)))))))......((((((....((((.((((.....))))))))......)))))).... ( -32.00)
>DroYak_CAF1 150213 95 - 1
--AAUCUGGAUU-UUC--UGGGGCUCAGCCCUAGAAAAUAUUCGGAAUUCCCGCGAGUUUUUGCUGCUUGAAUAUGUCGACGGCUUCAAUACUUGUCAUU
--..((((((((-(((--((((((...))))))))))..)))))))......((((((....((((.((((.....))))))))......)))))).... ( -32.00)
>consensus
AAAAUCUGGAUU_UUC_GUGGGGUUCAGCCCUAGAAAAUAUUCGGAAUUCCCGCGAGUUUUUGCCGCUCGAAUAUGUCGACGGCUUCAAUACUUGUCAUU
....(((((((..(((...(((......)))..)))...)))))))......((((((....((((.((((.....))))))))......)))))).... (-23.70 = -22.86 +  -0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:10 2006