Locus 6563

Sequence ID	3L_DroMel_CAF1
Location	17,377,911 – 17,378,024
Length	113
Max. P	0.615188

overview

Window 4

Location	17,377,911 – 17,378,024
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	86.82
Mean single sequence MFE	-29.61
Consensus MFE	-19.29
Energy contribution	-20.93
Covariance contribution	1.64
Combinations/Pair	1.04
Mean z-score	-1.98
Structure conservation index	0.65
SVM decision value	-0.02
SVM RNA-class probability	0.524522
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17377911 113 + 23771897
CACUUGAUAAAGGUUCUGACGAGGGCAGCAUACAUAUAAAUAUGUAUAGUGACUAUACUAUCCUAUAUAUAGAAAUGCCGGUGGUGCCACCAGCCGCCAACUUCAUCGCCACC
...........(((..(((.(..(((.((...........(((((((((.((........)))))))))))........((((....)))).)).)))..).)))..)))... ( -30.10)
>DroSec_CAF1 4824 111 + 1
CACUUGAUAAAGGUUCUGACGAGGGCAGCAUACAUACAAAUAUGUAUAGGGAG--UACUAUCCUAUAUAUAGAAAUGCCGGUGCUGCCACCAGCCACCAACUUCAUCGCCACC
....(((....(((.(((.....((((((((.........(((((((((((..--.....))))))))))).........))))))))..)))..)))....)))........ ( -31.37)
>DroSim_CAF1 4529 111 + 1
CACUUGAUAAAGGUUCUGACGAGGGCAGCAUACAUAUAAAUAUGUACAGUGAG--UACUAUCCUAUAUAUAGAAAUGCCGGUGGUGCCACCAGCCACCAACUUCGUCGCCACC
...........(((..(((((((((((...((.(((((.(((.((((.....)--))))))..))))).))....))))((((((.......))))))...)))))))..))) ( -32.80)
>DroEre_CAF1 4935 101 + 1
CACUUGAUAAAGGUUCUGACGAGGGCAGCAUGUAC------UCGUAUAGUGAG--UACUAUCCUAUAUAUAGACAUGCCGGUGGUGCCACCAG----CAACUUCAACGCCACC
...........(((..(((.(...((.((((((..------..((((((.((.--.....))))))))....)))))).((((....)))).)----)..).)))..)))... ( -29.00)
>DroYak_CAF1 5807 95 + 1
CACUUGAUAAAGGUUCUGACGAGGGCAGCAUA------------UAUAGUGAG--UACUAUCCUAUAUAUAGAAAUGGCGGUGGUGCCACCAG----CAACUUCAACGCCACC
..((((.((.......)).))))(((...(((------------(((((.((.--.....)))))))))).(((...((((((....)))).)----)...)))...)))... ( -24.80)
>consensus
CACUUGAUAAAGGUUCUGACGAGGGCAGCAUACAUA_AAAUAUGUAUAGUGAG__UACUAUCCUAUAUAUAGAAAUGCCGGUGGUGCCACCAGCC_CCAACUUCAUCGCCACC
...........(((..(((.(..((((.............(((((((((.((........)))))))))))....))))((((....)))).........).)))..)))... (-19.29 = -20.93 +   1.64)

alignment

secondary structure

dotplot

Window 5

Location	17,377,911 – 17,378,024
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	86.82
Mean single sequence MFE	-34.12
Consensus MFE	-22.52
Energy contribution	-23.16
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.10
Structure conservation index	0.66
SVM decision value	0.17
SVM RNA-class probability	0.615188
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17377911 113 - 23771897
GGUGGCGAUGAAGUUGGCGGCUGGUGGCACCACCGGCAUUUCUAUAUAUAGGAUAGUAUAGUCACUAUACAUAUUUAUAUGUAUGCUGCCCUCGUCAGAACCUUUAUCAAGUG
(((...(((((.(..(((((((((((....))))))).....(((((((((.(((((((((...)))))).))))))))))))))))..).)))))...)))........... ( -37.40)
>DroSec_CAF1 4824 111 - 1
GGUGGCGAUGAAGUUGGUGGCUGGUGGCAGCACCGGCAUUUCUAUAUAUAGGAUAGUA--CUCCCUAUACAUAUUUGUAUGUAUGCUGCCCUCGUCAGAACCUUUAUCAAGUG
......(((((((.(..((((.((.(((((((...((((...(((.((((((......--...)))))).))).....)))).))))))))).))))..).)))))))..... ( -35.30)
>DroSim_CAF1 4529 111 - 1
GGUGGCGACGAAGUUGGUGGCUGGUGGCACCACCGGCAUUUCUAUAUAUAGGAUAGUA--CUCACUGUACAUAUUUAUAUGUAUGCUGCCCUCGUCAGAACCUUUAUCAAGUG
(((...(((((.(..(((.(((((((....))))))).....(((((((((.((((((--(.....)))).)))))))))))).)))..).)))))...)))........... ( -36.50)
>DroEre_CAF1 4935 101 - 1
GGUGGCGUUGAAGUUG----CUGGUGGCACCACCGGCAUGUCUAUAUAUAGGAUAGUA--CUCACUAUACGA------GUACAUGCUGCCCUCGUCAGAACCUUUAUCAAGUG
((..((((......((----((((((....))))))))(((((.......)))))(((--(((.......))------))))))))..))....................... ( -33.60)
>DroYak_CAF1 5807 95 - 1
GGUGGCGUUGAAGUUG----CUGGUGGCACCACCGCCAUUUCUAUAUAUAGGAUAGUA--CUCACUAUA------------UAUGCUGCCCUCGUCAGAACCUUUAUCAAGUG
((..((...(((((.(----(.((((....)))))).))))).((((((((((.....--.)).)))))------------)))))..))....................... ( -27.80)
>consensus
GGUGGCGAUGAAGUUGG_GGCUGGUGGCACCACCGGCAUUUCUAUAUAUAGGAUAGUA__CUCACUAUACAUAUUU_UAUGUAUGCUGCCCUCGUCAGAACCUUUAUCAAGUG
((..(((..(((((.....(((((((....))))))))))))....(((((((........)).)))))..............)))..))....................... (-22.52 = -23.16 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:26 2006