Locus 8266

Sequence ID	3L_DroMel_CAF1
Location	21,717,753 – 21,717,913
Length	160
Max. P	0.940283

overview

Window 4

Location	21,717,753 – 21,717,873
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.93
Mean single sequence MFE	-18.92
Consensus MFE	-10.82
Energy contribution	-10.83
Covariance contribution	0.00
Combinations/Pair	1.12
Mean z-score	-1.99
Structure conservation index	0.57
SVM decision value	0.00
SVM RNA-class probability	0.535085
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21717753 120 + 23771897
CAGCCCAGUCCACCCACUCCUACUCCUACUGCAGAGGCUGUCAUUGAAUUUUAAUUUAAUCCAAUGCAAGUCGAAUGCAAACAAAAAAUUGCAUCUGACUCUAUUACAAUGCAAAGACAA
.((((((((..................))))....))))((((((((((....)))))))....(((((((((.((((((........)))))).))))).........))))..))).. ( -22.57)
>DroPse_CAF1 26114 108 + 1
------GCUCCUCCUUCUCCUGCU------UCUGCUGCUGUCAUUGAAUUUUAAUUUAAUUCAAUUCAAGCCAAAAACAAACACAAAAUUGCAUCUGACUCUAUUACAAUGGCAAGACAA
------...............((.------...))...((((((((((((.......))))))))....((((....................................))))..)))). ( -12.72)
>DroSim_CAF1 3963 120 + 1
CAGCCCAGUCCACCCACUCCUACUCCUACUGCAGAGGCUGUCAUUGAAUUUUAAUUUAAUCCAAUGCAAGCCAAAUGCAAACAAAAAAUUGCAUCUGACUCUAUUACAAUGCAAAGACAA
.......(((...................((((..((((..(((((.(((.......))).)))))..))))...)))).........((((((.((.........)))))))).))).. ( -22.00)
>DroYak_CAF1 50420 108 + 1
------------ACUACUUCCACUCCUACUCCAGAGGCUGUCAUUGAAUUUUAAUUUAAUCCAAUGCAAGCCAAAUGCAAACAAAAAAUUGCAUCUGACUCUAUUACAAUGCAAAGACGA
------------...................((((((((..(((((.(((.......))).)))))..))))...(((((........)))))))))....................... ( -18.40)
>consensus
______AGUCCACCCACUCCUACUCCUACUGCAGAGGCUGUCAUUGAAUUUUAAUUUAAUCCAAUGCAAGCCAAAUGCAAACAAAAAAUUGCAUCUGACUCUAUUACAAUGCAAAGACAA
......................................(((((((((((....)))))))....((((((.((.((((((........)))))).)).)).........))))..)))). (-10.82 = -10.83 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	21,717,753 – 21,717,873
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.93
Mean single sequence MFE	-31.32
Consensus MFE	-22.61
Energy contribution	-22.55
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-2.19
Structure conservation index	0.72
SVM decision value	1.29
SVM RNA-class probability	0.940283
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21717753 120 - 23771897
UUGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUCGACUUGCAUUGGAUUAAAUUAAAAUUCAAUGACAGCCUCUGCAGUAGGAGUAGGAGUGGGUGGACUGGGCUG
..((((.(.((((((....(((((..((((((........))))))..))))).(((((((((.......)))))))))))..(((((.(....).)).))))))).).))))....... ( -32.40)
>DroPse_CAF1 26114 108 - 1
UUGUCUUGCCAUUGUAAUAGAGUCAGAUGCAAUUUUGUGUUUGUUUUUGGCUUGAAUUGAAUUAAAUUAAAAUUCAAUGACAGCAGCAGA------AGCAGGAGAAGGAGGAGC------
((.((((((..((((..(((((.((((((((....)))))))).)))))(((...((((((((.......))))))))...))).)))).------.)))))).))........------ ( -27.70)
>DroSim_CAF1 3963 120 - 1
UUGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUUGGCUUGCAUUGGAUUAAAUUAAAAUUCAAUGACAGCCUCUGCAGUAGGAGUAGGAGUGGGUGGACUGGGCUG
..((((.(.((((((....(((((((((((((........))))))))))))).(((((((((.......)))))))))))..(((((.(....).)).))))))).).))))....... ( -35.40)
>DroYak_CAF1 50420 108 - 1
UCGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUUGGCUUGCAUUGGAUUAAAUUAAAAUUCAAUGACAGCCUCUGGAGUAGGAGUGGAAGUAGU------------
......((((.((((....(((((((((((((........))))))))))))).(((((((((.......)))))))))))))(((((......)))).)...)))).------------ ( -29.80)
>consensus
UUGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUUGGCUUGCAUUGGAUUAAAUUAAAAUUCAAUGACAGCCUCUGCAGUAGGAGUAGGAGUAGGUGGACU______
..(((..............(((((((((((((........)))))))))))))..((((((((.......)))))))))))....................................... (-22.61 = -22.55 +  -0.06)

alignment

secondary structure

dotplot

Window 6

Location	21,717,793 – 21,717,913
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.67
Mean single sequence MFE	-26.78
Consensus MFE	-22.44
Energy contribution	-23.04
Covariance contribution	0.60
Combinations/Pair	1.15
Mean z-score	-1.76
Structure conservation index	0.84
SVM decision value	1.27
SVM RNA-class probability	0.938761
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21717793 120 - 23771897
UAAAAAAAUGUUCCCAGCUUUUUAUUAUCACCGGGCGAUCUUGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUCGACUUGCAUUGGAUUAAAUUAAAAUUCAAUGA
((((((..((....))..)))))).(((.((...((((........))))...)).)))(((((..((((((........))))))..))))).(((((((((.......))))))))). ( -26.10)
>DroPse_CAF1 26142 120 - 1
UACCAAAAUUUUCCCAGCUUUUUAUUAUCGCCGGGUGAUCUUGUCUUGCCAUUGUAAUAGAGUCAGAUGCAAUUUUGUGUUUGUUUUUGGCUUGAAUUGAAUUAAAUUAAAAUUCAAUGA
...(((.(((..(((.((...........)).))).))).)))((..((((....((((((..((((......))))..))))))..))))..))((((((((.......)))))))).. ( -24.10)
>DroSim_CAF1 4003 120 - 1
UAAAAAAAUGUUCCCAGCUUUUUAUUAUCACCGGGCGAUCUUGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUUGGCUUGCAUUGGAUUAAAUUAAAAUUCAAUGA
((((((..((....))..)))))).(((.((...((((........))))...)).)))(((((((((((((........))))))))))))).(((((((((.......))))))))). ( -29.10)
>DroPer_CAF1 25257 120 - 1
UACCAAAAUUUUCCCAGCUUUUUAUUAUCGCCGGGUGAUCUUGUCUUGCCAUUGUAAUAGAGUCAGAUGCAAUUUUGUGUUUGUUUUUGGCUUGAAUUGAAUUAAAUUAAAAUUCAAUGA
...(((.(((..(((.((...........)).))).))).)))((..((((....((((((..((((......))))..))))))..))))..))((((((((.......)))))))).. ( -24.10)
>DroYak_CAF1 50448 120 - 1
UAAAAAAAUGUUCCCAGUUUUUUAUUAUCACCGGGCGAUCUCGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUUGGCUUGCAUUGGAUUAAAUUAAAAUUCAAUGA
(((((((.((....)).)))))))........(((((....))))).............(((((((((((((........))))))))))))).(((((((((.......))))))))). ( -30.50)
>consensus
UAAAAAAAUGUUCCCAGCUUUUUAUUAUCACCGGGCGAUCUUGUCUUUGCAUUGUAAUAGAGUCAGAUGCAAUUUUUUGUUUGCAUUUGGCUUGCAUUGGAUUAAAUUAAAAUUCAAUGA
............(((.((...........)).)))........................(((((((((((((........))))))))))))).(((((((((.......))))))))). (-22.44 = -23.04 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:53 2006