Locus 959

Sequence ID	2R_DroMel_CAF1
Location	4,104,626 – 4,104,742
Length	116
Max. P	0.692237

overview

Window 0

Location	4,104,626 – 4,104,742
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.47
Mean single sequence MFE	-27.86
Consensus MFE	-19.25
Energy contribution	-18.75
Covariance contribution	-0.50
Combinations/Pair	1.26
Mean z-score	-1.68
Structure conservation index	0.69
SVM decision value	0.23
SVM RNA-class probability	0.645677
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4104626 116 + 20766785
AUUUUUCCCCAUUGCUUCAGUUAUUUGCCUUUAUUCCUGGCUAGUGGCGUACUCUUUUUACGCCGCCUUAGGAGGACCUCUCUUCAUCUGAAUGUGAUCCAUUGCCAAGUA----AUAAA
...................((((((((.(.....((((((...((((((((.......)))))))).))))))(((..((.((((....))).).)))))...).))))))----))... ( -26.80)
>DroSec_CAF1 8784 116 + 1
AUUAUUUCCCAAUACUUUAGUUGUAUGCCUUUAUUUCUGGCUAGUGGCGUACUCCUUUUACGCCGCCUUGGGAGGACCUCUCUUCAUCUGAAUGCGAUCCUUUGCAAAGUA----AUAAA
....(((((((((((.......))))(((.........)))..((((((((.......))))))))..))))))).................(((((....))))).....----..... ( -29.10)
>DroSim_CAF1 12578 116 + 1
AUUAUUUCCCAAUACUUUAGUUGUAUGCAUUUAUUUCUGGCUAGUGGCGUACUCCUUUUACGCCGCCUUAGGAGGACCUCUCUUCAUCUGAAUGCGAUCCUUUGCAAAGUA----AUAAA
(((((((..((((((.......))))(((((((.......(((((((((((.......))))))))..)))(((((....)))))...))))))).......))..)))))----))... ( -27.50)
>DroYak_CAF1 1680 120 + 1
ACUGUUUUCGACUUCCUCAGUUAUAUGUCUAUAUUUCUGGCUGGUGGCAUACUCUUUUUACGCCGCCUUAGGAGGCCCGCUAUUCAUCUGAAGGGGAUCCUCUACCAAGAAGCUAUUGAA
......(((((......(((..((((....))))..)))(((((((((.............))))))...((((((((....(((....))).)))..))))).......)))..))))) ( -28.02)
>consensus
AUUAUUUCCCAAUACUUCAGUUAUAUGCCUUUAUUUCUGGCUAGUGGCGUACUCCUUUUACGCCGCCUUAGGAGGACCUCUCUUCAUCUGAAUGCGAUCCUUUGCAAAGUA____AUAAA
............(((.((((.............(((((((...((((((((.......)))))))).))))))).............)))).(((((....)))))..)))......... (-19.25 = -18.75 +  -0.50)

alignment

secondary structure

dotplot

Window 1

Location	4,104,626 – 4,104,742
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.47
Mean single sequence MFE	-29.42
Consensus MFE	-20.31
Energy contribution	-20.50
Covariance contribution	0.19
Combinations/Pair	1.14
Mean z-score	-1.75
Structure conservation index	0.69
SVM decision value	0.33
SVM RNA-class probability	0.692237
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4104626 116 - 20766785
UUUAU----UACUUGGCAAUGGAUCACAUUCAGAUGAAGAGAGGUCCUCCUAAGGCGGCGUAAAAAGAGUACGCCACUAGCCAGGAAUAAAGGCAAAUAACUGAAGCAAUGGGGAAAAAU
(((((----(.((((((...(((((.(.(((....)))..).)))))......((.((((((.......)))))).)).))))))))))))............................. ( -29.90)
>DroSec_CAF1 8784 116 - 1
UUUAU----UACUUUGCAAAGGAUCGCAUUCAGAUGAAGAGAGGUCCUCCCAAGGCGGCGUAAAAGGAGUACGCCACUAGCCAGAAAUAAAGGCAUACAACUAAAGUAUUGGGAAAUAAU
.((((----(..........(((((...(((....)))....)))))((((((.((((((((.......))))))....(((.........)))...........)).))))))))))). ( -31.90)
>DroSim_CAF1 12578 116 - 1
UUUAU----UACUUUGCAAAGGAUCGCAUUCAGAUGAAGAGAGGUCCUCCUAAGGCGGCGUAAAAGGAGUACGCCACUAGCCAGAAAUAAAUGCAUACAACUAAAGUAUUGGGAAAUAAU
((((.----(((((((((.((((((...(((....)))....)))))).....(((((((((.......))))))....))).........))))........))))).))))....... ( -26.40)
>DroYak_CAF1 1680 120 - 1
UUCAAUAGCUUCUUGGUAGAGGAUCCCCUUCAGAUGAAUAGCGGGCCUCCUAAGGCGGCGUAAAAAGAGUAUGCCACCAGCCAGAAAUAUAGACAUAUAACUGAGGAAGUCGAAAACAGU
.......((((((((((.((((..(((((((....))..)).)))))))....((.((((((.......)))))).)).))).....((((....))))....))))))).......... ( -29.50)
>consensus
UUUAU____UACUUGGCAAAGGAUCGCAUUCAGAUGAAGAGAGGUCCUCCUAAGGCGGCGUAAAAAGAGUACGCCACUAGCCAGAAAUAAAGGCAUACAACUAAAGUAUUGGGAAAUAAU
............(((((...(((((...(((....)))....)))))......((.((((((.......)))))).)).))))).................................... (-20.31 = -20.50 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:47 2006