Locus 544

Sequence ID	3L_DroMel_CAF1
Location	1,573,705 – 1,573,866
Length	161
Max. P	0.984879

overview

Window 1

Location	1,573,705 – 1,573,796
Length	91
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	80.53
Mean single sequence MFE	-21.30
Consensus MFE	-11.67
Energy contribution	-14.87
Covariance contribution	3.20
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.55
SVM decision value	0.94
SVM RNA-class probability	0.886603
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1573705 91 + 23771897
CA---AACUGCUGCCCACAUUCCUUGUGU--UUGUCU-CUGUUGAUUUGUUUCCAAUUUCCUACAACGAUACAAGCCAACAUAAGCAAGUAGCCCCU
..---....(((((.((((.....)))).--(((..(-.(((((..((((.((..............)).))))..))))).)..)))))))).... ( -19.04)
>DroSec_CAF1 17996 93 + 1
CA---AACUGCUGCCCACAUUCCUUGUGUCUUUGGCU-UUGCUGGUUUGUUUCCAAUUUCCUACAACGCUACAAGCCAACAUGAGCAAGUAGCUCAU
..---....(((((.((((.....))))......(((-(((.((((((((....................)))))))).)).))))..))))).... ( -22.95)
>DroSim_CAF1 18365 81 + 1
CA---AACUGCUGCCCACAUUCCUUGUGU-------------UGGUUUGUUUCCAAUUUCCUACAACGCUACAAGCCAACACGACCAAGUAGCUCCU
..---....(((((.........((((((-------------((((((((....................))))))))))))))....))))).... ( -21.57)
>DroEre_CAF1 24968 94 + 1
UUGG-ACCUGCUGCCCACAUUCCUGGUGU--UUGGCUUUUGUUGGUUUCUUGCCAAUUUCCUACAACGAUACAAGCCAACAUGAGCUAGUAACCCCU
.(((-.........))).......(((..--(((((((.(((((((((.(((..............)))...))))))))).)))))))..)))... ( -20.84)
>DroYak_CAF1 19044 92 + 1
CAGAUAUCUGCUGCCCACAUUCCUUGUAC--UUCGCU-UUGUUGGUUUGUUGCCAAUUUCCUAGAACGCUAGAUGCCAACAUGAGCGAGUAUCCC--
(((....)))...............((((--(.((((-(((((((((((....)))....((((....))))..))))))).))))))))))...-- ( -22.10)
>consensus
CA___AACUGCUGCCCACAUUCCUUGUGU__UUGGCU_UUGUUGGUUUGUUUCCAAUUUCCUACAACGCUACAAGCCAACAUGAGCAAGUAGCCCCU
.........(((((.((((.....))))......(((..(((((((((((....................)))))))))))..)))..))))).... (-11.67 = -14.87 +   3.20)

alignment

secondary structure

dotplot

Window 2

Location	1,573,756 – 1,573,866
Length	110
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	77.70
Mean single sequence MFE	-31.44
Consensus MFE	-17.66
Energy contribution	-18.70
Covariance contribution	1.04
Combinations/Pair	1.15
Mean z-score	-2.48
Structure conservation index	0.56
SVM decision value	1.99
SVM RNA-class probability	0.984879
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1573756 110 + 23771897
UUCCUACAACGAUACAAGCCAACAUAAGCAAGUAGCCCCUCCACCGACCGAUAGCCUCCAUGGCUUACAUGCUCACAUUGGCGUUGGCUUGGGAUCGUCA------AUCGUCAUCA
........(((((.(((((((((....((.....)).................(((....((((......)).))....))))))))))))..)))))..------.......... ( -29.40)
>DroSec_CAF1 18049 105 + 1
UUCCUACAACGCUACAAGCCAACAUGAGCAAGUAGCUCAUCCAC----CGAUAGCCAUCAUAGCUUACAUGAUCACAUUGGCGUUGGUUUGGGGUCGUCA------AUCGUCAU-C
........((((..(((((((((((((((.....))))))...(----((((.(..(((((.......)))))..)))))).)))))))))..).)))..------........-. ( -30.10)
>DroSim_CAF1 18406 106 + 1
UUCCUACAACGCUACAAGCCAACACGACCAAGUAGCUCCUCCAC----CGAUAGCCACCAUAGCUCACAUGCUCACAUUGGCGUUGGCUUGGGGUCGUCA------AUCGUCAUCC
........((((..(((((((((((......))...........----.....((((....(((......))).....)))))))))))))..).)))..------.......... ( -28.10)
>DroEre_CAF1 25022 108 + 1
UUCCUACAACGAUACAAGCCAACAUGAGCUAGUAACCCCUCCUG----CU-CAGC--CCAAAGCUUACAAGCUCACAUUGGCGUUGGCUUGGGGUCGUCAUCGAGAGUAGUCAU-C
...((((..((((.(((((((((.(((((..(........)..)----))-))((--(...((((....))))......))))))))))))..))))((.....))))))....-. ( -35.60)
>DroYak_CAF1 19098 95 + 1
UUCCUAGAACGCUAGAUGCCAACAUGAGCGAGUAUCCC--------------------CAUGGCUUACAAGCUCACAUUGGCGUUGGCUUGGGAUCGUCAUCUAGCGUCGUCAU-C
......((.(((((((((((((..(((((..(((..((--------------------...))..)))..)))))..)))))...(((........))))))))))))).....-. ( -34.00)
>consensus
UUCCUACAACGCUACAAGCCAACAUGAGCAAGUAGCCCCUCCAC____CGAUAGCC_CCAUAGCUUACAUGCUCACAUUGGCGUUGGCUUGGGGUCGUCA______AUCGUCAU_C
.(((((....((((...(((((..((((((.((((((........................)))).)).))))))..)))))..)))).)))))...................... (-17.66 = -18.70 +   1.04)

alignment

secondary structure

dotplot

Window 3

Location	1,573,756 – 1,573,866
Length	110
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	77.70
Mean single sequence MFE	-35.94
Consensus MFE	-22.82
Energy contribution	-23.50
Covariance contribution	0.68
Combinations/Pair	1.23
Mean z-score	-1.76
Structure conservation index	0.63
SVM decision value	0.53
SVM RNA-class probability	0.770418
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1573756 110 - 23771897
UGAUGACGAU------UGACGAUCCCAAGCCAACGCCAAUGUGAGCAUGUAAGCCAUGGAGGCUAUCGGUCGGUGGAGGGGCUACUUGCUUAUGUUGGCUUGUAUCGUUGUAGGAA
..........------.((((((..(((((((((......(((((((.(((.(((.......(((((....)))))...)))))).)))))))))))))))).))))))....... ( -37.70)
>DroSec_CAF1 18049 105 - 1
G-AUGACGAU------UGACGACCCCAAACCAACGCCAAUGUGAUCAUGUAAGCUAUGAUGGCUAUCG----GUGGAUGAGCUACUUGCUCAUGUUGGCUUGUAGCGUUGUAGGAA
.-........------.((((.(..(((.((((((((.((((.((((((.....)))))).)).)).)----))..((((((.....))))))))))).)))..)))))....... ( -31.40)
>DroSim_CAF1 18406 106 - 1
GGAUGACGAU------UGACGACCCCAAGCCAACGCCAAUGUGAGCAUGUGAGCUAUGGUGGCUAUCG----GUGGAGGAGCUACUUGGUCGUGUUGGCUUGUAGCGUUGUAGGAA
..........------.((((.(..(((((((((((..(((....)))..((.(...(((((((.((.----...))..))))))).).)))))))))))))..)))))....... ( -36.10)
>DroEre_CAF1 25022 108 - 1
G-AUGACUACUCUCGAUGACGACCCCAAGCCAACGCCAAUGUGAGCUUGUAAGCUUUGG--GCUG-AG----CAGGAGGGGUUACUAGCUCAUGUUGGCUUGUAUCGUUGUAGGAA
.-....((((...(((((.......((((((((((((.....(((((....)))))..)--))((-((----(...((......)).))))).))))))))))))))..))))... ( -38.61)
>DroYak_CAF1 19098 95 - 1
G-AUGACGACGCUAGAUGACGAUCCCAAGCCAACGCCAAUGUGAGCUUGUAAGCCAUG--------------------GGGAUACUCGCUCAUGUUGGCAUCUAGCGUUCUAGGAA
.-.....((((((((((...(....)........((((((((((((..(((..((...--------------------.)).)))..))))))))))))))))))))))....... ( -35.90)
>consensus
G_AUGACGAU______UGACGACCCCAAGCCAACGCCAAUGUGAGCAUGUAAGCUAUGG_GGCUAUCG____GUGGAGGGGCUACUUGCUCAUGUUGGCUUGUAGCGUUGUAGGAA
.................((((....((((((((((......((((((.(((.(((.......((((......))))...)))))).))))))))))))))))...))))....... (-22.82 = -23.50 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:57 2006