Locus 2300

Sequence ID	3L_DroMel_CAF1
Location	6,466,594 – 6,466,725
Length	131
Max. P	0.839217

overview

Window 1

Location	6,466,594 – 6,466,702
Length	108
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.24
Mean single sequence MFE	-32.80
Consensus MFE	-20.30
Energy contribution	-19.52
Covariance contribution	-0.78
Combinations/Pair	1.31
Mean z-score	-1.71
Structure conservation index	0.62
SVM decision value	0.74
SVM RNA-class probability	0.839217
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6466594 108 + 23771897
AAAACUCGUUCCAGAAGCUGUCUAUCCCGCGGCAGGCAUUGCAUUGAAAUCUGCUGAGCAAUGAAGUUUAGCAAGCAACCAAUCUCCGCCCACUGGAAGAUAA-----AGAGU
...((((.((((((..(((((.......))))).(((...(.((((.....((((((((......))))))))......)))))...)))..)))))).....-----.)))) ( -29.90)
>DroVir_CAF1 1337 110 + 1
AGCACACGCUCAAGCAGCUGCUUGUCGCGUGGCAGGCACUGCGUAGAUAUCUGCUGGGCAAUAAAGUUCAGCAAGCAACCAAUUUCGGCCCACUAAAAA---UGAUUAAAAGA
.((.(((((.(((((....)))))..))))))).(((..............((((((((......))))))))..............))).........---........... ( -32.69)
>DroGri_CAF1 1358 105 + 1
AGCACACGUUCCAGCAGCUGCUUGUCCCGCGGCAGGCACUGCGUCGAUAUCUGUUGGGCAAUGAAGUUCAACAGGCAACCAAUUUCCGCCCACUGAAAG---GGA-----AGA
.((...((.....((((.((((((((....))))))))))))..))....(((((((((......)))))))))))........((..(((.......)---)).-----.)) ( -35.10)
>DroEre_CAF1 1331 107 + 1
AAAACUCGUUCCAAGAGCUGUCUAUCUCGCGGCAGGCAUUGCAUCGAAAUCUGCUGAGCAAUGAAGUUCAGCAGGCAGCCAAUCUCCGCCCACUGGAAGAUGA-----AAAG-
.....((.(((((.(((........)))((((..(((..(((........(((((((((......))))))))))))))).....))))....)))))))...-----....- ( -30.80)
>DroMoj_CAF1 1352 110 + 1
AGCACACGCUCCAGCAGCUGCUUAUCUCGCGGCAGGCACUGCGUCGAUAUCUGCUGAGCAAUAAAGUUCAGCAAGCAGCCAAUCUCCGCCCACUGCAAAACGAGAUUAA---A
.......((....)).((((((((((.(((((......)))))..))))..((((((((......)))))))))))))).((((((.((.....)).....))))))..---. ( -35.00)
>DroAna_CAF1 1331 106 + 1
AACACCCGCUCGAGGAGCUGCCUGUCUCGCGGCAGGCACUGCAUCGAUAUCUGCUGAGCUAUGAAGUUCAACAAACAUCCGAUCUCGGCCCACUAGAG--UGA-----AGAUA
.........(((((.((.((((((((....)))))))))).).))))(((((((((((....((.(((.....))).))....)))))).(((....)--)).-----))))) ( -33.30)
>consensus
AACACACGCUCCAGCAGCUGCCUAUCUCGCGGCAGGCACUGCAUCGAUAUCUGCUGAGCAAUGAAGUUCAGCAAGCAACCAAUCUCCGCCCACUGGAAG_UGA_____A_AGA
................(((((.......))))).(((..............((((((((......))))))))..............)))....................... (-20.30 = -19.52 +  -0.78)

alignment

secondary structure

dotplot

Window 2

Location	6,466,634 – 6,466,725
Length	91
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	79.01
Mean single sequence MFE	-20.68
Consensus MFE	-14.54
Energy contribution	-15.35
Covariance contribution	0.81
Combinations/Pair	1.22
Mean z-score	-1.20
Structure conservation index	0.70
SVM decision value	0.20
SVM RNA-class probability	0.632151
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6466634 91 + 23771897
GCAUUGAAAUCUGCUGAGCAAUGAAGUUUAGCAAGCAACCAAUCUCCGCCCACUGGAAGAUAA-----AGAGUUU-UU--UGUUGGAUGACUAG-CAAU-U
((.........((((((((......))))))))((((.((....((((.....)))).(((((-----((....)-))--)))))).)).)).)-)...-. ( -18.90)
>DroVir_CAF1 1377 97 + 1
GCGUAGAUAUCUGCUGGGCAAUAAAGUUCAGCAAGCAACCAAUUUCGGCCCACUAAAAA---UGAUUAAAAGAUU-AAGCCUUCAGAUUAUAAAUAAAUCC
...(((.....((((((((......)))))))).....((......))....)))...(---(((((..(((...-....)))..)))))).......... ( -14.50)
>DroSec_CAF1 1371 91 + 1
GCAUCGAAAUCUGCUGAGCAAUGAAGUUCAGCAGGCAGCCAAUCUCCGCCCACUGGAAAAUAA-----AAACCCU-GU--UGUAGGAUGACUAA-CAAU-C
.((((.....(((((((((......)))))))))(((((.....((((.....))))......-----.......-))--)))..)))).....-....-. ( -21.97)
>DroSim_CAF1 1371 91 + 1
GCAUUGAAAUCUGCUGAGCAAUGAAGUUCAGCAGGCACCCAAUCUCCGCCCACUGGAAAAUAA-----AAACCUU-GU--UGUAGGAUGACUAA-CAAU-C
..((((...((((((((((......))))))))))((.((....((((.....)))).(((((-----.....))-))--)...)).)).....-))))-. ( -20.80)
>DroEre_CAF1 1371 87 + 1
GCAUCGAAAUCUGCUGAGCAAUGAAGUUCAGCAGGCAGCCAAUCUCCGCCCACUGGAAGAUGA-----AAAG-----U--UGUAGGAUGACUGA-CAAU-C
.((((.....(((((((((......)))))))))(((((..(((((((.....))).))))..-----...)-----)--)))..)))).....-....-. ( -27.30)
>DroYak_CAF1 1371 92 + 1
GCAACGAAAUCUGCUGAGCAAUGAAGUUCAGCAGGCAGCCAAUCUCCGCCCACUGGAAGAUAA-----AAAGAUUAAU--UGUAUUAUGACUGA-CUAU-C
...((((..((((((((((......))))))))))......(((((((.....))).))))..-----.........)--)))...........-....-. ( -20.60)
>consensus
GCAUCGAAAUCUGCUGAGCAAUGAAGUUCAGCAGGCAGCCAAUCUCCGCCCACUGGAAAAUAA_____AAAGAUU_AU__UGUAGGAUGACUAA_CAAU_C
.((((....((((((((((......)))))))))).........((((.....))))............................))))............ (-14.54 = -15.35 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:59 2006