Locus 6280

Sequence ID 3L_DroMel_CAF1
Location 16,726,250 – 16,726,354
Length 104
Max. P 0.946004
window10072 window10073

overview

Window 2

Location 16,726,250 – 16,726,354
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.89
Mean single sequence MFE -27.78
Consensus MFE -15.60
Energy contribution -17.10
Covariance contribution 1.50
Combinations/Pair 1.12
Mean z-score -1.79
Structure conservation index 0.56
SVM decision value 0.82
SVM RNA-class probability 0.859887
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16726250 104 + 23771897
UUUUGUAGCUUUUCGCUGCAGCAGCAGAUCAAUUUCCAGCGACAGCUGUCGAAUCAAGAAUUGAUUUUCCCUCGAGACUC--AA---------GAAACUGAGAAACUGCAGGAAA-----
...((((((.....))))))((((.((((((((((....((((....))))......))))))))))..........(((--(.---------.....))))...))))......----- ( -28.20)
>DroSec_CAF1 33584 90 + 1
UU--------------UGCAGCAGCAGAUCAAUUUCCAGCGACAGCUGUCGAAUCAAGAAUCGAUUUUCCCUCGAUACCC--AA---------GAAAUUGAGAAACUGCAGGAAA-----
..--------------....((((....((((((((((((....))))...........(((((.......)))))....--..---------))))))))....))))......----- ( -23.00)
>DroSim_CAF1 38128 90 + 1
UU--------------UGCAGCAGCAGACCAAUUUCCAGCGACAGCUGUCGAAUCAAGAAUCGAUUUUCCCUCGAGACCC--AA---------GAAAUUGAGAAACUGCAAGAAA-----
((--------------(((((...(....(((((((((((....))))((((.....(((......)))..)))).....--..---------))))))).)...)))))))...----- ( -19.40)
>DroEre_CAF1 34129 109 + 1
UUUUGCUGCUUUUCGCUGCAGCGGCAGAUCAAUUUCCAGCGACAGCUGUCGAAUUAGGAAUUGAUUUUCCCCCGAGACUA--AA---------GGAAUCAAGAAACUGCAGGAGGCGAAA
.((((((.....((.((((((.((.(((((((((((...((((....)))).....))))))))))).)).((.......--..---------))..........)))))))))))))). ( -32.60)
>DroYak_CAF1 37030 108 + 1
-UUUGCCGCUUUUCGCUGCAGCGGCAGAUCAAUUUUCAGCGACAGCUGUCGAAUUAAGAAUUGAUUUUCCCUCGAGACUA--AA---------GGAAUCGAGAAACUGCAGGAGGCGAAA
-((((((.....((.((((((.((.(((((((((((...((((....)))).....))))))))))).))(((((..(..--..---------.)..)))))...)))))))))))))). ( -38.00)
>DroAna_CAF1 29130 120 + 1
UUUUGCAUCUUUUCACUGCGCCAGCAGAUCAAUUUCCAGCGACAGUUGUCGAAUUAAAAAUUGAUUUUCUCUCGAGAGCAUCAACCUUGGUUCAUAAUUACGUAUCUACAGGAGGGCCCA
....((.........((((....)))).....(((((...(((....)))(((((((...(((((.((((....)))).)))))..))))))).................)))))))... ( -25.50)
>consensus
UUUUGC_GCUUUUCGCUGCAGCAGCAGAUCAAUUUCCAGCGACAGCUGUCGAAUCAAGAAUUGAUUUUCCCUCGAGACCA__AA_________GAAAUUGAGAAACUGCAGGAAA_____
...............((((((....((((((((((....((((....))))......))))))))))...(((((......................)))))...))))))......... (-15.60 = -17.10 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 16,726,250 – 16,726,354
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.89
Mean single sequence MFE -29.90
Consensus MFE -17.68
Energy contribution -17.47
Covariance contribution -0.22
Combinations/Pair 1.35
Mean z-score -1.95
Structure conservation index 0.59
SVM decision value 1.36
SVM RNA-class probability 0.946004
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16726250 104 - 23771897
-----UUUCCUGCAGUUUCUCAGUUUC---------UU--GAGUCUCGAGGGAAAAUCAAUUCUUGAUUCGACAGCUGUCGCUGGAAAUUGAUCUGCUGCUGCAGCGAAAAGCUACAAAA
-----(((((((((((...((((((((---------((--(((((..(((..........)))..)))))))((((....))))))))))))......))))))).)))).......... ( -32.70)
>DroSec_CAF1 33584 90 - 1
-----UUUCCUGCAGUUUCUCAAUUUC---------UU--GGGUAUCGAGGGAAAAUCGAUUCUUGAUUCGACAGCUGUCGCUGGAAAUUGAUCUGCUGCUGCA--------------AA
-----......(((((...((((((((---------(.--.((.(((((.......))))).))..).....((((....))))))))))))...)))))....--------------.. ( -28.70)
>DroSim_CAF1 38128 90 - 1
-----UUUCUUGCAGUUUCUCAAUUUC---------UU--GGGUCUCGAGGGAAAAUCGAUUCUUGAUUCGACAGCUGUCGCUGGAAAUUGGUCUGCUGCUGCA--------------AA
-----....(((((((...((((((((---------(.--.((..((((.......))))..))..).....((((....))))))))))))......))))))--------------). ( -27.30)
>DroEre_CAF1 34129 109 - 1
UUUCGCCUCCUGCAGUUUCUUGAUUCC---------UU--UAGUCUCGGGGGAAAAUCAAUUCCUAAUUCGACAGCUGUCGCUGGAAAUUGAUCUGCCGCUGCAGCGAAAAGCAGCAAAA
((((((....((((((..(((((..(.---------..--..)..)))))((...(((((((((.....((((....))))..)).)))))))...)))))))))))))).......... ( -30.10)
>DroYak_CAF1 37030 108 - 1
UUUCGCCUCCUGCAGUUUCUCGAUUCC---------UU--UAGUCUCGAGGGAAAAUCAAUUCUUAAUUCGACAGCUGUCGCUGAAAAUUGAUCUGCCGCUGCAGCGAAAAGCGGCAAA-
....((((((((((((..(((((..(.---------..--..)..)))))((...(((((((.(((...((((....)))).))).)))))))...))))))))).)).....)))...- ( -33.30)
>DroAna_CAF1 29130 120 - 1
UGGGCCCUCCUGUAGAUACGUAAUUAUGAACCAAGGUUGAUGCUCUCGAGAGAAAAUCAAUUUUUAAUUCGACAACUGUCGCUGGAAAUUGAUCUGCUGGCGCAGUGAAAAGAUGCAAAA
...(((.....(((((........(((.(((....))).)))(((....)))....((((((((((...((((....)))).))))))))))))))).)))(((.(....)..))).... ( -27.30)
>consensus
_____CCUCCUGCAGUUUCUCAAUUUC_________UU__GAGUCUCGAGGGAAAAUCAAUUCUUAAUUCGACAGCUGUCGCUGGAAAUUGAUCUGCUGCUGCAGCGAAAAGC_GCAAAA
.........(((((((...((((((....................(((((((((......)))))...))))((((....))))..))))))......)))))))............... (-17.68 = -17.47 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:34 2006