Locus 5462

Sequence ID	3L_DroMel_CAF1
Location	14,941,385 – 14,941,493
Length	108
Max. P	0.832721

overview

Window 8

Location	14,941,385 – 14,941,493
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.92
Mean single sequence MFE	-36.07
Consensus MFE	-23.88
Energy contribution	-24.30
Covariance contribution	0.42
Combinations/Pair	1.17
Mean z-score	-2.45
Structure conservation index	0.66
SVM decision value	0.72
SVM RNA-class probability	0.832721
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14941385 108 + 23771897
-----AUUCUCAACAUGUGGGCCAGUUUUGGGUAAAGAUGCGAAAGGUCCUGUCUGCAGAUCCU------U-CAAAGAUGUGGGACAUUCCCACGGCACCAAACCAUGUGUUGGGUUUUU
-----...(((((((((((((((.......)))...(.((((((.((..(((....)))..)))------)-).....((((((.....))))))))).)...))))))))))))..... ( -38.90)
>DroSec_CAF1 121695 107 + 1
-----AUUCUCAACAUGUGGGCCAGUUUUGGGUUAGGAUGCGAUAGGUCCUGUCUGCAGAUCCU------U-CAAAGAUGUGGGACAUUCCCACGGCACCACA-CAUGUGUUGGGUUUUU
-----...(((((((((((((((..((((((...((((((((((((...))))).)))..))))------)-)))))..(((((.....)))))))).)))))-....)))))))..... ( -41.00)
>DroSim_CAF1 119439 107 + 1
-----ACUCUCAACAUGUGGGCUAGUUUUGGGUAAAGAUGCGAAAGAUCCUGUCUGCAGAUCCU------U-CAAAGAUGUGGGACAUUCCCACGGCACCAAA-CAUGUGUUGGGUUUUU
-----...(((((((((((.(((.......)))...(.((((((.((((.((....)))))).)------)-).....((((((.....))))))))).)...-)))))))))))..... ( -33.20)
>DroEre_CAF1 116442 107 + 1
-----UUUCUCAACAUGUGGGCCUGCUUUGGGUAAGGAUGCGAAAGGUCCUGUCUGCAGAUCCU------U-CAAAGAUGUGGGACAUUCCCACGGCACCAAA-CAUGUGUUGGGUUUUU
-----...(((((((((((.((((.....))))..((.((((((.((..(((....)))..)))------)-).....((((((.....)))))))))))...-)))))))))))..... ( -40.10)
>DroYak_CAF1 117404 107 + 1
-----AUUCUCAGCAUGUGGUCUUGCUUUGGGUUAAGAUGCGAAAGGUCCUGUCUGCAGAUCCU------U-CAAAGAUGUGGGACAUUCCCACGGCACCAAA-CAUGUGUUGGGUUUUU
-----...((((((((((((((((((.....).))))))(((((.((..(((....)))..)))------)-).....((((((.....))))))))......-)))))))))))..... ( -35.80)
>DroAna_CAF1 106693 113 + 1
AUUUUUUUCACAGCAUGUCUACCACAU---GGUCCUAA--CUCACAAUCCUUACUUCAGAUCCUGUGGUAUCUGAGAAUGUGGGACAUUCCCUUGGCAG-AAA-CAUGUGUUGGGCUUAU
................(((((.(((((---(((((...--..((((.((......((((((((...)).)))))))).)))))))).(((........)-)).-)))))).))))).... ( -27.40)
>consensus
_____AUUCUCAACAUGUGGGCCAGUUUUGGGUAAAGAUGCGAAAGGUCCUGUCUGCAGAUCCU______U_CAAAGAUGUGGGACAUUCCCACGGCACCAAA_CAUGUGUUGGGUUUUU
........(((((((((((.(((.......))).....(((....((((.((....))))))................((((((.....)))))))))......)))))))))))..... (-23.88 = -24.30 +   0.42)

alignment

secondary structure

dotplot

Window 9

Location	14,941,385 – 14,941,493
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.92
Mean single sequence MFE	-30.50
Consensus MFE	-18.37
Energy contribution	-19.40
Covariance contribution	1.03
Combinations/Pair	1.12
Mean z-score	-2.04
Structure conservation index	0.60
SVM decision value	0.16
SVM RNA-class probability	0.610907
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14941385 108 - 23771897
AAAAACCCAACACAUGGUUUGGUGCCGUGGGAAUGUCCCACAUCUUUG-A------AGGAUCUGCAGACAGGACCUUUCGCAUCUUUACCCAAAACUGGCCCACAUGUUGAGAAU-----
.......(((((..(((...(((((.(((((.....)))))......(-(------(((.((((....)))).))))).))))).....(((....))).)))..))))).....----- ( -32.10)
>DroSec_CAF1 121695 107 - 1
AAAAACCCAACACAUG-UGUGGUGCCGUGGGAAUGUCCCACAUCUUUG-A------AGGAUCUGCAGACAGGACCUAUCGCAUCCUAACCCAAAACUGGCCCACAUGUUGAGAAU-----
.......(((((....-(((((.((((((((.....)))))......(-(------(((.((((....)))).))).))..................))))))))))))).....----- ( -33.20)
>DroSim_CAF1 119439 107 - 1
AAAAACCCAACACAUG-UUUGGUGCCGUGGGAAUGUCCCACAUCUUUG-A------AGGAUCUGCAGACAGGAUCUUUCGCAUCUUUACCCAAAACUAGCCCACAUGUUGAGAGU-----
...........(((((-(..((.((.(((((.....)))))......(-(------(((((((.......)))))))))...................)))))))))).......----- ( -28.90)
>DroEre_CAF1 116442 107 - 1
AAAAACCCAACACAUG-UUUGGUGCCGUGGGAAUGUCCCACAUCUUUG-A------AGGAUCUGCAGACAGGACCUUUCGCAUCCUUACCCAAAGCAGGCCCACAUGUUGAGAAA-----
...........(((((-(..((.((((((((.....)))))..(((((-(------((((..(((.((.((...)).))))))))))...)))))..))))))))))).......----- ( -31.40)
>DroYak_CAF1 117404 107 - 1
AAAAACCCAACACAUG-UUUGGUGCCGUGGGAAUGUCCCACAUCUUUG-A------AGGAUCUGCAGACAGGACCUUUCGCAUCUUAACCCAAAGCAAGACCACAUGCUGAGAAU-----
...............(-((.(((((.(((((.....)))))......(-(------(((.((((....)))).))))).)))))..)))....((((........))))......----- ( -26.50)
>DroAna_CAF1 106693 113 - 1
AUAAGCCCAACACAUG-UUU-CUGCCAAGGGAAUGUCCCACAUUCUCAGAUACCACAGGAUCUGAAGUAAGGAUUGUGAG--UUAGGACC---AUGUGGUAGACAUGCUGUGAAAAAAAU
.........(((((((-((.-.......(((((((.....)))))))...(((((((((.(((((..((.......))..--))))).))---.))))))))))))).)))......... ( -30.90)
>consensus
AAAAACCCAACACAUG_UUUGGUGCCGUGGGAAUGUCCCACAUCUUUG_A______AGGAUCUGCAGACAGGACCUUUCGCAUCUUUACCCAAAACUGGCCCACAUGUUGAGAAU_____
..........((((((...(((.((((((((.....)))))...............(((.((((....)))).))).....................)))))))))).)).......... (-18.37 = -19.40 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:55 2006