Locus 2659

Sequence ID	2R_DroMel_CAF1
Location	9,386,730 – 9,386,847
Length	117
Max. P	0.862024

overview

Window 3

Location	9,386,730 – 9,386,830
Length	100
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	77.80
Mean single sequence MFE	-33.07
Consensus MFE	-23.63
Energy contribution	-23.93
Covariance contribution	0.31
Combinations/Pair	1.18
Mean z-score	-1.48
Structure conservation index	0.71
SVM decision value	0.83
SVM RNA-class probability	0.862024
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9386730 100 - 20766785
AUCUCUGAGCAGUCGUAUCACGCCCACACGUGACACGCCCGACAGAGAUCGCCUGCCGCACUAUGGCCCCCGAUUCUCGCCAAGGUAAGUCCUU---GAA--------AUC
.((((((..(.(.(((.(((((......))))).))).).).))))))(((...((((.....))))...))).......(((((.....))))---)..--------... ( -28.30)
>DroVir_CAF1 10152 101 - 1
UCGCCUGUACAGUCGUGUUACGCCCACGCGUGAUACGCCCGACAGAGAUCGCCUGCCGCACUAUGGCCCCCGUUUCUCGCCAAGGUAAGUGGCC---CGCCGCU-------
..((((((...(.((((((((((....)))))))))))...)))).....((..((((((((.((((...........)))).)))..))))).---.)).)).------- ( -35.80)
>DroPse_CAF1 8626 110 - 1
AUCUGUGUGCAGUCGUGUCACGCCCACACGUGACACGCCCGACAGAGAUCGUCUGCCGCACUACGGCCCCAGAUUCUCGCCAAGGUAAGUGCACCCCAACAC-ACAACACA
...((((((.....((((((((......))))))))(((.....((((((....((((.....))))....)).)))).....))).............)))-)))..... ( -35.60)
>DroWil_CAF1 11119 107 - 1
CACGUAACGUAGUCGUGUCACGCCCACACGUGAUACACCCGACAGAGAUCGCCUGCCUCACUAUGGCCCACGAUUCUCGCCAAGGUAAGUUAUC---AACAG-CCAAGAGA
...(((((......((((((((......))))))))(((.....(((((((...(((.......)))...))).)))).....)))..))))).---.....-........ ( -28.80)
>DroMoj_CAF1 19339 108 - 1
UUGGCUGUGCAGUCGUGUUACGCCCACGCGUGAUACGCCCGACAGAGAUCGCCUGCCGCAUUAUGGCCCACGUUUCUCGCCAAGGUAAGUGACC---AACCGACCAAUCGA
((((((((.(.(.((((((((((....)))))))))).).))))((((.((...((((.....))))...))..)))))))))(((..((....---.))..)))...... ( -36.30)
>DroPer_CAF1 10411 103 - 1
AUCUGUGUGCAGUCGUGUCACGCCCACACGUGACACGCCCGACAGAGAUCGUCUGCCGCACUACGGCCCCAGAUUCUCGCCAAGGUAAGUCCACCCCAAC--------ACA
....((((...(.(((((((((......))))))))))..(((.((((((....((((.....))))....)).))))((....))..))).......))--------)). ( -33.60)
>consensus
AUCUCUGUGCAGUCGUGUCACGCCCACACGUGACACGCCCGACAGAGAUCGCCUGCCGCACUAUGGCCCCCGAUUCUCGCCAAGGUAAGUGCAC___AAC_G______ACA
..............((((((((......))))))))(((.....(((((((...((((.....))))...))).)))).....)))......................... (-23.63 = -23.93 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	9,386,755 – 9,386,847
Length	92
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	84.34
Mean single sequence MFE	-24.85
Consensus MFE	-17.39
Energy contribution	-19.50
Covariance contribution	2.11
Combinations/Pair	1.17
Mean z-score	-2.06
Structure conservation index	0.70
SVM decision value	-0.01
SVM RNA-class probability	0.526759
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9386755 92 - 20766785
CUAUGUCAAAAACCA-AAAUCUCUGAGCAGUCGUAUCACGCCCACACGUGACACGCCCGACAGAGAUCGCCUGCCGCACUAUGGCCCCCGAUU
...............-...((((((..(.(.(((.(((((......))))).))).).).))))))(((...((((.....))))...))).. ( -22.60)
>DroPse_CAF1 8661 92 - 1
CAAUGUACA-AACCAAAUAUCUGUGUGCAGUCGUGUCACGCCCACACGUGACACGCCCGACAGAGAUCGUCUGCCGCACUACGGCCCCAGAUU
.........-........((((.(((.(.(.(((((((((......))))))))).).)))).)))).((((((((.....))))...)))). ( -28.30)
>DroSim_CAF1 8952 91 - 1
CUAUGUCAA-AACCA-AAAUCUCUGAGCAGUCGUAUCACGCCCACACGUGAUACUCCCGACAGAGAUCGCCUGCCGCACUAUGGCCCCCGAUU
.........-.....-...((((((..(.(..((((((((......))))))))..).).))))))(((...((((.....))))...))).. ( -24.50)
>DroWil_CAF1 11151 83 - 1
-------AA-AA-AA-AACACGUAACGUAGUCGUGUCACGCCCACACGUGAUACACCCGACAGAGAUCGCCUGCCUCACUAUGGCCCACGAUU
-------..-..-..-....(((..((((((.((((((((......))))))))........(((.........)))))))))....)))... ( -20.20)
>DroYak_CAF1 8999 91 - 1
CUAUGUCAA-AUGCA-AAAUCUCUGAGCAGUCGUAUCACGCCCACACGUGACACGCCCGACAGAGAUCGCCUGCCUCACUACGGGCCCCGAUU
....(((..-.....-..(((((((..(.(.(((.(((((......))))).))).).).))))))).(((((........)))))...))). ( -25.20)
>DroPer_CAF1 10439 92 - 1
CAAUGUACA-AACCAAAUAUCUGUGUGCAGUCGUGUCACGCCCACACGUGACACGCCCGACAGAGAUCGUCUGCCGCACUACGGCCCCAGAUU
.........-........((((.(((.(.(.(((((((((......))))))))).).)))).)))).((((((((.....))))...)))). ( -28.30)
>consensus
CUAUGUCAA_AACCA_AAAUCUCUGAGCAGUCGUAUCACGCCCACACGUGACACGCCCGACAGAGAUCGCCUGCCGCACUACGGCCCCCGAUU
...................((((((....(.(((((((((......))))))))).)...))))))(((...((((.....))))...))).. (-17.39 = -19.50 +   2.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:35 2006