Locus 5542

Sequence ID	X_DroMel_CAF1
Location	14,340,358 – 14,340,518
Length	160
Max. P	0.992513

overview

Window 7

Location	14,340,358 – 14,340,478
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.38
Mean single sequence MFE	-41.98
Consensus MFE	-35.35
Energy contribution	-35.35
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-2.24
Structure conservation index	0.84
SVM decision value	2.33
SVM RNA-class probability	0.992513
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14340358 120 + 22224390
AUUCAGAAUUCAGCGGAAGGGGGGCCGAGCAUAAAUUGCAAUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUGCAAUGCAUGCGUUGCACUUUUGUGCUCCGC
............(((((.((((((....(((.....)))..)))))).((((((...(.((....)).)..)))))).(((((((((((...)))))))))))((((....))))))))) ( -43.30)
>DroSec_CAF1 52369 119 + 1
AUUCAGAAUUCAGCGGAAGGGGG-CCGAGCAUAAAUUGCAAUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCUUCGC
.....(((....(((((((((((-....(((.....)))....))))..(((((...(.((....)).)..)))))((((((((((((.....)))))))))))).)))))))..))).. ( -42.70)
>DroSim_CAF1 50078 118 + 1
AUUCAGAAUUCAGCGGAAGGGGG--CGAGCAUAAAUUGCAAUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCUUCGC
.....(((....(((((((((((--...(((.....)))....))))..(((((...(.((....)).)..)))))((((((((((((.....)))))))))))).)))))))..))).. ( -42.30)
>DroEre_CAF1 51308 118 + 1
AUUCAGAACUCGGCGGAAG-GGG-CCGAGCAUAAAUUGCCAUUCCCCACAGCGAUCGACAUGGAAAUAUAUGCGCUGCAGCGUGUGCAUCCACUGCACGCGUUGCAGUUUUGUGCCUCGC
..................(-(((-(((((((((.(((.((((((............)).)))).))).)))))(((((((((((((((.....))))))))))))))).))).))))).. ( -45.50)
>DroYak_CAF1 54911 119 + 1
AUUCAGAAUUCAGCGGAUGAGGG-CAGAGCAUAAAUUGCAGUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAUCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCGCCGC
............((((.((.(((-....(((.....)))....)))))((((((...(.((....)).)..))))))...((((((((.....))))))))..((((....)))).)))) ( -36.10)
>consensus
AUUCAGAAUUCAGCGGAAGGGGG_CCGAGCAUAAAUUGCAAUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCUUCGC
............((((....(((.....(((.....)))....)))((((((((.................))))(((((((((((((.....)))))))))))))....))))..)))) (-35.35 = -35.35 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	14,340,398 – 14,340,518
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-38.28
Consensus MFE	-33.23
Energy contribution	-33.67
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.36
Structure conservation index	0.87
SVM decision value	0.52
SVM RNA-class probability	0.765953
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14340398 120 + 22224390
AUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUGCAAUGCAUGCGUUGCACUUUUGUGCUCCGCCGAUUAAUUGCAGCAGUUCUGGGCUAAGGGAUAAAGGAUA
..((((((((((((...(.((....)).)..))))((((((((((((((...))))))))))))))....))))....(((.(..(((((...))))).).)))...))))......... ( -37.20)
>DroSec_CAF1 52408 120 + 1
AUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCUUCGCCGAUUAAUUGCAGUAGUUCUGGGUUAAGGGAUAAAGGAUA
..((((((((((((...(.((....)).)..))))(((((((((((((.....)))))))))))))....)))).........((((((.(((.....)))))))))))))......... ( -36.40)
>DroSim_CAF1 50116 120 + 1
AUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCUUCGCCGAUUAAUUGCAGCAGUUCUGGGUUAAGGGAUAAAGGAUA
....((((.(((..........(((.....)))(((((((((((((((.....))))))))))((((....))))..............))))).))).))))................. ( -36.10)
>DroEre_CAF1 51346 120 + 1
AUUCCCCACAGCGAUCGACAUGGAAAUAUAUGCGCUGCAGCGUGUGCAUCCACUGCACGCGUUGCAGUUUUGUGCCUCGCCGAUUAAUUGCAGCGGCGCUGGGUUAAGGGAUACAGGAUA
..(((((((((.....(.((((......)))))(((((((((((((((.....))))))))))))))).)))))((.(((((...........)))))..)).....))))......... ( -45.80)
>DroYak_CAF1 54950 120 + 1
GUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAUCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCGCCGCCGAUUAAUUGCAGCGCUUCUGGGUUAAGGGAUAAAGGAUA
....((((.(((..........(((.....)))(((((((((.(((((.....)))))(((.(((((....))))).)))))).....)))))))))..))))................. ( -35.90)
>consensus
AUUCCCCACAGCGAUCGACAUGGAAAUAUAUUCGCUGCAGCGUGUGCAUCCAUUGCAUGCGUUGCACUUUUGUGCUUCGCCGAUUAAUUGCAGCAGUUCUGGGUUAAGGGAUAAAGGAUA
..((((((((((((.................))))(((((((((((((.....)))))))))))))....)))).........((((((.(((.....)))))))))))))......... (-33.23 = -33.67 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	14,340,398 – 14,340,518
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.83
Mean single sequence MFE	-35.98
Consensus MFE	-29.96
Energy contribution	-30.12
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.70
Structure conservation index	0.83
SVM decision value	1.01
SVM RNA-class probability	0.900518
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14340398 120 - 22224390
UAUCCUUUAUCCCUUAGCCCAGAACUGCUGCAAUUAAUCGGCGGAGCACAAAAGUGCAACGCAUGCAUUGCAUGCACACGCUGCAGCGAAUAUAUUUCCAUGUCGAUCGCUGUGGGGAAU
.........(((((.(((......((((((........)))))).((((....))))...((((((...))))))....)))(((((((..((((....))))...)))))))))))).. ( -39.30)
>DroSec_CAF1 52408 120 - 1
UAUCCUUUAUCCCUUAACCCAGAACUACUGCAAUUAAUCGGCGAAGCACAAAAGUGCAACGCAUGCAAUGGAUGCACACGCUGCAGCGAAUAUAUUUCCAUGUCGAUCGCUGUGGGGAAU
.........(((((...............((.........(((..((((....))))..))).((((.....))))...)).(((((((..((((....))))...)))))))))))).. ( -31.70)
>DroSim_CAF1 50116 120 - 1
UAUCCUUUAUCCCUUAACCCAGAACUGCUGCAAUUAAUCGGCGAAGCACAAAAGUGCAACGCAUGCAAUGGAUGCACACGCUGCAGCGAAUAUAUUUCCAUGUCGAUCGCUGUGGGGAAU
.........(((((.....(((....((((((........(((..((((....))))..))).((((.....)))).....))))))(((.....)))...........))).))))).. ( -32.30)
>DroEre_CAF1 51346 120 - 1
UAUCCUGUAUCCCUUAACCCAGCGCCGCUGCAAUUAAUCGGCGAGGCACAAAACUGCAACGCGUGCAGUGGAUGCACACGCUGCAGCGCAUAUAUUUCCAUGUCGAUCGCUGUGGGGAAU
.........(((((.....(((((..((((((........(((..(((......)))..)))(((((.....)))))....))))))((((........))))....))))).))))).. ( -39.90)
>DroYak_CAF1 54950 120 - 1
UAUCCUUUAUCCCUUAACCCAGAAGCGCUGCAAUUAAUCGGCGGCGCACAAAAGUGCAACGCAUGCAAUGGAUGCACACGAUGCAGCGAAUAUAUUUCCAUGUCGAUCGCUGUGGGGAAC
.................((((..(((((((((.....((((((..((((....))))..))).((((.....))))..)))))))))(((.....)))..........))).)))).... ( -36.70)
>consensus
UAUCCUUUAUCCCUUAACCCAGAACUGCUGCAAUUAAUCGGCGAAGCACAAAAGUGCAACGCAUGCAAUGGAUGCACACGCUGCAGCGAAUAUAUUUCCAUGUCGAUCGCUGUGGGGAAU
.........(((((.....(((...(((((((........(((..((((....))))..))).((((.....)))).....))))))).((((......))))......))).))))).. (-29.96 = -30.12 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:33 2006