Locus 3670

Sequence ID	X_DroMel_CAF1
Location	9,815,579 – 9,815,749
Length	170
Max. P	0.993582

overview

Window 3

Location	9,815,579 – 9,815,696
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-35.08
Consensus MFE	-31.78
Energy contribution	-32.42
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.91
SVM decision value	1.08
SVM RNA-class probability	0.912547
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9815579 117 - 22224390
GCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCACCUCAGCAAACAAAUUCCGAACUGGAGGCGAAUUUCCAGGAUAGCAGCGAUCCCGACUUGAAUCCUAUCAAC
((((......)))).((((((((......((((((...........))))))..............(((((((....)))))))))))))))..........((((......)))). ( -34.40)
>DroSec_CAF1 10876 117 - 1
GCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCGGAACUGGAGGCAAAUUUCCAGGGUACCAGCGAUCCCGACUUGAAUCCUAUCAAC
((.((((.....)))).))..(((..((((((((.....((((((....)))...............((((((....)))))))))..))))))))..))).((((......)))). ( -37.60)
>DroSim_CAF1 6667 117 - 1
GCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCGGAACUGGAGGCGAAUUUCCAGGAUACCAGCGAUCCCGACUUGAAUCCUAUCAAC
((.((((.....)))).))..(((..((((((((........(((....)))..............(((((((....)))))))....))))))))..))).((((......)))). ( -36.30)
>DroEre_CAF1 6807 117 - 1
GCCGUGCUAUCGGCAUUGCUAUCGGUAACGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCCGAACUGGAGGCGAGAUUCCAGGAUACCAGCGAUCCCGACCUGAAUCCCAUCAAU
((((......)))).......((((...((((((........(((....)))..............((((((......))))))....))))))...))))................ ( -33.60)
>DroYak_CAF1 8687 117 - 1
GCCGUGCUAUCGGCACUGCUAUCGCUAACGCUGGGCUAUCCCGCUCCACAGCAAACAAACUCCGAACUGGAGGCGAGUUUCCAGGAUACCAGCGAUCCCGACUUGAAUCCCAUCAAU
((.((((.....)))).))..(((....((((((..(((((.(((....)))((((...((((.....))))....))))...)))))))))))....))).((((......)))). ( -33.50)
>consensus
GCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCCGAACUGGAGGCGAAUUUCCAGGAUACCAGCGAUCCCGACUUGAAUCCUAUCAAC
((.((((.....)))).))..(((..((((((((........((......))..............(((((((....)))))))....))))))))..)))................ (-31.78 = -32.42 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	9,815,619 – 9,815,736
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-39.36
Consensus MFE	-34.66
Energy contribution	-34.58
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-1.98
Structure conservation index	0.88
SVM decision value	2.41
SVM RNA-class probability	0.993582
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9815619 117 - 22224390
AAUUAUGCAGUUCACCAGGAGCCGUUUAUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCACCUCAGCAAACAAAUUCCGAACUGGAGGCGAA
.....(.((((((....((((..((((........(((((((.((((.....)))).))))))).....((((((...........))))))))))...)))))))))).)...... ( -34.80)
>DroSec_CAF1 10916 117 - 1
AAUUAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCGGAACUGGAGGCAAA
.....(((......((((...(((((((((.....(((((((.((((.....)))).))))))).....(((((((......)))...)))).))))))..)))..))))..))).. ( -39.60)
>DroSim_CAF1 6707 117 - 1
AAUAAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCGGAACUGGAGGCGAA
.....(((......((((...(((((((((.....(((((((.((((.....)))).))))))).....(((((((......)))...)))).))))))..)))..))))..))).. ( -38.90)
>DroEre_CAF1 6847 117 - 1
AAAUAUGCAGUUCACCAGGAGUCAUUUGUUGAUAUCGAUGGCCGUGCUAUCGGCAUUGCUAUCGGUAACGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCCGAACUGGAGGCGAG
.....(.((((((....(((((..((((((((((((((((((.((((.....)))).))))))))))..((.(((....)))))...))))))))...))))))))))).)...... ( -43.00)
>DroYak_CAF1 8727 117 - 1
AAUUAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGCUAACGCUGGGCUAUCCCGCUCCACAGCAAACAAACUCCGAACUGGAGGCGAG
.....(.((((((....((((..(((((((......((((((.((((.....)))).))))))((....))(((((......)).))).)))))))...)))))))))).)...... ( -40.50)
>consensus
AAUUAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUCCCGCUCCUCAGCAAACAAAUUCCGAACUGGAGGCGAA
.....(.((((((....(....)(((((((.....(((((((.((((.....)))).))))))).....(((((((......)))...)))).)))))))...)))))).)...... (-34.66 = -34.58 +  -0.08)

alignment

secondary structure

dotplot

Window 5

Location	9,815,656 – 9,815,749
Length	93
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.27
Mean single sequence MFE	-28.92
Consensus MFE	-20.42
Energy contribution	-20.12
Covariance contribution	-0.30
Combinations/Pair	1.44
Mean z-score	-1.00
Structure conservation index	0.71
SVM decision value	0.15
SVM RNA-class probability	0.609187
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9815656 93 - 22224390
----------------------GCUUGCAGAAA-----CUAAUUAUGCAGUUCACCAGGAGCCGUUUAUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUC
----------------------(((((((....-----.......)))))....((((((...((.....))...(((((((.((((.....)))).)))))))...)).)))))).... ( -26.80)
>DroSec_CAF1 10953 93 - 1
----------------------GCUUGCAGAAA-----CUAAUUAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUC
----------------------((((((.....-----.((((...((.((((.....)))).))..))))....(((((((.((((.....)))).))))))).....)).)))).... ( -27.00)
>DroSim_CAF1 6744 93 - 1
----------------------GCUUGCAGAAA-----CUAAUAAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAUCGCUGGGCUUUC
----------------------((((((.....-----.((((((.((.((((.....)))).))))))))....(((((((.((((.....)))).))))))).....)).)))).... ( -28.00)
>DroEre_CAF1 6884 93 - 1
----------------------GCUUGCAGAAA-----CUAAAUAUGCAGUUCACCAGGAGUCAUUUGUUGAUAUCGAUGGCCGUGCUAUCGGCAUUGCUAUCGGUAACGCUGGGCUUUC
----------------------(((((((....-----.......)))))....((((..((((.....))))(((((((((.((((.....)))).)))))))))....)))))).... ( -29.90)
>DroYak_CAF1 8764 98 - 1
----------------------GCUUGCAGAAAACUACUUAAUUAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGCUAACGCUGGGCUAUC
----------------------.((((..((..(((.(........).)))))..))))((((.............((((((.((((.....)))).))))))((....))..))))... ( -27.30)
>DroAna_CAF1 6706 116 - 1
CCAACCUCUCCUCUUCCUGUCACUUUCCAGAAGA----GCAGAGAUGCAGUUCCCCGUGCACCGAGUGUUGCUGUCGAUGGCCCUGUUAUCGGUGUCGCUGUCGCUGACGGCCGCCGCCC
.....((((.((((((.((........)))))))----).))))..((((..((.((.(((........)))...))..))..))))...(((((..((((((...)))))))))))... ( -34.50)
>consensus
______________________GCUUGCAGAAA_____CUAAUUAUGCAGUUCACCAGGAGCCGUUUGUUACUAUCGAUGGCCGUGCUAUCGGCACUGCUAUCGUUAACGCUGGGCUUUC
......................((((((...........((((...((.((((.....)))).))..))))....(((((((.((((.....)))).))))))).....)).)))).... (-20.42 = -20.12 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:17 2006