Locus 5947

Sequence ID	X_DroMel_CAF1
Location	15,339,387 – 15,339,522
Length	135
Max. P	0.993694

overview

Window 6

Location	15,339,387 – 15,339,501
Length	114
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	95.32
Mean single sequence MFE	-38.60
Consensus MFE	-32.92
Energy contribution	-32.70
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.56
Structure conservation index	0.85
SVM decision value	0.68
SVM RNA-class probability	0.821563
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15339387 114 - 22224390
UCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAACUGAUUUUGGAGAUUGGCCAACUGGAGUUUGUGCUGAUCCUGACUGAUCUUCAUCUGAAUGGACUUC
(((..(((.((((((((((...(((((.(((((.((((((.......))))))..)))))...((.(((....))).)))))))....)))))..))))).)))...))).... ( -33.70)
>DroSim_CAF1 184 114 - 1
UCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAACUGAUUUUGGAGAUUGGCCAACUGGAGUUUGUGCUGAUCCUGACUGUUCUUCAUCUGAAUGGACUUC
(((..(((..(((((((((...(((((.(((((.((((((.......))))))..)))))...((.(((....))).)))))))....)))))))))....)))...))).... ( -35.20)
>DroYak_CAF1 215 114 - 1
UCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAGCUGAUUUUGGAGAUUGGCUACCUGGAUUUUGUGCUGAUCCUGACUGAUCUUCAGCUGAACGGAUUUC
(((..((((((((((((((....((((((((((.(((((((.....)))))))..)))))..)))))...(((((.......))))).)))))..)))))))))...))).... ( -46.90)
>consensus
UCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAACUGAUUUUGGAGAUUGGCCAACUGGAGUUUGUGCUGAUCCUGACUGAUCUUCAUCUGAAUGGACUUC
(((..(((.((((((((((...(((((.(((((.((((((.......))))))..)))))....((....)).......)))))....)))))..))))).)))...))).... (-32.92 = -32.70 +  -0.22)

alignment

secondary structure

dotplot

Window 7

Location	15,339,427 – 15,339,522
Length	95
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	60.89
Mean single sequence MFE	-31.30
Consensus MFE	-9.52
Energy contribution	-9.32
Covariance contribution	-0.20
Combinations/Pair	1.42
Mean z-score	-2.49
Structure conservation index	0.30
SVM decision value	0.36
SVM RNA-class probability	0.704109
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15339427 95 + 22224390
CUCCAGUUGGCCAAUCUCCAAAA------UCAGUUGCAAGCCGAUCAGGAGAAGCUAAGAGAACUGCUCCAGCUGCAGGACAAACUGGAGCAGCAAAAGGA----------
.(((..(((((...(((((...(------((.((.....)).)))..))))).))))).....(((((((((.(........).))))))))).....)))---------- ( -30.10)
>DroVir_CAF1 20437 100 + 1
---UGGCGAACUGAUC--GAGCGUGUGCGUCAGGUUGAUGCCGAGCGCGAGAAGCUG------CAACUUGAGUUGGAUGAGGUUGUCAAACAGGCGAAGGAAAAGAAAACU
---((((((.((.(((--.(((...(((((..(((....)))..)))))....))).------((((....))))))).)).))))))....................... ( -28.90)
>DroSim_CAF1 224 95 + 1
CUCCAGUUGGCCAAUCUCCAAAA------UCAGUUGCAAGCCGAUCAGGAGAAGCUAAGAGAACUGCUCCAGCUGCAGGACAAACUGGAGCAGCAAAAGGA----------
.(((..(((((...(((((...(------((.((.....)).)))..))))).))))).....(((((((((.(........).))))))))).....)))---------- ( -30.10)
>DroYak_CAF1 255 95 + 1
AUCCAGGUAGCCAAUCUCCAAAA------UCAGCUGCAAGCCGAUCAGGAGAAGCUAAGAGAACUGCUCCAGCUGCAGGACAAACUGGAGCAGCAAAAGGA----------
.(((...((((...(((((...(------((.((.....)).)))..))))).))))......(((((((((.(........).))))))))).....)))---------- ( -31.70)
>DroMoj_CAF1 23391 100 + 1
---CGGUGAGCUGAUC--GAGCGCGUCCGGCAAGCGGAUGCCGAGCGGGACAAAUUG------CAGCGCGAGCUGGAGGAGCUGGUGAAGCAGUCCAAGGAGAAGAAAACG
---..((...((..((--..(((((((((.....)))))))...)).((((...((.------((((....)))).))..(((.....))).))))...))..))...)). ( -35.70)
>consensus
_UCCAGUUAGCCAAUCUCCAAAA______UCAGGUGCAAGCCGAUCAGGAGAAGCUAAGAGAACUGCUCCAGCUGCAGGACAAACUGGAGCAGCAAAAGGA__________
........................................((.....((((...............)))).(((.(((......))).))).......))........... ( -9.52 =  -9.32 +  -0.20)

alignment

secondary structure

dotplot

Window 8

Location	15,339,427 – 15,339,522
Length	95
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	60.89
Mean single sequence MFE	-31.48
Consensus MFE	-13.67
Energy contribution	-14.75
Covariance contribution	1.08
Combinations/Pair	1.50
Mean z-score	-2.80
Structure conservation index	0.43
SVM decision value	2.42
SVM RNA-class probability	0.993694
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15339427 95 - 22224390
----------UCCUUUUGCUGCUCCAGUUUGUCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAACUGA------UUUUGGAGAUUGGCCAACUGGAG
----------(((..((((((((((((((.(.....))))))))))))........((((((((.((((((.......))))------))..)))))..))))))..))). ( -37.00)
>DroVir_CAF1 20437 100 - 1
AGUUUUCUUUUCCUUCGCCUGUUUGACAACCUCAUCCAACUCAAGUUG------CAGCUUCUCGCGCUCGGCAUCAACCUGACGCACACGCUC--GAUCAGUUCGCCA---
...................((..(((.....)))..)).........(------(((((..(((.((...((.((.....)).))....)).)--))..)))).))..--- ( -14.50)
>DroSim_CAF1 224 95 - 1
----------UCCUUUUGCUGCUCCAGUUUGUCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAACUGA------UUUUGGAGAUUGGCCAACUGGAG
----------(((..((((((((((((((.(.....))))))))))))........((((((((.((((((.......))))------))..)))))..))))))..))). ( -37.00)
>DroYak_CAF1 255 95 - 1
----------UCCUUUUGCUGCUCCAGUUUGUCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAGCUGA------UUUUGGAGAUUGGCUACCUGGAU
----------(((....((((((((((((.(.....))))))))))))).....((((((((((.(((((((.....)))))------))..)))))..)))))...))). ( -43.60)
>DroMoj_CAF1 23391 100 - 1
CGUUUUCUUCUCCUUGGACUGCUUCACCAGCUCCUCCAGCUCGCGCUG------CAAUUUGUCCCGCUCGGCAUCCGCUUGCCGGACGCGCUC--GAUCAGCUCACCG---
.............(((((..(((.....)))...)))))...(.((((------....(((..(((..(((((......)))))..)).)..)--)).)))).)....--- ( -25.30)
>consensus
__________UCCUUUUGCUGCUCCAGUUUGUCCUGCAGCUGGAGCAGUUCUCUUAGCUUCUCCUGAUCGGCUUGCAACUGA______UUUUGGAGAUUGGCUAACUGGA_
.................((((((((((((........)))))))))))).......((((((((.((((((.......)))).......)).)))))..)))......... (-13.67 = -14.75 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:12 2006