Locus 7725

Sequence ID	2L_DroMel_CAF1
Location	21,835,353 – 21,835,531
Length	178
Max. P	0.956760

overview

Window 1

Location	21,835,353 – 21,835,465
Length	112
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	96.41
Mean single sequence MFE	-29.42
Consensus MFE	-26.85
Energy contribution	-27.60
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.35
Structure conservation index	0.91
SVM decision value	1.27
SVM RNA-class probability	0.937915
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21835353 112 - 22407834
UUCCGUCAGCAGCACAACAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGACAUGAAGUUGACAGCUCAAUGCGCUCGAAAAAAAAAAC
.....(((((..........(((((((.....((((((...(((((...........)))))..)))))).......)))))))...((.....))))).)).......... ( -27.20)
>DroSec_CAF1 122622 111 - 1
UUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGACGUGAAGUUGACAGCUCAAUGCGCUCUAAAA-AAAAAC
....((((((..(((((((((.(((((...)))))......(((((...........)))))..)))))).....)))..)))))).((.....)).........-...... ( -30.80)
>DroSim_CAF1 69895 111 - 1
UUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGACGUGAAGUUGACAGCUCAAUGCGCUCUAAAA-AAAAAC
....((((((..(((((((((.(((((...)))))......(((((...........)))))..)))))).....)))..)))))).((.....)).........-...... ( -30.80)
>DroEre_CAF1 83899 110 - 1
UUCCGUCAGCAGCACAGCAACAGCGUCCAAGAGGCAACAACUUCGGGGCAAACGAAAACGAAAAGUUGCUGAGACAUGAAGUUGACAGCUCAAUGCGCUCCAAAA--AAAAC
....((((((..(((((((((...((((..(((.......)))..))))...((....))....))))))).....))..)))))).((.....)).........--..... ( -28.90)
>consensus
UUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGACAUGAAGUUGACAGCUCAAUGCGCUCUAAAA_AAAAAC
....((((((..(((((((((.(((((...)))))......(((((..(....)...)))))..))))))).....))..)))))).((.....))................ (-26.85 = -27.60 +   0.75)

alignment

secondary structure

dotplot

Window 2

Location	21,835,391 – 21,835,491
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	97.20
Mean single sequence MFE	-30.60
Consensus MFE	-26.44
Energy contribution	-26.52
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.59
Structure conservation index	0.86
SVM decision value	0.66
SVM RNA-class probability	0.814098
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21835391 100 - 22407834
CCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAACAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGA
.....((((((........))))))......((((((((.........(((((...)))))......(((((...........)))))..)))))))).. ( -29.90)
>DroSec_CAF1 122659 100 - 1
CCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGA
((.....))....(((((((((........))))).))))(((((((.(((((...)))))......(((((...........)))))..)))))))... ( -31.80)
>DroSim_CAF1 69932 100 - 1
CCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGA
((.....))....(((((((((........))))).))))(((((((.(((((...)))))......(((((...........)))))..)))))))... ( -31.80)
>DroEre_CAF1 83935 100 - 1
CCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCGUCCAAGAGGCAACAACUUCGGGGCAAACGAAAACGAAAAGUUGCUGAGA
((.....))....(((((((((........))))).))))(((((((...((((..(((.......)))..))))...((....))....)))))))... ( -30.00)
>DroYak_CAF1 74832 100 - 1
CCUGAUUGGUCUUUGCUUUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCGCCCAAGAGGCAACAACAUCGGGGCAAACGAAAACGAAAAGUUGCUGAGA
.....((((((........))))))......((((((((...((....))((((....(....).......))))...............)))))))).. ( -29.50)
>consensus
CCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACAACUUCGGGGCAAACGAAACCGAAAAGUUGCUGAGA
((.....))....(((((((((........))))).))))(((((((.((.((((((.(....)..))).)))))...((....))....)))))))... (-26.44 = -26.52 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	21,835,426 – 21,835,531
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	97.52
Mean single sequence MFE	-34.32
Consensus MFE	-32.28
Energy contribution	-32.92
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.94
SVM decision value	1.47
SVM RNA-class probability	0.956760
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21835426 105 - 22407834
CAAGUGGAAAUCCUUUUGGCCGAAAGGAGGCAGCAACCGACCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAACAACAGCUUCCAAGAGGCAACA
((((.((....)).))))(((....((((((.......((((.....))))..(((((((((........))))).))))........))))))....))).... ( -35.60)
>DroSec_CAF1 122694 105 - 1
CAAGUGGAAAUCCUUUUGGCCGAAAGGAGGCAGCAACCGACCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACA
((((.((....)).))))(((....((((((.((....((((.....))))..(((((((((........))))).))))..))....))))))....))).... ( -35.70)
>DroSim_CAF1 69967 105 - 1
CAAGUGGAAAUCCUUUUGGCCGAAAGGAGGCAGCAACCGACCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACA
((((.((....)).))))(((....((((((.((....((((.....))))..(((((((((........))))).))))..))....))))))....))).... ( -35.70)
>DroEre_CAF1 83970 105 - 1
CAAGUGGAAAUCCUUUUGGCCGAAAGGAGGCAGCAACCGACCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCGUCCAAGAGGCAACA
((((.((....)).))))(((....(((.((.((....((((.....))))..(((((((((........))))).))))..))....)).)))....))).... ( -34.00)
>DroYak_CAF1 74867 105 - 1
CAAGUGGAAAUCCUUUAGGCCGGAAGGAGGCAGCAACCGACCUGAUUGGUCUUUGCUUUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCGCCCAAGAGGCAACA
...........(((((.((((((((...((((((((..((((.....)))).)))))...)))...)))))...((......))......)))..)))))..... ( -30.60)
>consensus
CAAGUGGAAAUCCUUUUGGCCGAAAGGAGGCAGCAACCGACCUGAUUGGUCUUUGCUCUGGCCAGAUUCCGUCAGCAGCACAGCAACAGCUUCCAAGAGGCAACA
((((.((....)).))))(((....((((((.......((((.....))))..(((((((((........))))).))))........))))))....))).... (-32.28 = -32.92 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:36 2006