Locus 7929

Sequence ID	3R_DroMel_CAF1
Location	21,256,797 – 21,256,933
Length	136
Max. P	0.990413

overview

Window 1

Location	21,256,797 – 21,256,895
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	83.06
Mean single sequence MFE	-26.18
Consensus MFE	-17.72
Energy contribution	-17.84
Covariance contribution	0.12
Combinations/Pair	1.23
Mean z-score	-3.12
Structure conservation index	0.68
SVM decision value	2.21
SVM RNA-class probability	0.990413
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21256797 98 + 27905053
CGCUUAUUGUUCCGUUGCCGGAACUUUGUUUACAUUUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUUCAGUCAUCGUAGCAGCUC
.(((((((((((((....))))))((((((......((((((((.....)))))))).)))))))))))....(((((..........).)))))).. ( -24.70)
>DroSec_CAF1 81785 88 + 1
CGCUUAUUGUUCCGUUGCCGGAACUUUGUUUACACAUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUACUGCCAU----------C
.((.....((((((....))))))((((((.....(((((((((.....)))))))))))))))..........))...........----------. ( -23.40)
>DroSim_CAF1 84509 98 + 1
CGCUUAUUGUUCCGUUGCCGGAACUUUGUUUACAUUUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUACAGCCAUCGUAGCAGCUC
...(((((((((((....))))))((((((......((((((((.....)))))))).))))))))))).....(((((((.......)))).))).. ( -27.90)
>DroYak_CAF1 91336 98 + 1
CGCUUAUUGUUCUGCUGCCGGAACUUUGUUUACAUUUGCCAUCACUUUCUGGUGGCAUAAUAAAAAUAAUUUUUGCUCUGCAGUCAUCGCAGCAGCUC
........((((((....)))))).((((((..(((((((((((.....)))))))).)))..)))))).....(((((((.......)))).))).. ( -26.00)
>DroAna_CAF1 75821 94 + 1
UGCUUAUUGUCCUGUCGCCGG-GCUUUGUUUACACACACAAUCACUUU-UGGUGGCAGGACGA-AAUAAU-UUCGCUUUACAGUCGUCUUGGCAGCUC
.(((..(((((((((((((((-(..((((........)))).....))-))))))))))))))-......-...(((..((....))...)))))).. ( -28.90)
>consensus
CGCUUAUUGUUCCGUUGCCGGAACUUUGUUUACAUUUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUACAGUCAUCGUAGCAGCUC
.((.....((((((....))))))((((((......((((((((.....)))))))).))))))..........))...................... (-17.72 = -17.84 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	21,256,797 – 21,256,895
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	83.06
Mean single sequence MFE	-25.60
Consensus MFE	-15.78
Energy contribution	-16.46
Covariance contribution	0.68
Combinations/Pair	1.13
Mean z-score	-2.58
Structure conservation index	0.62
SVM decision value	1.13
SVM RNA-class probability	0.919157
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21256797 98 - 27905053
GAGCUGCUACGAUGACUGAAGAGCAAAAAUUAUUUUUGUUAUGCCACCAGAAAAUGAUGGCAAAUGUAAACAAAGUUCCGGCAACGGAACAAUAAGCG
..(((..((((..........(((((((.....))))))).(((((.((.....)).)))))..))))......((((((....))))))....))). ( -28.20)
>DroSec_CAF1 81785 88 - 1
G----------AUGGCAGUAGAGCAAAAAUUAUUUUUGUUAUGCCACCAGAAAAUGAUGGCAUGUGUAAACAAAGUUCCGGCAACGGAACAAUAAGCG
(----------.(((((....(((((((.....))))))).))))).)...........((.(((....)))..((((((....)))))).....)). ( -27.10)
>DroSim_CAF1 84509 98 - 1
GAGCUGCUACGAUGGCUGUAGAGCAAAAAUUAUUUUUGUUAUGCCACCAGAAAAUGAUGGCAAAUGUAAACAAAGUUCCGGCAACGGAACAAUAAGCG
..(((.(((((.....)))))(((((((.....))))))).(((((.((.....)).)))))............((((((....))))))....))). ( -29.30)
>DroYak_CAF1 91336 98 - 1
GAGCUGCUGCGAUGACUGCAGAGCAAAAAUUAUUUUUAUUAUGCCACCAGAAAGUGAUGGCAAAUGUAAACAAAGUUCCGGCAGCAGAACAAUAAGCG
(..(((((((...((((((...))..........(((((..(((((.((.....)).)))))...)))))...))))...)))))))..)........ ( -23.20)
>DroAna_CAF1 75821 94 - 1
GAGCUGCCAAGACGACUGUAAAGCGAA-AUUAUU-UCGUCCUGCCACCA-AAAGUGAUUGUGUGUGUAAACAAAGC-CCGGCGACAGGACAAUAAGCA
..(((.......((.((....))))..-......-..((((((.(.((.-...((..((((........)))).))-..)).).))))))....))). ( -20.20)
>consensus
GAGCUGCUACGAUGACUGUAGAGCAAAAAUUAUUUUUGUUAUGCCACCAGAAAAUGAUGGCAAAUGUAAACAAAGUUCCGGCAACGGAACAAUAAGCG
......................((.................(((((.((.....)).)))))............((((((....)))))).....)). (-15.78 = -16.46 +   0.68)

alignment

secondary structure

dotplot

Window 3

Location	21,256,827 – 21,256,933
Length	106
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	79.96
Mean single sequence MFE	-23.22
Consensus MFE	-13.42
Energy contribution	-14.70
Covariance contribution	1.28
Combinations/Pair	1.12
Mean z-score	-2.20
Structure conservation index	0.58
SVM decision value	0.94
SVM RNA-class probability	0.885475
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21256827 106 + 27905053
UACAUUUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUUCAGUCAUCGUAGCAGCUCAUCA--AAGAUAGUUGUAUAAGGCAUUUAUGCAAGCCAAA
(((...((((((((.....))))))))...(((((.....))))).............)))((((((.(((.--..)))))))))....(((..........)))... ( -21.70)
>DroSec_CAF1 81815 96 + 1
UACACAUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUACUGCCAU----------CAUCA--AAGAUAGUUGAAGAAGGCAUUUAUGCAAGCCAAA
.....(((((((((.....))))))))).............(((((.....((((.(----------(.(((--(......)))).)).)))).....)))))..... ( -26.20)
>DroSim_CAF1 84539 106 + 1
UACAUUUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUACAGCCAUCGUAGCAGCUCAUCA--AAGAUAGUUGAACAAGGCAUUUAUGCAAGCCAAA
......((((((((.....))))))))..............(((((......(((...((..(((((.(((.--..)))))))).))..)))......)))))..... ( -22.90)
>DroYak_CAF1 91366 102 + 1
UACAUUUGCCAUCACUUUCUGGUGGCAUAAUAAAAAUAAUUUUUGCUCUGCAGUCAUCGCAGCAGCUCAUCA--AAGAUAGUUGAACAAGGCAUU----CAAGCCAAA
......((((((((.....)))))))).................(((((((.......)))).)))...(((--(......))))....(((...----...)))... ( -24.90)
>DroAna_CAF1 75850 96 + 1
UACACACACAAUCACUUU-UGGUGGCAGGACGA-AAUAAU-UUCGCUUUACAGUCGUCUUGGCAGCUCAUCAAAAAGAUAGUUGAACAGGGCAUUUAUC---------
....(((.(((......)-))))).((((((((-..(((.-......)))...))))))))...((((.((((........))))...)))).......--------- ( -20.40)
>consensus
UACAUUUGCCAUCAUUUUCUGGUGGCAUAACAAAAAUAAUUUUUGCUCUACAGUCAUCGUAGCAGCUCAUCA__AAGAUAGUUGAACAAGGCAUUUAUGCAAGCCAAA
......((((((((.....))))))))...(((((.....))))).......(((.......(((((.(((.....)))))))).....)))................ (-13.42 = -14.70 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:20 2006