Locus 272

Sequence ID	2R_DroMel_CAF1
Location	1,669,562 – 1,669,692
Length	130
Max. P	0.995800

overview

Window 6

Location	1,669,562 – 1,669,653
Length	91
Sequences	3
Columns	91
Reading direction	reverse
Mean pairwise identity	91.18
Mean single sequence MFE	-24.40
Consensus MFE	-24.00
Energy contribution	-24.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.98
SVM decision value	0.57
SVM RNA-class probability	0.784115
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1669562 91 - 20766785
CCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCAGUUAAGCACACAAAAAAAUUA
((((((((.......))))).....((((((.....)))))).((((.........))))..)))..((......)).............. ( -25.20)
>DroPse_CAF1 84213 90 - 1
CCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCUCUGAAA-CAUCGUAAAAUUC
((((((((.......))))).....((((((.....)))))).((((.........))))..)))............-............. ( -24.00)
>DroPer_CAF1 78143 90 - 1
CCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCUCUGAAA-CAUCGUAAAAUUC
((((((((.......))))).....((((((.....)))))).((((.........))))..)))............-............. ( -24.00)
>consensus
CCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCUCUGAAA_CAUCGUAAAAUUC
((((((((.......))))).....((((((.....)))))).((((.........))))..))).......................... (-24.00 = -24.00 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	1,669,573 – 1,669,692
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	75.50
Mean single sequence MFE	-39.68
Consensus MFE	-32.30
Energy contribution	-32.67
Covariance contribution	0.38
Combinations/Pair	1.08
Mean z-score	-2.02
Structure conservation index	0.81
SVM decision value	2.19
SVM RNA-class probability	0.989987
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1669573 119 + 20766785
UGUGCUUAACUGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGCAUACGAAAU-CAAAAUUUUUGCUAUGCGUUCUCC
.(((((.(((((((.....)))......))))))))).((((((..((((((....))))))..).))))).......((((((((((((((((.-......))))).))))))))))). ( -46.10)
>DroPse_CAF1 84224 108 + 1
UG-UUUCAGAGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGU--UAUAA-------CUUUUUUGUAUUCUCUUU--
..-....(((((((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))..--(((((-------.....)))))..))))..-- ( -39.70)
>DroEre_CAF1 60507 107 + 1
CUUAUUUAAGGGCCUCCGUGGCGCAAUUGAUUAGCGUGUUCGACUGUUAACCAACAUUUUGGUGGUUCCAGUCCACCCGGGGGCGCGUAUCAAUUUCGGGGUUUUUU-------------
.......(((((((.(((......(((((((..((((.((((..((((....))))....(((((.......))))))))).))))..))))))).)))))))))).------------- ( -32.40)
>DroPer_CAF1 78154 108 + 1
UG-UUUCAGAGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGU--AACAA-------CUUUUUUGUAUUCUCUUU--
..-....(((((((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))..--.((((-------.....))))...))))..-- ( -40.50)
>consensus
UG_UUUCAAAGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGC__AACAA_______CUUUUUUGUAUUCUCUUU__
...........(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).................................... (-32.30 = -32.67 +   0.38)

alignment

secondary structure

dotplot

Window 8

Location	1,669,573 – 1,669,692
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	75.50
Mean single sequence MFE	-32.62
Consensus MFE	-26.98
Energy contribution	-26.85
Covariance contribution	-0.13
Combinations/Pair	1.10
Mean z-score	-2.17
Structure conservation index	0.83
SVM decision value	2.62
SVM RNA-class probability	0.995800
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1669573 119 - 20766785
GGAGAACGCAUAGCAAAAAUUUUG-AUUUCGUAUGCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCAGUUAAGCACA
.(..((((((((..(((.......-.)))..)))))(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).)))...)... ( -36.30)
>DroPse_CAF1 84224 108 - 1
--AAAGAGAAUACAAAAAAG-------UUAUA--ACGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCUCUGAAA-CA
--..((((...........(-------(....--))(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))))))....-.. ( -33.10)
>DroEre_CAF1 60507 107 - 1
-------------AAAAAACCCCGAAAUUGAUACGCGCCCCCGGGUGGACUGGAACCACCAAAAUGUUGGUUAACAGUCGAACACGCUAAUCAAUUGCGCCACGGAGGCCCUUAAAUAAG
-------------......(((((.(((((((...((((....))))(((((.(((((.(.....).)))))..)))))..........)))))))......))).))............ ( -27.10)
>DroPer_CAF1 78154 108 - 1
--AAAGAGAAUACAAAAAAG-------UUGUU--ACGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCUCUGAAA-CA
--..((((...((((.....-------)))).--..(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))))))....-.. ( -34.00)
>consensus
__AAAGAGAAUACAAAAAAG_______UUGUU__ACGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCUCUAAAA_CA
....................................(((.((((((((.......)))))......(((((.....)))))..((((.........))))..))).)))........... (-26.98 = -26.85 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:14 2006