Locus 5674

Sequence ID	2R_DroMel_CAF1
Location	18,008,308 – 18,008,427
Length	119
Max. P	0.854528

overview

Window 8

Location	18,008,308 – 18,008,427
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.49
Mean single sequence MFE	-43.82
Consensus MFE	-39.76
Energy contribution	-40.20
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.47
Structure conservation index	0.91
SVM decision value	0.80
SVM RNA-class probability	0.854528
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18008308 119 + 20766785
UGAGGCCGGCACGGCAUGUAUUUGGAAAACCAUUUCGCUGGCUGCCUGGUCCUUUGUGAACCUUAAAGCUGCUCGGUCUC-AAAUGGAAGCUCGCAUUGGAAGUGGUUUUUCCAGGGGCG
(((((((((((((((.......(((....)))....))))(((....(((.(.....).)))....)))))).)))))))-).......((((...(((((((.....))))))))))). ( -39.50)
>DroSec_CAF1 22435 119 + 1
UGAGGCCGGCUCGGCAUGUAUUUGGAAAACCAUUUCGCUGACUGCCUGGUCCUUUGUGGACCUUAAAGCUGCUCGGUCUC-AAAUGGAAGCUCGCAUUGGAAGUGGUUUUUCCAGGGGCG
((((((((((..((((.((...(((((.....)))))...)))))).(((((.....)))))........)).)))))))-).......((((...(((((((.....))))))))))). ( -43.80)
>DroSim_CAF1 21370 119 + 1
UGAGGCCGGCACGGCAUGUAUUUGGAAAACCAUUUCGCUGGCUGCCUGGUCCUUUGUGGACCUUAAAGCUGCUCGGUCUC-AAAUGGAAGCUCGCAUUGGAAGUGGUUUUUCCAGGGGCG
(((((((((((((((.......(((....)))....))))(((....(((((.....)))))....)))))).)))))))-).......((((...(((((((.....))))))))))). ( -46.30)
>DroEre_CAF1 23790 119 + 1
UGAGGCCGGCACGGCAUGUAUUUGGAAAACCAUUUCGCUGGCUGGCUGGUCCUUUGUGGACCUUAAAGCUGCUCGGUCUC-AAAUGGAAGUUCGCAUUGGUAGUGGUUUUUCCAGGGGCG
(((((((((((((((.......(((....)))....))))(((....(((((.....)))))....)))))).)))))))-)..((((((.((((.......))))..))))))...... ( -43.90)
>DroYak_CAF1 21103 120 + 1
UGAGGCCGGCACGGCAUGUAUUUGGAAAACCAUUUCGCUGGCUGGCUGGUCCUUUGUGGACCUUAAAGCUGCUCGGUCUCGAAAUGGAAGCUCGCAUUGGAAGUGGUUUUUCCAGGGGCG
.((((((((((((((.......(((....)))....))))(((....(((((.....)))))....)))))).))))))).........((((...(((((((.....))))))))))). ( -45.60)
>consensus
UGAGGCCGGCACGGCAUGUAUUUGGAAAACCAUUUCGCUGGCUGCCUGGUCCUUUGUGGACCUUAAAGCUGCUCGGUCUC_AAAUGGAAGCUCGCAUUGGAAGUGGUUUUUCCAGGGGCG
.(((((((((.((((.......(((....)))....))))(((....(((((.....)))))....))).)).))))))).........((((...(((((((.....))))))))))). (-39.76 = -40.20 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	18,008,308 – 18,008,427
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.49
Mean single sequence MFE	-34.04
Consensus MFE	-30.80
Energy contribution	-30.88
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.38
Structure conservation index	0.90
SVM decision value	0.50
SVM RNA-class probability	0.761479
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18008308 119 - 20766785
CGCCCCUGGAAAAACCACUUCCAAUGCGAGCUUCCAUUU-GAGACCGAGCAGCUUUAAGGUUCACAAAGGACCAGGCAGCCAGCGAAAUGGUUUUCCAAAUACAUGCCGUGCCGGCCUCA
(((...(((((.......)))))..)))..........(-(((.(((.(((.......(((((.....))))).((((((((......))))............)))).)))))).)))) ( -34.00)
>DroSec_CAF1 22435 119 - 1
CGCCCCUGGAAAAACCACUUCCAAUGCGAGCUUCCAUUU-GAGACCGAGCAGCUUUAAGGUCCACAAAGGACCAGGCAGUCAGCGAAAUGGUUUUCCAAAUACAUGCCGAGCCGGCCUCA
(((...(((((.......)))))..)))..........(-(((.(((.((........(((((.....))))).((((((....((((....)))).....)).))))..))))).)))) ( -35.30)
>DroSim_CAF1 21370 119 - 1
CGCCCCUGGAAAAACCACUUCCAAUGCGAGCUUCCAUUU-GAGACCGAGCAGCUUUAAGGUCCACAAAGGACCAGGCAGCCAGCGAAAUGGUUUUCCAAAUACAUGCCGUGCCGGCCUCA
(((...(((((.......)))))..)))..........(-(((.(((.(((.......(((((.....))))).((((((((......))))............)))).)))))).)))) ( -36.90)
>DroEre_CAF1 23790 119 - 1
CGCCCCUGGAAAAACCACUACCAAUGCGAACUUCCAUUU-GAGACCGAGCAGCUUUAAGGUCCACAAAGGACCAGCCAGCCAGCGAAAUGGUUUUCCAAAUACAUGCCGUGCCGGCCUCA
(((...(((...........)))..)))..........(-(((.(((.(((((.....(((((.....)))))....(((((......)))))............))..)))))).)))) ( -30.20)
>DroYak_CAF1 21103 120 - 1
CGCCCCUGGAAAAACCACUUCCAAUGCGAGCUUCCAUUUCGAGACCGAGCAGCUUUAAGGUCCACAAAGGACCAGCCAGCCAGCGAAAUGGUUUUCCAAAUACAUGCCGUGCCGGCCUCA
(((...(((((.......)))))..)))............(((.(((.(((((.....(((((.....)))))....(((((......)))))............))..)))))).))). ( -33.80)
>consensus
CGCCCCUGGAAAAACCACUUCCAAUGCGAGCUUCCAUUU_GAGACCGAGCAGCUUUAAGGUCCACAAAGGACCAGGCAGCCAGCGAAAUGGUUUUCCAAAUACAUGCCGUGCCGGCCUCA
(((...(((((.......)))))..)))............(((.(((.(((((.....(((((.....))))).(..(((((......)))))..).........))..)))))).))). (-30.80 = -30.88 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:32 2006