Locus 2966

Sequence ID	X_DroMel_CAF1
Location	7,903,979 – 7,904,139
Length	160
Max. P	0.953961

overview

Window 9

Location	7,903,979 – 7,904,099
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-38.27
Consensus MFE	-34.73
Energy contribution	-35.07
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.91
SVM decision value	0.86
SVM RNA-class probability	0.867774
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7903979 120 + 22224390
GCGGGUCUGAUAAAGAGUCAUGGGAUGGAAGGGGGUGGGAAAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCA
(((..(((.....)))((((((........(((((..(..........)..))))).((((..((((((((((((....))))))).))))).))))......))))))....))).... ( -35.60)
>DroSec_CAF1 4588 120 + 1
GCGAUUCUGAUAAAGAGGCUUCGGCUGGAAGGGGGUGGGAAAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCA
....((((.....))))(((((((((....(((((..(..........)..))))).......((((((((((((....))))))).))))).))))))....((((....)))).))). ( -38.50)
>DroSim_CAF1 7708 120 + 1
GCGAGUCUGAUAAAGAGGCUUCGGCUGGAAGGGGGUGGGAAAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCA
.(((((((.......)))).)))((((...(((((..(..........)..))))).((((..((((((((((((....))))))).))))).))))......((((....)))))))). ( -40.70)
>consensus
GCGAGUCUGAUAAAGAGGCUUCGGCUGGAAGGGGGUGGGAAAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCA
..(..(((.....)))..)....((((...(((((..(..........)..))))).((((..((((((((((((....))))))).))))).))))......((((....)))))))). (-34.73 = -35.07 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	7,904,019 – 7,904,139
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.03
Mean single sequence MFE	-40.00
Consensus MFE	-39.50
Energy contribution	-39.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-4.21
Structure conservation index	0.99
SVM decision value	1.05
SVM RNA-class probability	0.906780
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7904019 120 + 22224390
AAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCAAAUGCAGAAGCCGAAGAAGAAGCAGAGGCAUCAGAAGAAG
.......(.(((((((.((((..((((((((((((....))))))).))))).))))(((((.((((....))))..((....))..)))))...........))))))).)........ ( -39.50)
>DroSec_CAF1 4628 120 + 1
AAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCAAAUGCAGAAGCCGAAGAAGAAGCAGAGGCAUCGCAAGAAG
.........(((((((.((((..((((((((((((....))))))).))))).))))(((((.((((....))))..((....))..)))))...........)))))))((....)).. ( -41.50)
>DroSim_CAF1 7748 120 + 1
AAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCAAAUGCAGAAGCCGAAGAAGAAGCAGAGGCAUCACAAGAAG
.......(.(((((((.((((..((((((((((((....))))))).))))).))))(((((.((((....))))..((....))..)))))...........))))))).)........ ( -39.50)
>DroYak_CAF1 7848 120 + 1
AAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCAAAUGCAGAAGCCGAAGAAGAAGCAGAGGCAUCAGAAGAAG
.......(.(((((((.((((..((((((((((((....))))))).))))).))))(((((.((((....))))..((....))..)))))...........))))))).)........ ( -39.50)
>consensus
AAGGGGAGCUGCCUCUAGGUUAAUAAAUCGUGCUAAUAGUGGCACGAAUUUAAAGCCGGUUUACAUGGCAACAUGCAGCAAAUGCAGAAGCCGAAGAAGAAGCAGAGGCAUCACAAGAAG
.......(.(((((((.((((..((((((((((((....))))))).))))).))))(((((.((((....))))..((....))..)))))...........))))))).)........ (-39.50 = -39.50 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	7,904,019 – 7,904,139
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.03
Mean single sequence MFE	-31.77
Consensus MFE	-31.60
Energy contribution	-31.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.97
Structure conservation index	0.99
SVM decision value	1.44
SVM RNA-class probability	0.953961
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7904019 120 - 22224390
CUUCUUCUGAUGCCUCUGCUUCUUCUUCGGCUUCUGCAUUUGCUGCAUGUUGCCAUGUAAACCGGCUUUAAAUUCGUGCCACUAUUAGCACGAUUUAUUAACCUAGAGGCAGCUCCCCUU
..........((((((((..........(((..(((((.....)))).)..))).........((...(((((.(((((........))))))))))....))))))))))......... ( -31.60)
>DroSec_CAF1 4628 120 - 1
CUUCUUGCGAUGCCUCUGCUUCUUCUUCGGCUUCUGCAUUUGCUGCAUGUUGCCAUGUAAACCGGCUUUAAAUUCGUGCCACUAUUAGCACGAUUUAUUAACCUAGAGGCAGCUCCCCUU
......((..((((((((..........(((..(((((.....)))).)..))).........((...(((((.(((((........))))))))))....))))))))))))....... ( -32.30)
>DroSim_CAF1 7748 120 - 1
CUUCUUGUGAUGCCUCUGCUUCUUCUUCGGCUUCUGCAUUUGCUGCAUGUUGCCAUGUAAACCGGCUUUAAAUUCGUGCCACUAUUAGCACGAUUUAUUAACCUAGAGGCAGCUCCCCUU
..........((((((((..........(((..(((((.....)))).)..))).........((...(((((.(((((........))))))))))....))))))))))......... ( -31.60)
>DroYak_CAF1 7848 120 - 1
CUUCUUCUGAUGCCUCUGCUUCUUCUUCGGCUUCUGCAUUUGCUGCAUGUUGCCAUGUAAACCGGCUUUAAAUUCGUGCCACUAUUAGCACGAUUUAUUAACCUAGAGGCAGCUCCCCUU
..........((((((((..........(((..(((((.....)))).)..))).........((...(((((.(((((........))))))))))....))))))))))......... ( -31.60)
>consensus
CUUCUUCUGAUGCCUCUGCUUCUUCUUCGGCUUCUGCAUUUGCUGCAUGUUGCCAUGUAAACCGGCUUUAAAUUCGUGCCACUAUUAGCACGAUUUAUUAACCUAGAGGCAGCUCCCCUU
..........((((((((..........(((..(((((.....)))).)..))).........((...(((((.(((((........))))))))))....))))))))))......... (-31.60 = -31.60 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:58 2006