Locus 5848

Sequence ID	2R_DroMel_CAF1
Location	18,499,695 – 18,499,891
Length	196
Max. P	0.938959

overview

Window 8

Location	18,499,695 – 18,499,811
Length	116
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	93.16
Mean single sequence MFE	-25.81
Consensus MFE	-21.28
Energy contribution	-22.03
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.82
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499695 116 + 20766785
GAUUAAUUAAGAACUAAAAAUGAAAUGGCAUAAAACCAAUCAAAUGGCCAAAUGGCCAAACGGCUUUCACCGCAAUUGCGAA-AACGUUCGCUCCAGAGCCGUUUGCUCAAGCUGCA
....................(((..(((.......))).)))..(((((....)))))..((((((...........(((((-....)))))....((((.....)))))))))).. ( -26.80)
>DroSec_CAF1 18491 109 + 1
GAUUAAUUAAGAACUAAAAAUUAAAUGGCAUAAAACCAAUCAAAUG--------GCCAAACGGCUUUCACCGCAAUUGCGAAAAACGUUCGCUCCAGAGCCGUUUGCUCAAGCUGCA
..........................(((......(((......))--------).(((((((((((..........(((((.....)))))...))))))))))).....)))... ( -22.32)
>DroSim_CAF1 7529 117 + 1
GAUUAAUUAAGAACUAAAAAUGAAAUGGCAUAAAACCAAUCAAAUGGCCAAAUGGCCAAACGGCUUUCACCGCAAUUGCGAAAAACGUUCGCUACAGUGCCGUUUGCUCAAGCUGCA
......................(((((((((.............(((((....)))))..(((......))).....(((((.....)))))....)))))))))((.......)). ( -28.30)
>consensus
GAUUAAUUAAGAACUAAAAAUGAAAUGGCAUAAAACCAAUCAAAUGGCCAAAUGGCCAAACGGCUUUCACCGCAAUUGCGAAAAACGUUCGCUCCAGAGCCGUUUGCUCAAGCUGCA
......................(((((((...............(((((....)))))..(((......))).....(((((.....)))))......)))))))((.......)). (-21.28 = -22.03 +   0.75)

alignment

secondary structure

dotplot

Window 9

Location	18,499,695 – 18,499,811
Length	116
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	93.16
Mean single sequence MFE	-33.23
Consensus MFE	-26.62
Energy contribution	-27.70
Covariance contribution	1.08
Combinations/Pair	1.00
Mean z-score	-2.26
Structure conservation index	0.80
SVM decision value	0.11
SVM RNA-class probability	0.589751
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499695 116 - 20766785
UGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUU-UUCGCAAUUGCGGUGAAAGCCGUUUGGCCAUUUGGCCAUUUGAUUGGUUUUAUGCCAUUUCAUUUUUAGUUCUUAAUUAAUC
....((((((((.....))))..))))(((((((-(((((.......))))))))((..(((((....)))))..))..((((.....))))...........)))).......... ( -34.70)
>DroSec_CAF1 18491 109 - 1
UGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUUUUUCGCAAUUGCGGUGAAAGCCGUUUGGC--------CAUUUGAUUGGUUUUAUGCCAUUUAAUUUUUAGUUCUUAAUUAAUC
....((((((((.....))))..))))((((.......((....(((((....)))))...))--------...((((.((((.....)))).))))......)))).......... ( -29.60)
>DroSim_CAF1 7529 117 - 1
UGCAGCUUGAGCAAACGGCACUGUAGCGAACGUUUUUCGCAAUUGCGGUGAAAGCCGUUUGGCCAUUUGGCCAUUUGAUUGGUUUUAUGCCAUUUCAUUUUUAGUUCUUAAUUAAUC
........((((((((((((((((((((((.....)))))...))))))....)))))))((((....))))...(((.((((.....))))..)))......)))).......... ( -35.40)
>consensus
UGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUUUUUCGCAAUUGCGGUGAAAGCCGUUUGGCCAUUUGGCCAUUUGAUUGGUUUUAUGCCAUUUCAUUUUUAGUUCUUAAUUAAUC
....(((.((((.....))))...)))((((.......((....))(((((((((((..(((((....)))))......))))))).))))............)))).......... (-26.62 = -27.70 +   1.08)

alignment

secondary structure

dotplot

Window 0

Location	18,499,735 – 18,499,851
Length	116
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	90.78
Mean single sequence MFE	-33.02
Consensus MFE	-27.37
Energy contribution	-28.79
Covariance contribution	1.42
Combinations/Pair	1.00
Mean z-score	-2.26
Structure conservation index	0.83
SVM decision value	0.44
SVM RNA-class probability	0.736018
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499735 116 + 20766785
CAAAUGGCCAAAUGGCCAAACGGCUUUCACCGCAAUUGCGAA-AACGUUCGCUCCAGAGCCGUUUGCUCAAGCUGCAAAAUAUGACUUCAAAUUAAUGCAAAGUGAGGUAGGUGCUC
.....((((....))))((((((((((..........(((((-....)))))...)))))))))).((((...((((.(((.((....)).)))..))))...)))).......... ( -31.92)
>DroSec_CAF1 18531 105 + 1
CAAAUG--------GCCAAACGGCUUUCACCGCAAUUGCGAAAAACGUUCGCUCCAGAGCCGUUUGCUCAAGCUGCAAAAUAUGACUUCAAAUUAAUGCAGAGUGAG----GUGCUC
.....(--------(((((((((((((..........(((((.....)))))...)))))))))))((((..(((((.(((.((....)).)))..)))))..))))----..))). ( -32.72)
>DroSim_CAF1 7569 113 + 1
CAAAUGGCCAAAUGGCCAAACGGCUUUCACCGCAAUUGCGAAAAACGUUCGCUACAGUGCCGUUUGCUCAAGCUGCAAAAUAUGACUUCAAAUUAAUGCAGAGUGAG----GUGCUC
.....((((....))))(((((((.......((....(((((.....)))))....))))))))).((((..(((((.(((.((....)).)))..)))))..))))----...... ( -34.41)
>consensus
CAAAUGGCCAAAUGGCCAAACGGCUUUCACCGCAAUUGCGAAAAACGUUCGCUCCAGAGCCGUUUGCUCAAGCUGCAAAAUAUGACUUCAAAUUAAUGCAGAGUGAG____GUGCUC
.....((((....))))((((((((((..........(((((.....)))))...)))))))))).((((..(((((.(((.((....)).)))..)))))..)))).......... (-27.37 = -28.79 +   1.42)

alignment

secondary structure

dotplot

Window 1

Location	18,499,735 – 18,499,851
Length	116
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	90.78
Mean single sequence MFE	-36.63
Consensus MFE	-33.44
Energy contribution	-34.30
Covariance contribution	0.86
Combinations/Pair	1.03
Mean z-score	-2.38
Structure conservation index	0.91
SVM decision value	1.27
SVM RNA-class probability	0.938959
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499735 116 - 20766785
GAGCACCUACCUCACUUUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUU-UUCGCAAUUGCGGUGAAAGCCGUUUGGCCAUUUGGCCAUUUG
((((......((((..(((((..(((.((....)).))).)))))..))))......))))....(((((....-)))))....(((((....))))).(((((....))))).... ( -38.40)
>DroSec_CAF1 18531 105 - 1
GAGCAC----CUCACUCUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUUUUUCGCAAUUGCGGUGAAAGCCGUUUGGC--------CAUUUG
((((..----((((..(((((..(((.((....)).))).)))))..))))......))))(((..((((((.(((((((.......))))))).)))))).)--------)).... ( -33.10)
>DroSim_CAF1 7569 113 - 1
GAGCAC----CUCACUCUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCACUGUAGCGAACGUUUUUCGCAAUUGCGGUGAAAGCCGUUUGGCCAUUUGGCCAUUUG
......----((((..(((((..(((.((....)).))).)))))..)))).((((((((((((((((((.....)))))...))))))....)))))))((((....))))..... ( -38.40)
>consensus
GAGCAC____CUCACUCUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUUUUUCGCAAUUGCGGUGAAAGCCGUUUGGCCAUUUGGCCAUUUG
((((......((((..(((((..(((.((....)).))).)))))..))))......))))....(((((.....)))))....(((((....))))).(((((....))))).... (-33.44 = -34.30 +   0.86)

alignment

secondary structure

dotplot

Window 2

Location	18,499,775 – 18,499,891
Length	116
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	95.39
Mean single sequence MFE	-30.63
Consensus MFE	-30.32
Energy contribution	-30.77
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-1.40
Structure conservation index	0.99
SVM decision value	0.10
SVM RNA-class probability	0.583173
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499775 116 - 20766785
GCUUCAUUUGUUGUGCAAAUAGGCGAAAUGCAUUGCCAUCGAGCACCUACCUCACUUUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUU-UU
((((((((((.....))))).(((((......)))))...((((......((((..(((((..(((.((....)).))).)))))..))))......)))).))))).......-.. ( -31.80)
>DroSec_CAF1 18563 113 - 1
GCUUCAUUUGUUGUGCAAAUAGGCGAAAUGCAUUGCCAUCGAGCAC----CUCACUCUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUUUUU
((((((((((.....))))).(((((......)))))...((((..----((((..(((((..(((.((....)).))).)))))..))))......)))).))))).......... ( -32.30)
>DroSim_CAF1 7609 113 - 1
GCUUCAUUUGUUGUGCAAAUAGGCGAAAUGCAUUGCCAUCGAGCAC----CUCACUCUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCACUGUAGCGAACGUUUUU
(((.((..((((((((.....(((((......))))).....))..----((((..(((((..(((.((....)).))).)))))..))))...)))))).)).))).......... ( -27.80)
>consensus
GCUUCAUUUGUUGUGCAAAUAGGCGAAAUGCAUUGCCAUCGAGCAC____CUCACUCUGCAUUAAUUUGAAGUCAUAUUUUGCAGCUUGAGCAAACGGCUCUGGAGCGAACGUUUUU
((((((((((.....))))).(((((......)))))...((((......((((..(((((..(((.((....)).))).)))))..))))......)))).))))).......... (-30.32 = -30.77 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:21 2006