Locus 3843

Sequence ID	X_DroMel_CAF1
Location	10,212,030 – 10,212,310
Length	280
Max. P	0.993953

overview

Window 4

Location	10,212,030 – 10,212,150
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.67
Mean single sequence MFE	-49.66
Consensus MFE	-43.90
Energy contribution	-43.62
Covariance contribution	-0.28
Combinations/Pair	1.11
Mean z-score	-1.17
Structure conservation index	0.88
SVM decision value	0.05
SVM RNA-class probability	0.560650
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10212030 120 - 22224390
CCCGAAGUGUGGAUGUGGCGGUCUUCCUGCGCCAACGGAUCGCCGCCUGGUUCGAUGAGAAUCGGGAUGCGACCAGUGGCGACAUGGAGGACUAUCAGAUGCGCGGUGGACCGUAAGUAC
.(((...((((.((.((..(((((((((((((((..((.((((..((((((((.....))))))))..))))))..))))).)).))))))))..)).)).)))).)))........... ( -57.30)
>DroSec_CAF1 8375 120 - 1
CCCGGAGUGUGGAUGUGGCGGUCUUCCUGCGCCAGCGGAUCGCCGCCUGGUUCGAUGAGAAUCGGGAUGCGAGCAGUGGCGACAUGGAGAACUAUCAGAUGCGCGGUGGACCGUAAGUAC
..((((.((((.((.((..(((..((((((((((.(...((((..((((((((.....))))))))..))))...)))))).)).)))..)))..)).)).)))).)...)))....... ( -48.80)
>DroSim_CAF1 8844 120 - 1
CCCGGAGUGUGGAUGUGGCGGUCUUCCUGCGCCAGCGGAUCGCCGCCUGGUUCGAUGAGAAUCGGGAUGCGAGCAGUGGCGACAUGGAGAACUAUCAGAUGCGCGGUGGACCGUAAGUAC
..((((.((((.((.((..(((..((((((((((.(...((((..((((((((.....))))))))..))))...)))))).)).)))..)))..)).)).)))).)...)))....... ( -48.80)
>DroEre_CAF1 9523 120 - 1
CCCGGAGCGUGGAUGUGGCGGUCUUUCUGCGCCAGAGGAUCGCCGCCUGGUUCGAUGAGAAUCGGUAUGCGAGCAGUGGCGACAUGGAGAACUACCAGAUGCGCGGGGGACCGUAAGUGC
......(((((.((.(((..(((((..(((((((..(..((((...(((((((.....)))))))...)))).)..))))).))..))).))..))).)).)))((....))......)) ( -47.20)
>DroYak_CAF1 9521 120 - 1
CCCGGAGCGUGGAUGUGGCGGUCUUUCUGCGCCAGAGAAUCGCCGCCUGGUUCGAUGAGAAUCGGGAUGCGACCAGUGGCGACAUUGAGAGCUACCAGAUGCGUGGAGGACCGUAAGUUC
..........((((...((((((((.(..(((.......((((..((((((((.....))))))))..)))).(((((....))))).............)))..)))))))))..)))) ( -46.20)
>consensus
CCCGGAGUGUGGAUGUGGCGGUCUUCCUGCGCCAGCGGAUCGCCGCCUGGUUCGAUGAGAAUCGGGAUGCGAGCAGUGGCGACAUGGAGAACUAUCAGAUGCGCGGUGGACCGUAAGUAC
........(((.((.(((..((((((.(((((((.....((((..((((((((.....))))))))..))))....))))).)).)))).))..))).)).)))((....))........ (-43.90 = -43.62 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	10,212,110 – 10,212,230
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-46.60
Consensus MFE	-44.36
Energy contribution	-44.72
Covariance contribution	0.36
Combinations/Pair	1.11
Mean z-score	-1.08
Structure conservation index	0.95
SVM decision value	0.12
SVM RNA-class probability	0.595537
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10212110 120 + 22224390
AUCCGUUGGCGCAGGAAGACCGCCACAUCCACACUUCGGGUGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGC
..(((((((((((.((.(((.(((((((((.......)))))..(((....)))......)))).)((...((((((((....)))))))).))..)).)).))))))).))))...... ( -49.40)
>DroSec_CAF1 8455 120 + 1
AUCCGCUGGCGCAGGAAGACCGCCACAUCCACACUCCGGGUGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGC
..(((((((((((.((.(((.(((((((((.......)))))..(((....)))......)))).)((...((((((((....)))))))).))..)).)).))))))).))))...... ( -51.80)
>DroSim_CAF1 8924 120 + 1
AUCCGCUGGCGCAGGAAGACCGCCACAUCCACACUCCGGGUGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGC
..(((((((((((.((.(((.(((((((((.......)))))..(((....)))......)))).)((...((((((((....)))))))).))..)).)).))))))).))))...... ( -51.80)
>DroEre_CAF1 9603 120 + 1
AUCCUCUGGCGCAGAAAGACCGCCACAUCCACGCUCCGGGUGAAGAGAAUGCUCAGAUUCUGGCCCGCAUAGCGAUACGUGUUCGUGUUCCGGCAUUCAUCGUGCGCCAUGCGGCACUGC
..........((((.......(((((((((.......)))))..(((....)))......))))((((((.(((.((((((...((((....)))).)).))))))).))))))..)))) ( -38.70)
>DroYak_CAF1 9601 120 + 1
AUUCUCUGGCGCAGAAAGACCGCCACAUCCACGCUCCGGGUGAACAGGAUGCUCAGAUUCUGGCCCGCAUAGCGAUAUGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGC
......((((((.....(((((.(((((...((((.(((((...((((((......)))))))))))...))))..)))))..)).)))(((((....))))))))))).(((....))) ( -41.30)
>consensus
AUCCGCUGGCGCAGGAAGACCGCCACAUCCACACUCCGGGUGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGC
..(((((((((((.((.((..(((.(((((.......)))))...(((((......))))))))..((...((((((((....)))))))).))..)).)).))))))).))))...... (-44.36 = -44.72 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	10,212,150 – 10,212,270
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-50.36
Consensus MFE	-42.88
Energy contribution	-42.76
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.85
SVM decision value	0.50
SVM RNA-class probability	0.760561
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10212150 120 + 22224390
UGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGCAGCGCAUUGUAGGCGGCCAGUUGGGCCAGUGUCGUGUCCC
....(((....))).(((.(((((((((...((((((((....)))))))).((((.....)))))))..((.((.((((((....)))))))).))......)))))).)))....... ( -49.40)
>DroSec_CAF1 8495 120 + 1
UGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGCAGCGCAUUGUAUGCGGCCAGUUGGGCCAGUGUCGUGUCCC
.((.((.(..((((((...(((((((.((((((((((((....))))))))(((....)))((((((..((((....))))))))))..)))))))))))))))))...).))...)).. ( -49.60)
>DroSim_CAF1 8964 120 + 1
UGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGCAGCGCAUUGUAUGCGGCCAGUUGGGCCAGUGUCGUGUCCC
.((.((.(..((((((...(((((((.((((((((((((....))))))))(((....)))((((((..((((....))))))))))..)))))))))))))))))...).))...)).. ( -49.60)
>DroEre_CAF1 9643 120 + 1
UGAAGAGAAUGCUCAGAUUCUGGCCCGCAUAGCGAUACGUGUUCGUGUUCCGGCAUUCAUCGUGCGCCAUGCGGCACUGCAGCGCAUUGUAGGCGGCCAAUUGGGCCAGUGUGGCGUCCC
........((((.((.(..(((((((((((.(((.((((((...((((....)))).)).))))))).))))(((.((((((....))))))...)))....)))))))).))))))... ( -46.80)
>DroYak_CAF1 9641 120 + 1
UGAACAGGAUGCUCAGAUUCUGGCCCGCAUAGCGAUAUGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGCAGCGCAUUGUAGGCGGCCAGUUGGGCCAGUGUCGCAUCCC
......((((((...(((.(((((((((...((((((((....))))))))(((...((((((((((..((((....))))))))))....))))))).).)))))))).))))))))). ( -56.40)
>consensus
UGAAGAGAAUGCUCAGAUUCUGGCCGGCAUAGCGAUACGUGUUCGUGUUGCGGCAUUCGUCGUGCGCCAUGCGGCACUGCAGCGCAUUGUAGGCGGCCAGUUGGGCCAGUGUCGUGUCCC
.....(((((......)))))(((..((((.((((((((....))))))))(((....))))))))))((((((((((.....((.......))((((.....))))))))))))))... (-42.88 = -42.76 +  -0.12)

alignment

secondary structure

dotplot

Window 7

Location	10,212,190 – 10,212,310
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.67
Mean single sequence MFE	-47.58
Consensus MFE	-43.80
Energy contribution	-44.28
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.92
SVM decision value	2.44
SVM RNA-class probability	0.993953
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10212190 120 - 22224390
AGUGGCUUCCCCAGUGCCGUCCAAAUGGCCACAAUGUCCUGGGACACGACACUGGCCCAACUGGCCGCCUACAAUGCGCUGCAGUGCCGCAUGGCGCACGACGAAUGCCGCAACACGAAC
.((((((((..((((((.((((....((.(.....).))..))))........((((.....)))).........))))))..(((((....))))).....))).)))))......... ( -41.70)
>DroSec_CAF1 8535 120 - 1
AGUGGCUUCCCCAGUGCCGGCCAAAUGGCCACAAUGGCCUGGGACACGACACUGGCCCAACUGGCCGCAUACAAUGCGCUGCAGUGCCGCAUGGCGCACGACGAAUGCCGCAACACGAAC
.((((((((..((((((((((((...((((.....))))((((.((......)).))))..))))))........))))))..(((((....))))).....))).)))))......... ( -49.40)
>DroSim_CAF1 9004 120 - 1
AGUGGCUUCCCCAGUGCCGUCCAAAUGGCCACAAUGGCCUGGGACACGACACUGGCCCAACUGGCCGCAUACAAUGCGCUGCAGUGCCGCAUGGCGCACGACGAAUGCCGCAACACGAAC
.((((((((..((((((.((((....((((.....))))..))))........((((.....)))).........))))))..(((((....))))).....))).)))))......... ( -48.80)
>DroEre_CAF1 9683 120 - 1
AGUGGCUUCCCCAGCGCCGUCCAGAUGGCCACAAUGGCCUGGGACGCCACACUGGCCCAAUUGGCCGCCUACAAUGCGCUGCAGUGCCGCAUGGCGCACGAUGAAUGCCGGAACACGAAC
.(((((...(((((.(((((((....)).....))))))))))..))))).(((((...((((..((((....((((((......).)))))))))..))))....)))))......... ( -48.70)
>DroYak_CAF1 9681 120 - 1
AGUGGCUUCCCCAGUGCCGUGCAAAUGGCCACAAUGGCCUGGGAUGCGACACUGGCCCAACUGGCCGCCUACAAUGCGCUGCAGUGCCGCAUGGCGCACGACGAAUGCCGCAACACGAAC
.((((((((....(((((((((....((((.....))))..((.((((.....((((.....))))(((......).))))))...))))))))))).....))).)))))......... ( -49.30)
>consensus
AGUGGCUUCCCCAGUGCCGUCCAAAUGGCCACAAUGGCCUGGGACACGACACUGGCCCAACUGGCCGCCUACAAUGCGCUGCAGUGCCGCAUGGCGCACGACGAAUGCCGCAACACGAAC
.((((((((..((((((.((((....((((.....))))..))))........((((.....)))).........))))))..(((((....))))).....))).)))))......... (-43.80 = -44.28 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:08 2006