Locus 6234

Sequence ID	X_DroMel_CAF1
Location	15,834,968 – 15,835,128
Length	160
Max. P	0.848781

overview

Window 4

Location	15,834,968 – 15,835,088
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.22
Mean single sequence MFE	-44.82
Consensus MFE	-31.43
Energy contribution	-30.30
Covariance contribution	-1.13
Combinations/Pair	1.48
Mean z-score	-1.45
Structure conservation index	0.70
SVM decision value	0.20
SVM RNA-class probability	0.628975
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15834968 120 - 22224390
CACUUCACCGGACGCCUGUCCACGCAACGUGCGUUUCAUUUGCAGCUGUCUUCAGAAGGCUGUGAUGGCCAAAUGGCCGACAGAGCGGCUCGUUCGCACACGCGUCGUCUCUGGCUUUAU
.........((((....))))((((.....)))).....(..(((((.((....)).)))))..)(((((....))))).(((((((((.(((......))).)))).)))))....... ( -44.20)
>DroVir_CAF1 2202 120 - 1
CACAUCGCCGGACGCCUGUCCGCGCAACGUACGCUACAUAUGCAAUUGCCUGCAGAAGGCUGUCGUGGCCAAAUGGCCAACGGAACGCUUGGUGCGGACACGUGUCGUCUCUGGUUUUAU
......(((((((((.(((((((((..(((..((.......))....((((.....))))..((((((((....)))).)))).)))....))))))))).))))).....))))..... ( -46.30)
>DroGri_CAF1 2487 120 - 1
CACAUCGCCGGAUGCCUGUCCGCGCAAUGUGCGCUACAUUUGCAACUGCCUGCAGAAGGCGGUCGUUGCCAAAUGGCAAACGGAGCGUUUGGUGCGUACGCGUGUCGUCUCCGGUUUUAU
......((((((.((.....(((((...((((((..((..(((.(((((((.....)))))))(((((((....))).))))..)))..))..)))))))))))..)).))))))..... ( -50.30)
>DroWil_CAF1 2629 120 - 1
CACAUCCCCGGACGCCUGUCCGCGUAAUGUACGCUAUAUUUGCAAUUGCCUUCAGAAGGCGGUGGUCGCCAAAUGGCCAACGGAGCGUCUGGUGCGUACUAGGGUCGUUUCUGGUUUCAU
.......(((((((((((((((((((...))))).............((((.....))))))((((((.....)))))))))).))))))))((...(((((((....)))))))..)). ( -40.60)
>DroMoj_CAF1 585 120 - 1
CACGUCGCCGGACGCUUGUCCGCGCAACGUGCGCUACAUCUGCAACUGCUUGCAGAAGGCGGUCGUGGCCAAGUGGCCGACGGAGCGUUUGGUGCGCACGCGCGUCGUAUCCGGUUUUAU
......((((((..(.....(((((...((((((.((.(((((((....)))))))(((((.((((((((....)))).))))..))))).)))))))))))))..)..))))))..... ( -54.60)
>DroAna_CAF1 5034 120 - 1
UACUUCACCAGAUGCUUGCCCGCGAAAUGUGCGCUAUAUUUGUAACUGCCUUCAGAAAGCUGUAAUGGCUAAAUGGCCAACAGAACGUUUGGUCCGUACCCGUGUUGUAUCUGGAUUUAU
.......((((((((.....((((....(((((...((..(((..(((....)))....((((..(((((....))))))))).)))..))...))))).))))..))))))))...... ( -32.90)
>consensus
CACAUCGCCGGACGCCUGUCCGCGCAACGUGCGCUACAUUUGCAACUGCCUGCAGAAGGCGGUCGUGGCCAAAUGGCCAACGGAGCGUUUGGUGCGUACACGUGUCGUCUCUGGUUUUAU
.......(((((.((......((((...((((((..((..(((.((.((((.....)))).))..(((((....))))).....)))..))..))))))..)))).)).)))))...... (-31.43 = -30.30 +  -1.13)

alignment

secondary structure

dotplot

Window 5

Location	15,835,008 – 15,835,128
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.61
Mean single sequence MFE	-44.90
Consensus MFE	-33.41
Energy contribution	-36.75
Covariance contribution	3.34
Combinations/Pair	1.35
Mean z-score	-2.42
Structure conservation index	0.74
SVM decision value	0.78
SVM RNA-class probability	0.848781
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15835008 120 + 22224390
UCGGCCAUUUGGCCAUCACAGCCUUCUGAAGACAGCUGCAAAUGAAACGCACGUUGCGUGGACAGGCGUCCGGUGAAGUGAAUAUCGACUGGGUGACCAGAUCGAGGAUUUGCAAUAGAA
..((((....)))).((((.(((((((...(.(((((((.........))).)))))..))).)))).....)))).(..(((.((((((((....)))).))))..)))..)....... ( -44.70)
>DroVir_CAF1 2242 120 + 1
UUGGCCAUUUGGCCACGACAGCCUUCUGCAGGCAAUUGCAUAUGUAGCGUACGUUGCGCGGACAGGCGUCCGGCGAUGUGAAUAUCGAUUGGGUGACCAGAUCGAGUAUCUGCAGCAGGA
.(((((....)))))......(((.((((((((....)).......((.((((((((.(((((....)))))))))))))....((((((((....))).)))))))..)))))).))). ( -53.80)
>DroGri_CAF1 2527 120 + 1
UUUGCCAUUUGGCAACGACCGCCUUCUGCAGGCAGUUGCAAAUGUAGCGCACAUUGCGCGGACAGGCAUCCGGCGAUGUGAAUAUGGAUUGGGUGACCAGAUCGAGUAUCUGCAGCAGGA
.(((((....)))))......(((.(((((((..(((((....))))).((((((((.((((......))))))))))))....(((.((((....)))).)))....))))))).))). ( -49.80)
>DroWil_CAF1 2669 120 + 1
UUGGCCAUUUGGCGACCACCGCCUUCUGAAGGCAAUUGCAAAUAUAGCGUACAUUACGCGGACAGGCGUCCGGGGAUGUGAAUAUCGAUUGAGUGACGAGAUCGAGAAUUUGCAGCAGGA
...(((....))).....((((((.....))))..((((((((......((((((.(.(((((....))))).)))))))....((((((.........))))))..))))))))..)). ( -38.00)
>DroMoj_CAF1 625 120 + 1
UCGGCCACUUGGCCACGACCGCCUUCUGCAAGCAGUUGCAGAUGUAGCGCACGUUGCGCGGACAAGCGUCCGGCGACGUGAAUAUCGACUGGGUGACCAGGUCGAGUAUCUGCAAGAGGA
..((((....)))).......(((((((....)))(((((((((.....((((((((.(((((....)))))))))))))....((((((((....))).))))).))))))))))))). ( -60.00)
>DroAna_CAF1 5074 120 + 1
UUGGCCAUUUAGCCAUUACAGCUUUCUGAAGGCAGUUACAAAUAUAGCGCACAUUUCGCGGGCAAGCAUCUGGUGAAGUAAAUAUUGACUGCGUUACAAGAUCAAGAAUUUGCAAAAGAA
.((((......)))).....((.((((.((.(((((((........(....)(((((((.((.......)).)))))))......))))))).)).........))))...))....... ( -23.10)
>consensus
UUGGCCAUUUGGCCACGACAGCCUUCUGAAGGCAGUUGCAAAUGUAGCGCACAUUGCGCGGACAGGCGUCCGGCGAUGUGAAUAUCGACUGGGUGACCAGAUCGAGUAUCUGCAACAGGA
..((((....))))......((((.....))))..((((((((......((((((((.(((((....)))))))))))))....((((((((....)))).))))..))))))))..... (-33.41 = -36.75 +   3.34)

alignment

secondary structure

dotplot

Window 6

Location	15,835,008 – 15,835,128
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.61
Mean single sequence MFE	-36.98
Consensus MFE	-29.07
Energy contribution	-27.92
Covariance contribution	-1.16
Combinations/Pair	1.50
Mean z-score	-1.50
Structure conservation index	0.79
SVM decision value	0.18
SVM RNA-class probability	0.619392
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15835008 120 - 22224390
UUCUAUUGCAAAUCCUCGAUCUGGUCACCCAGUCGAUAUUCACUUCACCGGACGCCUGUCCACGCAACGUGCGUUUCAUUUGCAGCUGUCUUCAGAAGGCUGUGAUGGCCAAAUGGCCGA
.....((((......((((.((((....)))))))).............((((....))))..))))............(..(((((.((....)).)))))..)(((((....))))). ( -37.10)
>DroVir_CAF1 2242 120 - 1
UCCUGCUGCAGAUACUCGAUCUGGUCACCCAAUCGAUAUUCACAUCGCCGGACGCCUGUCCGCGCAACGUACGCUACAUAUGCAAUUGCCUGCAGAAGGCUGUCGUGGCCAAAUGGCCAA
.(((.((((((.((((((((.(((....))))))))..........(((((((....))))).))...))).((.......))......)))))).)))......(((((....))))). ( -41.50)
>DroGri_CAF1 2527 120 - 1
UCCUGCUGCAGAUACUCGAUCUGGUCACCCAAUCCAUAUUCACAUCGCCGGAUGCCUGUCCGCGCAAUGUGCGCUACAUUUGCAACUGCCUGCAGAAGGCGGUCGUUGCCAAAUGGCAAA
......(((((((....(((.(((....))))))......(((((.(((((((....))))).)).)))))......)))))))(((((((.....)))))))..(((((....))))). ( -40.40)
>DroWil_CAF1 2669 120 - 1
UCCUGCUGCAAAUUCUCGAUCUCGUCACUCAAUCGAUAUUCACAUCCCCGGACGCCUGUCCGCGUAAUGUACGCUAUAUUUGCAAUUGCCUUCAGAAGGCGGUGGUCGCCAAAUGGCCAA
......(((((((..(((((...........))))).....((((..((((((....))))).)..)))).......)))))))(((((((.....)))))))(((((.....))))).. ( -31.20)
>DroMoj_CAF1 625 120 - 1
UCCUCUUGCAGAUACUCGACCUGGUCACCCAGUCGAUAUUCACGUCGCCGGACGCUUGUCCGCGCAACGUGCGCUACAUCUGCAACUGCUUGCAGAAGGCGGUCGUGGCCAAGUGGCCGA
......(((((((..(((((.(((....))))))))....(((((.(((((((....))))).)).)))))......)))))))(((((((.....)))))))..(((((....))))). ( -50.90)
>DroAna_CAF1 5074 120 - 1
UUCUUUUGCAAAUUCUUGAUCUUGUAACGCAGUCAAUAUUUACUUCACCAGAUGCUUGCCCGCGAAAUGUGCGCUAUAUUUGUAACUGCCUUCAGAAAGCUGUAAUGGCUAAAUGGCCAA
.....((((((..(....)..)))))).(((((...............((((((...((.(((.....))).))..))))))...(((....)))...)))))..(((((....))))). ( -20.80)
>consensus
UCCUGCUGCAAAUACUCGAUCUGGUCACCCAAUCGAUAUUCACAUCGCCGGACGCCUGUCCGCGCAACGUGCGCUACAUUUGCAACUGCCUGCAGAAGGCGGUCGUGGCCAAAUGGCCAA
......(((((((..(((((.(((....)))))))).............((((....))))((((.....))))...)))))))((.((((.....)))).))..(((((....))))). (-29.07 = -27.92 +  -1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:57 2006