Locus 6315

Sequence ID	X_DroMel_CAF1
Location	15,976,859 – 15,977,055
Length	196
Max. P	0.999565

overview

Window 7

Location	15,976,859 – 15,976,979
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-46.84
Consensus MFE	-46.72
Energy contribution	-46.56
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.33
Structure conservation index	1.00
SVM decision value	3.73
SVM RNA-class probability	0.999565
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15976859 120 + 22224390
UGGCCAAAAACUGUUGCCAACUCGAUCGAGCACUUCGAGCGGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCCAUAUUUUGAUC
..(((.....((((((((..(((....)))(((..(((((.(.((((.....))))..).)))))..))).))))))))....)))(((((((((.....)))))))))........... ( -49.00)
>DroSec_CAF1 44659 120 + 1
UGGCCAAAAACUGUUGCCAACUCGAUCGAGCACUUCGAGCGGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCUAUAUUUUGAUC
..(((.....((((((((..(((....)))(((..(((((.(.((((.....))))..).)))))..))).))))))))....)))(((((((((.....)))))))))........... ( -46.30)
>DroSim_CAF1 35784 120 + 1
UGGCCAAAAACUGUUGCCAACUCGAUCGAGCACUUCGAGCGGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCUAUAUUUUGAUC
..(((.....((((((((..(((....)))(((..(((((.(.((((.....))))..).)))))..))).))))))))....)))(((((((((.....)))))))))........... ( -46.30)
>DroEre_CAF1 43552 118 + 1
UGGCCAAAAACUGUUGCCAACUCGAUCGAGCACUUCGAGCGGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCU--AUUUCGAUC
..(((.....((((((((..(((....)))(((..(((((.(.((((.....))))..).)))))..))).))))))))....)))(((((((((.....)))))))))--......... ( -46.30)
>DroYak_CAF1 27411 118 + 1
UGGCCAAAAACUGUUGCCAACUCGAUCGAGCACUUCGAGCGGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCU--AUUUUGAUC
..(((.....((((((((..(((....)))(((..(((((.(.((((.....))))..).)))))..))).))))))))....)))(((((((((.....)))))))))--......... ( -46.30)
>consensus
UGGCCAAAAACUGUUGCCAACUCGAUCGAGCACUUCGAGCGGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCUAUAUUUUGAUC
..(((.....((((((((..(((....)))(((..(((((.(.((((.....))))..).)))))..))).))))))))....)))(((((((((.....)))))))))........... (-46.72 = -46.56 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	15,976,899 – 15,977,019
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.47
Mean single sequence MFE	-38.20
Consensus MFE	-32.48
Energy contribution	-32.12
Covariance contribution	-0.36
Combinations/Pair	1.13
Mean z-score	-1.45
Structure conservation index	0.85
SVM decision value	0.03
SVM RNA-class probability	0.547453
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15976899 120 + 22224390
GGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCCAUAUUUUGAUCGUUAUGAUUUCUAUACUCGCCAAGGUGUUAUUACAUCGAA
....(((..(((((((....((((.((((......))))))))((((((((((((.....))))))))).(((...((((.....))))...)))...))).))))))).....)))... ( -40.70)
>DroSec_CAF1 44699 120 + 1
GGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCUAUAUUUUGAUCGUUAUGAUUUCUGCACUCGCCAAUGUGUUAUUACGUCGUA
.((......(((((....((((.(((((.....)))))(((((((.(((((((((.....))))))))).......((((.....)))).)))).)))))))..)))))......))... ( -38.60)
>DroSim_CAF1 35824 120 + 1
GGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCUAUAUUUUGAUCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
....(((..((......((.((((.((((......)))))))).))(((((((((.....)))))))))....))..)))........................................ ( -30.00)
>DroEre_CAF1 43592 118 + 1
GGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCU--AUUUCGAUCGUUAUGAUUUCUGCACUCCCGAAGGUGUUAUUACGGCGAA
....(((((((......((.((((.((((......)))))))).))(((((((((.....)))))))))--..)))))))((..((((....(((((......))))).))))..))... ( -42.50)
>DroYak_CAF1 27451 118 + 1
GGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCU--AUUUUGAUCGUUAUGAUUUCUGCACACUCCAAGGUGUUAUUACGGCGAA
....(((..((......((.((((.((((......)))))))).))(((((((((.....)))))))))--..))..)))((..((((....((((........)))).))))..))... ( -39.20)
>consensus
GGAAGAUUGAACAUCUGGUGGCUUGCUGUGAGGUAGCGGAGGCGGCGGCCCAUUGGAUCACAGUGGGCUAUAUUUUGAUCGUUAUGAUUUCUGCACUCGCCAAGGUGUUAUUACGGCGAA
....(((((((......((.((((.((((......)))))))).))(((((((((.....)))))))))....)))))))............((((........))))............ (-32.48 = -32.12 +  -0.36)

alignment

secondary structure

dotplot

Window 9

Location	15,976,939 – 15,977,055
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.16
Mean single sequence MFE	-37.11
Consensus MFE	-24.99
Energy contribution	-25.30
Covariance contribution	0.31
Combinations/Pair	1.20
Mean z-score	-2.01
Structure conservation index	0.67
SVM decision value	0.82
SVM RNA-class probability	0.857837
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15976939 116 + 22224390
GGCGGCGGCCCAUUGGAUCACAGUGGGCCAUAUUUUGAUCGUUAUGAUUUCUAUACUCGCCAAGGUGUUAUUACAUCGAAUUUGGC--GAU-UUCUCGUGCCACAUUCAGGAUAU-UUUG
(((((.(((((((((.....))))))))).(((...((((.....))))...))).)))))..(((((....)))))((((.((((--(..-......))))).)))).......-.... ( -41.00)
>DroSec_CAF1 44739 117 + 1
GGCGGCGGCCCAUUGGAUCACAGUGGGCUAUAUUUUGAUCGUUAUGAUUUCUGCACUCGCCAAUGUGUUAUUACGUCGUAAUGUGU--UUUAUUUUUUCUCCACUUUCAGGAUAU-UUGU
......(((((((((.....)))))))))(((((((((..((((((((....((((........))))......))))))))(((.--.............)))..)))))))))-.... ( -30.84)
>DroEre_CAF1 43632 114 + 1
GGCGGCGGCCCAUUGGAUCACAGUGGGCU--AUUUCGAUCGUUAUGAUUUCUGCACUCCCGAAGGUGUUAUUACGGCGAACUUGCC--GAU-UACUCGGUUCACUUUCUGGUUGC-UUGG
(((((((((((((((.....)))))))))--.....((((((..((((....(((((......))))).))))..))))....(((--((.-...)))))))........)))))-)... ( -39.40)
>DroYak_CAF1 27491 117 + 1
GGCGGCGGCCCAUUGGAUCACAGUGGGCU--AUUUUGAUCGUUAUGAUUUCUGCACACUCCAAGGUGUUAUUACGGCGAAUUUGGCUGGUU-UUCCUGGGCCACUUUCAGCAUGUUUUGG
(((((((((((((((.....)))))))))--....(((((((..((((....((((........)))).))))..))))...(((((((..-..))..)))))...))))).)))).... ( -37.20)
>consensus
GGCGGCGGCCCAUUGGAUCACAGUGGGCU__AUUUUGAUCGUUAUGAUUUCUGCACUCGCCAAGGUGUUAUUACGGCGAAUUUGGC__GAU_UUCUCGGGCCACUUUCAGGAUAU_UUGG
...((((((((((((.....))))))))).........(((((.((((....((((........)))).)))).)))))....................))).................. (-24.99 = -25.30 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:29 2006