Locus 4810

Sequence ID	3L_DroMel_CAF1
Location	13,461,332 – 13,461,462
Length	130
Max. P	0.971466

overview

Window 1

Location	13,461,332 – 13,461,437
Length	105
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	93.78
Mean single sequence MFE	-27.82
Consensus MFE	-25.25
Energy contribution	-25.75
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.91
SVM decision value	1.44
SVM RNA-class probability	0.953775
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13461332 105 + 23771897
UUGGUUUUGGUUUUGUUCCAUUUACAUAUAUGCCAAUGCCAGGCUCGGGCGAUAUAUCCAGUUUUUCACUUGGAUAUCUCGGUGUAUAUAUUGUAAGGCACACAU
.............(((.((..(((((((((((((...(((.......)))((.((((((((........)))))))).))))))))))...))))))).)))... ( -26.90)
>DroSec_CAF1 30356 104 + 1
UUGGUUUUGGUUUUGUUCCAUUUACAUAUAUGCCAAUGCCAGGCUCGGGCGAUAUAUCCAGUUUUUCACUUGGAUAUCUCGGUGUAUAUA-UGUAAGGCACACGU
.............(((.((..(((((((((((((...(((.......)))((.((((((((........)))))))).)).).)))))))-))))))).)))... ( -29.10)
>DroSim_CAF1 27734 104 + 1
UUGGUUUUGGUUUUGUUCCAUUUACAUAUAUGCCAAUGCCAGGCUCGGGCGAUAUAUCCAGUUUUUCACUUGGAUAUCUCGGUGUAUAUA-UGUAAGGCACACGU
.............(((.((..(((((((((((((...(((.......)))((.((((((((........)))))))).)).).)))))))-))))))).)))... ( -29.10)
>DroEre_CAF1 27888 96 + 1
-------UGGUUUUGUUCCAUUUACAUAUAUGCCAAUGCCAGGCUCGGGCGAUAUAUCCAGUUUUUCACUUGGAUAUCUCGGUGUAUAUA-UGUA-UGCACAUGC
-------(((.......)))..((((((((((((...(((.......)))((.((((((((........)))))))).)).).)))))))-))))-......... ( -26.20)
>consensus
UUGGUUUUGGUUUUGUUCCAUUUACAUAUAUGCCAAUGCCAGGCUCGGGCGAUAUAUCCAGUUUUUCACUUGGAUAUCUCGGUGUAUAUA_UGUAAGGCACACGU
.............(((.((..(((((((((((((...(((.......)))((.((((((((........)))))))).))))))))))...))))))).)))... (-25.25 = -25.75 +   0.50)

alignment

secondary structure

dotplot

Window 2

Location	13,461,332 – 13,461,437
Length	105
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	93.78
Mean single sequence MFE	-27.15
Consensus MFE	-23.19
Energy contribution	-23.25
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-3.46
Structure conservation index	0.85
SVM decision value	1.68
SVM RNA-class probability	0.971466
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13461332 105 - 23771897
AUGUGUGCCUUACAAUAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUUGGCAUAUAUGUAAAUGGAACAAAACCAAAACCAA
(((((((((................((.(((((((.((.....))))))))).))(((.......)))...))))))))).....(((.......)))....... ( -26.60)
>DroSec_CAF1 30356 104 - 1
ACGUGUGCCUUACA-UAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUUGGCAUAUAUGUAAAUGGAACAAAACCAAAACCAA
...(((.(((((((-(((((....(((.(((((((.((.....))))))))).))).....(((.......)))))))))))))..)).)))............. ( -28.10)
>DroSim_CAF1 27734 104 - 1
ACGUGUGCCUUACA-UAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUUGGCAUAUAUGUAAAUGGAACAAAACCAAAACCAA
...(((.(((((((-(((((....(((.(((((((.((.....))))))))).))).....(((.......)))))))))))))..)).)))............. ( -28.10)
>DroEre_CAF1 27888 96 - 1
GCAUGUGCA-UACA-UAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUUGGCAUAUAUGUAAAUGGAACAAAACCA-------
((....)).-((((-(((((....(((.(((((((.((.....))))))))).))).....(((.......))))))))))))..(((.......)))------- ( -25.80)
>consensus
ACGUGUGCCUUACA_UAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUUGGCAUAUAUGUAAAUGGAACAAAACCAAAACCAA
..(((((((................((.(((((((.((.....))))))))).))(((.......)))...))))))).......(((.......)))....... (-23.19 = -23.25 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	13,461,366 – 13,461,462
Length	96
Sequences	3
Columns	96
Reading direction	reverse
Mean pairwise identity	95.10
Mean single sequence MFE	-23.47
Consensus MFE	-20.09
Energy contribution	-20.43
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.27
Structure conservation index	0.86
SVM decision value	0.41
SVM RNA-class probability	0.726918
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13461366 96 - 23771897
UAAGCCGCACACACAUCUCUCUCGUAUGUGUGCCUUACAAUAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUU
...((((((((((.((.......)).)))))))................(((.(((((((.((.....))))))))).))).........)))... ( -26.20)
>DroSec_CAF1 30390 94 - 1
CAAA-CGCACACACAUCUCUCGCGUACGUGUGCCUUACA-UAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUU
....-.((.((.....(((..(((((..((((.....))-))..)))...((.(((((((.((.....))))))))).))))..)))..))))... ( -22.10)
>DroSim_CAF1 27768 94 - 1
CAAA-CGCACAAACAUCUCUCGCGUACGUGUGCCUUACA-UAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUU
....-.((.((.....(((..(((((..((((.....))-))..)))...((.(((((((.((.....))))))))).))))..)))..))))... ( -22.10)
>consensus
CAAA_CGCACACACAUCUCUCGCGUACGUGUGCCUUACA_UAUAUACACCGAGAUAUCCAAGUGAAAAACUGGAUAUAUCGCCCGAGCCUGGCAUU
......((((((...............)))))).................((.(((((((.((.....))))))))).))(((.......)))... (-20.09 = -20.43 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:01 2006