Locus 4969

Sequence ID	3L_DroMel_CAF1
Location	13,725,031 – 13,725,121
Length	90
Max. P	0.939547

overview

Window 0

Location	13,725,031 – 13,725,121
Length	90
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.21
Mean single sequence MFE	-31.63
Consensus MFE	-18.71
Energy contribution	-18.02
Covariance contribution	-0.69
Combinations/Pair	1.20
Mean z-score	-2.34
Structure conservation index	0.59
SVM decision value	1.13
SVM RNA-class probability	0.919235
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13725031 90 + 23771897
GCAACGUCCCAC--GCUUUUGGAGUGCGAAUUUGCGUAAAUAUAAUUUAUUUACGCAAUUGCAAAGGA----------CCCGAGAAGGUUUCG---------------CAGGAUUAU
.....((((...--((........(((((..(((((((((((.....))))))))))))))))..(((----------.((.....)).))))---------------).))))... ( -25.00)
>DroPse_CAF1 124684 100 + 1
GCCAUGUCCCACGCGCUUUUGGAGUGCGAAUUUGCGUAAAUAUAAUUUAUUUACGCAAUGGCAAAGGA----------UCCGAGAAGGUUUCG--GCAUAGA-G----CAGGCACAU
(((..((((..(((((((...)))))))...(((((((((((.....))))))))))).......)))----------)((((((...)))))--)......-.----..))).... ( -34.10)
>DroEre_CAF1 138619 90 + 1
GCAACGUCCCAC--GCUUUUGGAGUGCGAAUUUGCGUAAAUAUAAUUUAUUUACGCAAUUGCAAGGGA----------CCGGAGAAGGCUUCG---------------CAGGAUUAU
((...(((((..--((((...))))((((..(((((((((((.....)))))))))))))))..))))----------).((((....)))))---------------)........ ( -30.90)
>DroYak_CAF1 142366 90 + 1
GCAACGUCCCAC--GCUUUUGGAGUGCGAAUUUGCGUAAAUAUAAUUUAUUUACGCAAUUGCCAAGGA----------CCGGAGAAGGCUUCG---------------CAGGAUUAU
((...((((...--((((...))))((((..(((((((((((.....)))))))))))))))...)))----------).((((....)))))---------------)........ ( -25.80)
>DroAna_CAF1 192847 115 + 1
GCGAGGCCCCCC--GUUUUUGGAGUGCGAAUUUGCGUAAAUAUAAUUUAUUUACGCAAUGGCCAACGAGCCAUGGCAGCCCUGGAAGGCUCACCCGGACGGAGGCAGUCAUGAUUAU
....((((..((--(....))).........(((((((((((.....))))))))))).)))).......((((((.((((((...((.....))...))).))).))))))..... ( -39.90)
>DroPer_CAF1 126076 100 + 1
GCCAUGUCCCACGCGCUUUUGGAGUGCGAAUUUGCGUAAAUAUAAUUUAUUUACGCAAUGGCAAAGGA----------UCCGAGAAGGUUUCG--GCAUAGA-G----CAGGCACAU
(((..((((..(((((((...)))))))...(((((((((((.....))))))))))).......)))----------)((((((...)))))--)......-.----..))).... ( -34.10)
>consensus
GCAACGUCCCAC__GCUUUUGGAGUGCGAAUUUGCGUAAAUAUAAUUUAUUUACGCAAUGGCAAAGGA__________CCCGAGAAGGCUUCG_______________CAGGAUUAU
(((((((((((........))).).)))...(((((((((((.....)))))))))))))))...................(((.....)))......................... (-18.71 = -18.02 +  -0.69)

alignment

secondary structure

dotplot

Window 1

Location	13,725,031 – 13,725,121
Length	90
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.21
Mean single sequence MFE	-28.82
Consensus MFE	-16.56
Energy contribution	-16.42
Covariance contribution	-0.14
Combinations/Pair	1.10
Mean z-score	-2.53
Structure conservation index	0.57
SVM decision value	1.28
SVM RNA-class probability	0.939547
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13725031 90 - 23771897
AUAAUCCUG---------------CGAAACCUUCUCGGG----------UCCUUUGCAAUUGCGUAAAUAAAUUAUAUUUACGCAAAUUCGCACUCCAAAAGC--GUGGGACGUUGC
....(((..---------------((..((((....)))----------)....((((((((((((((((.....))))))))).)))).))).........)--)..)))...... ( -24.90)
>DroPse_CAF1 124684 100 - 1
AUGUGCCUG----C-UCUAUGC--CGAAACCUUCUCGGA----------UCCUUUGCCAUUGCGUAAAUAAAUUAUAUUUACGCAAAUUCGCACUCCAAAAGCGCGUGGGACAUGGC
....(((((----.-.((((((--(((.......))(((----------.....(((..(((((((((((.....)))))))))))....))).)))....).))))))..)).))) ( -29.00)
>DroEre_CAF1 138619 90 - 1
AUAAUCCUG---------------CGAAGCCUUCUCCGG----------UCCCUUGCAAUUGCGUAAAUAAAUUAUAUUUACGCAAAUUCGCACUCCAAAAGC--GUGGGACGUUGC
....(((..---------------((..(((......))----------)....((((((((((((((((.....))))))))).)))).))).........)--)..)))...... ( -24.60)
>DroYak_CAF1 142366 90 - 1
AUAAUCCUG---------------CGAAGCCUUCUCCGG----------UCCUUGGCAAUUGCGUAAAUAAAUUAUAUUUACGCAAAUUCGCACUCCAAAAGC--GUGGGACGUUGC
....(((..---------------(((((((........----------.....)))..(((((((((((.....))))))))))).)))((.........))--)..)))...... ( -25.22)
>DroAna_CAF1 192847 115 - 1
AUAAUCAUGACUGCCUCCGUCCGGGUGAGCCUUCCAGGGCUGCCAUGGCUCGUUGGCCAUUGCGUAAAUAAAUUAUAUUUACGCAAAUUCGCACUCCAAAAAC--GGGGGGCCUCGC
.............(((((((...((.((((((....)))))((..(((((....)))))(((((((((((.....)))))))))))....)).).))....))--)))))....... ( -40.20)
>DroPer_CAF1 126076 100 - 1
AUGUGCCUG----C-UCUAUGC--CGAAACCUUCUCGGA----------UCCUUUGCCAUUGCGUAAAUAAAUUAUAUUUACGCAAAUUCGCACUCCAAAAGCGCGUGGGACAUGGC
....(((((----.-.((((((--(((.......))(((----------.....(((..(((((((((((.....)))))))))))....))).)))....).))))))..)).))) ( -29.00)
>consensus
AUAAUCCUG_______________CGAAACCUUCUCGGG__________UCCUUUGCAAUUGCGUAAAUAAAUUAUAUUUACGCAAAUUCGCACUCCAAAAGC__GUGGGACGUUGC
.......................................................(((((((((((((((.....)))))))))))..((.(((...........))).))..)))) (-16.56 = -16.42 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:11 2006