Locus 139

Sequence ID	X_DroMel_CAF1
Location	527,176 – 527,307
Length	131
Max. P	0.990698

overview

Window 8

Location	527,176 – 527,267
Length	91
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	85.28
Mean single sequence MFE	-28.28
Consensus MFE	-20.14
Energy contribution	-21.33
Covariance contribution	1.19
Combinations/Pair	1.12
Mean z-score	-2.06
Structure conservation index	0.71
SVM decision value	0.79
SVM RNA-class probability	0.850997
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 527176 91 + 22224390
UAUAUCGCCUUUCAGUAUGGACAG--GAACAGCGGCUAUAUCCUU-------------CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAA
.......(((.((......)).))--)...((.((..(((((...-------------.)))))..))))((((((((((((.....))))))))))))....... ( -28.80)
>DroSec_CAF1 13758 91 + 1
UAUAUCGCCUUUCAGUAUGGACAG--GAACAGCGGCUAUAUCCUU-------------CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAA
.......(((.((......)).))--)...((.((..(((((...-------------.)))))..))))((((((((((((.....))))))))))))....... ( -28.80)
>DroSim_CAF1 14071 91 + 1
UAUAUCGCCUUUCAGUAUGGACAG--GAACAGCGGCUAUAUCCUU-------------CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAA
.......(((.((......)).))--)...((.((..(((((...-------------.)))))..))))((((((((((((.....))))))))))))....... ( -28.80)
>DroEre_CAF1 18652 100 + 1
UAUAUCGCCUUUCAGUAUGGACAGCGGAACGGCGGCCAUAUCCUACUACCACCACGUA-GAUAUACCCCUCG-----GUCGCCAUAUUUGAGUGUGGCGUACAUAA
.....((((.((((((((((.(.((.((..((.((..(((((.(((.........)))-))))).)))))).-----)).)))))).)))))...))))....... ( -26.70)
>consensus
UAUAUCGCCUUUCAGUAUGGACAG__GAACAGCGGCUAUAUCCUU_____________CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAA
...............((((.((........((.((..(((((.................)))))..)))).(((((((((((.....))))))))))))).)))). (-20.14 = -21.33 +   1.19)

alignment

secondary structure

dotplot

Window 9

Location	527,214 – 527,307
Length	93
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	87.44
Mean single sequence MFE	-33.48
Consensus MFE	-25.06
Energy contribution	-26.62
Covariance contribution	1.56
Combinations/Pair	1.05
Mean z-score	-2.97
Structure conservation index	0.75
SVM decision value	1.67
SVM RNA-class probability	0.971014
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 527214 93 + 22224390
UCCUU-------------CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAAUAUGCAUGCACACGCAGCACAUUUGGGAGCAGUUCGAGUU
...((-------------(((..((((...((((((((((((.....)))))))))))).........(((.(((....)))))).....)))).....))))).. ( -36.10)
>DroSec_CAF1 13796 93 + 1
UCCUU-------------CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAAUAUGCAUGCACACGCAGCACAUUUGGGAGCAGUUCGAGUU
...((-------------(((..((((...((((((((((((.....)))))))))))).........(((.(((....)))))).....)))).....))))).. ( -36.10)
>DroSim_CAF1 14109 93 + 1
UCCUU-------------CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAAUAUGCAUGCACACGCAGCACAUUUGGGAGCAGUUCGAGUU
...((-------------(((..((((...((((((((((((.....)))))))))))).........(((.(((....)))))).....)))).....))))).. ( -36.10)
>DroEre_CAF1 18692 100 + 1
UCCUACUACCACCACGUA-GAUAUACCCCUCG-----GUCGCCAUAUUUGAGUGUGGCGUACAUAAUAUGCAUGCACACGCAGCACAUUUGGGAGCAGUUCGAGUU
.....((((......)))-)........((((-----..((((((((....)))))))((.(..(((.(((.(((....)))))).)))...).)).)..)))).. ( -25.60)
>consensus
UCCUU_____________CGGUAUCCCCCUCGCCACAUUCGCCAUAUGCGAGUGUGGCGUACAUAAUAUGCAUGCACACGCAGCACAUUUGGGAGCAGUUCGAGUU
..........................(((.((((((((((((.....)))))))))))).........(((.(((....)))))).....)))............. (-25.06 = -26.62 +   1.56)

alignment

secondary structure

dotplot

Window 0

Location	527,214 – 527,307
Length	93
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	87.44
Mean single sequence MFE	-37.67
Consensus MFE	-29.85
Energy contribution	-31.85
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-3.40
Structure conservation index	0.79
SVM decision value	2.23
SVM RNA-class probability	0.990698
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 527214 93 - 22224390
AACUCGAACUGCUCCCAAAUGUGCUGCGUGUGCAUGCAUAUUAUGUACGCCACACUCGCAUAUGGCGAAUGUGGCGAGGGGGAUACCG-------------AAGGA
...(((.....(((((.((((((((((....))).))))))).....(((((((.((((.....)))).))))))).)))))....))-------------).... ( -40.00)
>DroSec_CAF1 13796 93 - 1
AACUCGAACUGCUCCCAAAUGUGCUGCGUGUGCAUGCAUAUUAUGUACGCCACACUCGCAUAUGGCGAAUGUGGCGAGGGGGAUACCG-------------AAGGA
...(((.....(((((.((((((((((....))).))))))).....(((((((.((((.....)))).))))))).)))))....))-------------).... ( -40.00)
>DroSim_CAF1 14109 93 - 1
AACUCGAACUGCUCCCAAAUGUGCUGCGUGUGCAUGCAUAUUAUGUACGCCACACUCGCAUAUGGCGAAUGUGGCGAGGGGGAUACCG-------------AAGGA
...(((.....(((((.((((((((((....))).))))))).....(((((((.((((.....)))).))))))).)))))....))-------------).... ( -40.00)
>DroEre_CAF1 18692 100 - 1
AACUCGAACUGCUCCCAAAUGUGCUGCGUGUGCAUGCAUAUUAUGUACGCCACACUCAAAUAUGGCGAC-----CGAGGGGUAUAUC-UACGUGGUGGUAGUAGGA
.......(((((..((.((((((((((....))).)))))))((((((((((..........)))))((-----(....))).....-)))))))..))))).... ( -30.70)
>consensus
AACUCGAACUGCUCCCAAAUGUGCUGCGUGUGCAUGCAUAUUAUGUACGCCACACUCGCAUAUGGCGAAUGUGGCGAGGGGGAUACCG_____________AAGGA
...........(((((.((((((((((....))).))))))).....(((((((.((((.....)))).))))))).)))))........................ (-29.85 = -31.85 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:01 2006