Locus 7429

Sequence ID	3R_DroMel_CAF1
Location	19,792,071 – 19,792,188
Length	117
Max. P	0.984336

overview

Window 8

Location	19,792,071 – 19,792,163
Length	92
Sequences	3
Columns	101
Reading direction	forward
Mean pairwise identity	91.84
Mean single sequence MFE	-24.00
Consensus MFE	-21.87
Energy contribution	-21.87
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.91
SVM decision value	0.90
SVM RNA-class probability	0.877544
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19792071 92 + 27905053
AACACAUACUGCACUCGCAGCAGCCGCGAAUACUGCUCAUAUAACUGCAACAUCGAGAGACCUUUGCCGCUGCAAGCGCAACAGCAA---------CUGCA
................((((((((.(((((...(((..........)))...((....))..))))).)))))..((......))..---------.))). ( -23.20)
>DroEre_CAF1 22871 100 + 1
AACACAUACUGCACUCGCAGCAGCCGCGAAUACUGCUCAUAUAACUGCAACAUCGAGAGACCU-UGCCGCUGCAAGCGCAACAGCAACUUCAGCCACUGCA
..........(((...((.(((((.((((....(((..........)))...((....))..)-))).)))))..((......)).......))...))). ( -24.40)
>DroYak_CAF1 22669 92 + 1
AACACACACUGCACUCGCAGCAGCCGCGAUUACUGCUCAUAUAACUGCAACAUCGAGAGACCU-UGCCGCUGCAAGCGCAACAGCAA--------ACUGCA
.........(((.((.(((((....(((.....)))..........((((..((....))..)-))).))))).)).)))...((..--------...)). ( -24.40)
>consensus
AACACAUACUGCACUCGCAGCAGCCGCGAAUACUGCUCAUAUAACUGCAACAUCGAGAGACCU_UGCCGCUGCAAGCGCAACAGCAA________ACUGCA
.........(((.((.(((((....(((.....)))..........(((...((....))....))).))))).)).)))...(((...........))). (-21.87 = -21.87 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	19,792,071 – 19,792,163
Length	92
Sequences	3
Columns	101
Reading direction	reverse
Mean pairwise identity	91.84
Mean single sequence MFE	-38.87
Consensus MFE	-35.53
Energy contribution	-35.87
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.34
Structure conservation index	0.91
SVM decision value	1.97
SVM RNA-class probability	0.984336
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19792071 92 - 27905053
UGCAG---------UUGCUGUUGCGCUUGCAGCGGCAAAGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAUUCGCGGCUGCUGCGAGUGCAGUAUGUGUU
.(((.---------.((((...((((((((((((((...((.(((((.((((.......))))))).))...))...))))))))))))))))))..))). ( -35.90)
>DroEre_CAF1 22871 100 - 1
UGCAGUGGCUGAAGUUGCUGUUGCGCUUGCAGCGGCA-AGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAUUCGCGGCUGCUGCGAGUGCAGUAUGUGUU
.((((..((....))..))))(((((((((((((((.-.((.(((((.((((.......))))))).))...))...)))))))))))))))......... ( -42.90)
>DroYak_CAF1 22669 92 - 1
UGCAGU--------UUGCUGUUGCGCUUGCAGCGGCA-AGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAAUCGCGGCUGCUGCGAGUGCAGUGUGUGUU
.((((.--------...))))((((((((((((((((-(.(((....))).))((.(((((.......))))).)).)))))))))))))))......... ( -37.80)
>consensus
UGCAGU________UUGCUGUUGCGCUUGCAGCGGCA_AGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAUUCGCGGCUGCUGCGAGUGCAGUAUGUGUU
.(((((..........)))))(((((((((((((((...((.(((((.((((.......))))))).))...))...)))))))))))))))......... (-35.53 = -35.87 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	19,792,098 – 19,792,188
Length	90
Sequences	3
Columns	104
Reading direction	forward
Mean pairwise identity	88.59
Mean single sequence MFE	-25.01
Consensus MFE	-20.57
Energy contribution	-20.57
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.82
SVM decision value	0.13
SVM RNA-class probability	0.599084
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19792098 90 + 27905053
GAAUACUGCUCAUAUAACUGCAACAUCGAGAGACCUUUGCCGCUGCAAGCGCAACAGCAA---------CUGCAGCUGCAACAGCAUCCUCCAGCAGGA-----
.....(((((........(((....((....))...((((.((((((.((......))..---------.)))))).))))..)))......)))))..----- ( -26.44)
>DroEre_CAF1 22898 103 + 1
GAAUACUGCUCAUAUAACUGCAACAUCGAGAGACCU-UGCCGCUGCAAGCGCAACAGCAACUUCAGCCACUGCAGCUGCAACAGCAUCCUCCAGCAGGAACAGG
.....(((((.........((((..((....))..)-))).((((..((((((...((.......))...))).)))....)))).......)))))....... ( -25.70)
>DroYak_CAF1 22696 90 + 1
GAUUACUGCUCAUAUAACUGCAACAUCGAGAGACCU-UGCCGCUGCAAGCGCAACAGCAA--------ACUGCAACUGCAACAGCAUCCUCCAGCAGGA-----
.....(((((.........((((..((....))..)-))).((((...((......))..--------..(((....))).)))).......)))))..----- ( -22.90)
>consensus
GAAUACUGCUCAUAUAACUGCAACAUCGAGAGACCU_UGCCGCUGCAAGCGCAACAGCAA________ACUGCAGCUGCAACAGCAUCCUCCAGCAGGA_____
.....(((((.........(((...((....))....))).((((...((......))............(((....))).)))).......)))))....... (-20.57 = -20.57 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	19,792,098 – 19,792,188
Length	90
Sequences	3
Columns	104
Reading direction	reverse
Mean pairwise identity	88.59
Mean single sequence MFE	-36.73
Consensus MFE	-32.35
Energy contribution	-32.47
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.72
Structure conservation index	0.88
SVM decision value	1.46
SVM RNA-class probability	0.956306
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19792098 90 - 27905053
-----UCCUGCUGGAGGAUGCUGUUGCAGCUGCAG---------UUGCUGUUGCGCUUGCAGCGGCAAAGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAUUC
-----(((....)))((((((((((.(((((((((---------((((((((((....))))))))))..(((....))).)))))))....)))))))))))) ( -36.60)
>DroEre_CAF1 22898 103 - 1
CCUGUUCCUGCUGGAGGAUGCUGUUGCAGCUGCAGUGGCUGAAGUUGCUGUUGCGCUUGCAGCGGCA-AGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAUUC
.((((((((((.(((((.(((((((((((.(((((..((.......))..))))).)))))))))))-...))))).......))))......))))))..... ( -42.30)
>DroYak_CAF1 22696 90 - 1
-----UCCUGCUGGAGGAUGCUGUUGCAGUUGCAGU--------UUGCUGUUGCGCUUGCAGCGGCA-AGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAAUC
-----..(((((.(....((((((.((.((.((((.--------...)))).))))..))))))(((-(.(((....))).)))).......).)))))..... ( -31.30)
>consensus
_____UCCUGCUGGAGGAUGCUGUUGCAGCUGCAGU________UUGCUGUUGCGCUUGCAGCGGCA_AGGUCUCUCGAUGUUGCAGUUAUAUGAGCAGUAUUC
.....(((....)))((((((((((.(((((((((..........(((((((((....)))))))))...(((....))).)))))))....)))))))))))) (-32.35 = -32.47 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:47 2006