Locus 4530

Sequence ID	3R_DroMel_CAF1
Location	12,023,103 – 12,023,228
Length	125
Max. P	0.871771

overview

Window 3

Location	12,023,103 – 12,023,207
Length	104
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	86.75
Mean single sequence MFE	-22.40
Consensus MFE	-17.50
Energy contribution	-17.92
Covariance contribution	0.42
Combinations/Pair	1.12
Mean z-score	-2.50
Structure conservation index	0.78
SVM decision value	0.38
SVM RNA-class probability	0.712148
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12023103 104 + 27905053
ACUAUAUCU--AUGUAAAUGUUAAUGUAAUUCUAAGCCAGCGAAAUC-GUGUAACGAUAUCGCAUCAGAUAUCGGCAUACACAUACAUACGUUUAUAAAUCUAUAUG
.........--.(((((((((..(((((.(((.........)))...-(((((.(((((((......)))))))...))))).)))))))))))))).......... ( -23.90)
>DroPse_CAF1 9555 100 + 1
UCUAUAUCUAUAUGUAAAUGUUAAUGUAAUUCUAAGCCAGCGAAAUUUAAGCACCGAUAUCGCAUCAGAUAUCGGCCAAA----GCAUACGUAUAUAUAUGUAU---
..(((((.((((((((..((((.................((.........)).((((((((......))))))))....)----))))))))))).)))))...--- ( -23.10)
>DroSim_CAF1 1353 104 + 1
ACUAUAUCU--AUGUAAAUGUUAAUGUAAUUCUAAGCCAGCGAAAUG-GUGUAACGAUAUCGCAUCAGAUAUCGGCAUACACAUACAUACGUUUAUAAAUCUAUAUG
.........--.(((((((((..(((((.......((((......))-))(((.(((((((......)))))))...)))...)))))))))))))).......... ( -24.50)
>DroEre_CAF1 1343 102 + 1
ACUAUAUCU--AUGUAAAUGUUAAUAUAAUUCUAAGCCAGCGAAAUG-GUGUAACGAUAUCGCAUCAGAUAUCGGCAUAA--AUACAUACGUUUAUAAAUCUAUAUG
.........--.(((((((((...(((........((((......))-))....(((((((......)))))))......--)))...))))))))).......... ( -20.10)
>DroYak_CAF1 1342 102 + 1
ACUAUAUCU--AUGUAAAUGUUAAUAUAAUUCUAAGCCAGCGAAAUG-GUGUAAGGAUGUCGCAUCAGAUAUCGGCAUAA--UUACAUACGUUUAUAAAUCUAUAUG
.........--.(((((((((..............((((......))-))((((..((((((.((.....))))))))..--))))..))))))))).......... ( -19.70)
>DroPer_CAF1 9569 100 + 1
UCUAUAUCUAUAUGUAAAUGUUAAUGUAAUUCUAAGCCAGCGAAAUUUAAGCACCGAUAUCGCAUCAGAUAUCGGCCAAA----GCAUACGUAUAUAUAUGUAU---
..(((((.((((((((..((((.................((.........)).((((((((......))))))))....)----))))))))))).)))))...--- ( -23.10)
>consensus
ACUAUAUCU__AUGUAAAUGUUAAUGUAAUUCUAAGCCAGCGAAAUG_GUGUAACGAUAUCGCAUCAGAUAUCGGCAUAA__AUACAUACGUUUAUAAAUCUAUAUG
............(((((((((..(((((.......(((.((.........))...((((((......))))))))).......)))))))))))))).......... (-17.50 = -17.92 +   0.42)

alignment

secondary structure

dotplot

Window 4

Location	12,023,133 – 12,023,228
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	95.78
Mean single sequence MFE	-20.91
Consensus MFE	-16.62
Energy contribution	-16.22
Covariance contribution	-0.40
Combinations/Pair	1.09
Mean z-score	-2.12
Structure conservation index	0.79
SVM decision value	0.87
SVM RNA-class probability	0.871771
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12023133 95 + 27905053
UAAGCCAGCGAAAUCGUGUAACGAUAUCGCAUCAGAUAUCGGCAUACACAUACAUACGUUUAUAAAUCUAUAUGCCUACGUGUAGUUAAAAUUUA
......(((......(((((.(((((((......)))))))...)))))....((((((.((((......))))...)))))).)))........ ( -20.50)
>DroSec_CAF1 1376 95 + 1
UAAGCCAGCGAAAUGGUGUAACGAUAUCGCAUCAGAUAUCGGCAUACACAUACAUACGUUUAUAAAUCUAUAUGCCUACGUGUAGUUAAAAUUUA
(((((.......(((((((..(((((((......)))))))..)))).)))......))))).....(((((((....))))))).......... ( -20.92)
>DroSim_CAF1 1383 95 + 1
UAAGCCAGCGAAAUGGUGUAACGAUAUCGCAUCAGAUAUCGGCAUACACAUACAUACGUUUAUAAAUCUAUAUGCCUACGUGUAGUUAAAAUUUA
(((((.......(((((((..(((((((......)))))))..)))).)))......))))).....(((((((....))))))).......... ( -20.92)
>DroEre_CAF1 1373 93 + 1
UAAGCCAGCGAAAUGGUGUAACGAUAUCGCAUCAGAUAUCGGCAUAA--AUACAUACGUUUAUAAAUCUAUAUGCCUAUGUGUAGUUAAAAUUUA
...((((......))))....(((((((......)))))))......--(((((((.((.((((....)))).)).)))))))............ ( -21.30)
>DroYak_CAF1 1372 93 + 1
UAAGCCAGCGAAAUGGUGUAAGGAUGUCGCAUCAGAUAUCGGCAUAA--UUACAUACGUUUAUAAAUCUAUAUGCCUAUGUGUAGUUAAAAUUUA
...(((.(((......)))...((((((......))))))))).(((--(((((((.((.((((....)))).))...))))))))))....... ( -20.90)
>consensus
UAAGCCAGCGAAAUGGUGUAACGAUAUCGCAUCAGAUAUCGGCAUACACAUACAUACGUUUAUAAAUCUAUAUGCCUACGUGUAGUUAAAAUUUA
...(((.(((......)))...((((((......)))))))))..........((((((.((((......))))...))))))............ (-16.62 = -16.22 +  -0.40)

alignment

secondary structure

dotplot

Window 5

Location	12,023,133 – 12,023,228
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	95.78
Mean single sequence MFE	-19.43
Consensus MFE	-16.28
Energy contribution	-17.68
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.37
Structure conservation index	0.84
SVM decision value	0.02
SVM RNA-class probability	0.542398
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12023133 95 - 27905053
UAAAUUUUAACUACACGUAGGCAUAUAGAUUUAUAAACGUAUGUAUGUGUAUGCCGAUAUCUGAUGCGAUAUCGUUACACGAUUUCGCUGGCUUA
...................((((((((.((.((((....)))).)).))))))))..........((((.((((.....)))).))))....... ( -23.50)
>DroSec_CAF1 1376 95 - 1
UAAAUUUUAACUACACGUAGGCAUAUAGAUUUAUAAACGUAUGUAUGUGUAUGCCGAUAUCUGAUGCGAUAUCGUUACACCAUUUCGCUGGCUUA
.......((((........((((((((.((.((((....)))).)).))))))))((((((......))))))))))..(((......))).... ( -22.40)
>DroSim_CAF1 1383 95 - 1
UAAAUUUUAACUACACGUAGGCAUAUAGAUUUAUAAACGUAUGUAUGUGUAUGCCGAUAUCUGAUGCGAUAUCGUUACACCAUUUCGCUGGCUUA
.......((((........((((((((.((.((((....)))).)).))))))))((((((......))))))))))..(((......))).... ( -22.40)
>DroEre_CAF1 1373 93 - 1
UAAAUUUUAACUACACAUAGGCAUAUAGAUUUAUAAACGUAUGUAU--UUAUGCCGAUAUCUGAUGCGAUAUCGUUACACCAUUUCGCUGGCUUA
.......((((........((((((...((.(((....))).))..--.))))))((((((......))))))))))..(((......))).... ( -17.60)
>DroYak_CAF1 1372 93 - 1
UAAAUUUUAACUACACAUAGGCAUAUAGAUUUAUAAACGUAUGUAA--UUAUGCCGAUAUCUGAUGCGACAUCCUUACACCAUUUCGCUGGCUUA
...................((((((...((.(((....))).))..--.))))))..........((((...............))))....... ( -11.26)
>consensus
UAAAUUUUAACUACACGUAGGCAUAUAGAUUUAUAAACGUAUGUAUGUGUAUGCCGAUAUCUGAUGCGAUAUCGUUACACCAUUUCGCUGGCUUA
.......((((........((((((((.((.((((....)))).)).))))))))((((((......)))))))))).................. (-16.28 = -17.68 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:32 2006