Locus 1941

Sequence ID	X_DroMel_CAF1
Location	5,314,280 – 5,314,383
Length	103
Max. P	0.999868

overview

Window 1

Location	5,314,280 – 5,314,383
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.87
Mean single sequence MFE	-41.86
Consensus MFE	-37.22
Energy contribution	-37.42
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.93
Structure conservation index	0.89
SVM decision value	4.31
SVM RNA-class probability	0.999868
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5314280 103 + 22224390
UUUGUUCGCAGCU--------------UUCGGCUUUUGGCCAAAAAGGGCGACAAGGGGCCAAGUCAAUCAAAAGUUGGCCCACAGCUCAGCUGGCCAGCG---GCGAAUAAUAGAUGGA
.((((((((.(((--------------...(((.....)))......(((......(((((((.(........).))))))).((((...)))))))))).---))))))))........ ( -40.20)
>DroSec_CAF1 50761 106 + 1
UUUGUUCGCAGCU--------------UUCGGCUUGUGGCCAAAAAGGGCGACAAGGGGCCAAGUCAAUCAAAAGUUGGCCCACAGCUCAGCUGGCCAGCGGCGGCGAAUAAUAGAUGGA
.((((((((.(((--------------...(((((((.(((......))).)))).(((((((.(........).))))))).((((...)))))))...))).))))))))........ ( -44.00)
>DroSim_CAF1 42254 106 + 1
UUUGUUCGCAGCU--------------UUCGGCUUUUGGCCAAAAAGGGCGACAAGGGGCCAAGUCAAUCAAAAGUUGGCCCACAGCUCAGCUGGCCAGCGGCGGCGAAUAAUAGAUGGA
.((((((((.(((--------------....(((...(((((....((((......(((((((.(........).)))))))...))))...))))))))))).))))))))........ ( -40.80)
>DroEre_CAF1 53679 103 + 1
UUUGUUCGCAGCU--------------CUCGCCUUUUGGCCAAAAAGGGCGACAAGGGGCCAAGUCAAUCAAAAGUUGGCCCACAGCUCAGCUGGCCAGCG---GCGAAUAAUAGAUGGC
.((((((((.(((--------------.(((((((((......)))))))))....(((((((.(........).))))))).((((...))))...))).---))))))))........ ( -41.50)
>DroYak_CAF1 53698 117 + 1
UUUGUUCGCAGCUUUCUGCUUUCGGCUUUCGGCUUUUGGCCAAAAAGGGCGACAAGGGGCCAAGUCAAUCAAAAGUUGGCCCACAGCUCAGCUGGCCAGCG---GCGAAUAAUAGAUGGA
.((((((((((((....((.....))....)))).(((((((....((((......(((((((.(........).)))))))...))))...)))))))..---))))))))........ ( -42.80)
>consensus
UUUGUUCGCAGCU______________UUCGGCUUUUGGCCAAAAAGGGCGACAAGGGGCCAAGUCAAUCAAAAGUUGGCCCACAGCUCAGCUGGCCAGCG___GCGAAUAAUAGAUGGA
.((((((((.(((.................(((.....)))......(((......(((((((.(........).))))))).((((...))))))))))....))))))))........ (-37.22 = -37.42 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	5,314,280 – 5,314,383
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.87
Mean single sequence MFE	-35.36
Consensus MFE	-30.28
Energy contribution	-30.32
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.79
Structure conservation index	0.86
SVM decision value	1.56
SVM RNA-class probability	0.964024
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5314280 103 - 22224390
UCCAUCUAUUAUUCGC---CGCUGGCCAGCUGAGCUGUGGGCCAACUUUUGAUUGACUUGGCCCCUUGUCGCCCUUUUUGGCCAAAAGCCGAA--------------AGCUGCGAACAAA
...........(((((---.((((((((((...)))).(((((((.((......)).)))))))......)))...((((((.....))))))--------------))).))))).... ( -35.50)
>DroSec_CAF1 50761 106 - 1
UCCAUCUAUUAUUCGCCGCCGCUGGCCAGCUGAGCUGUGGGCCAACUUUUGAUUGACUUGGCCCCUUGUCGCCCUUUUUGGCCACAAGCCGAA--------------AGCUGCGAACAAA
...........(((((.((...((((((((...)))).(((((((.((......)).))))))).((((.(((......))).))))))))..--------------.)).))))).... ( -35.30)
>DroSim_CAF1 42254 106 - 1
UCCAUCUAUUAUUCGCCGCCGCUGGCCAGCUGAGCUGUGGGCCAACUUUUGAUUGACUUGGCCCCUUGUCGCCCUUUUUGGCCAAAAGCCGAA--------------AGCUGCGAACAAA
...........(((((.((....(((((((...)))).(((((((.((......)).)))))))......)))..(((((((.....))))))--------------))).))))).... ( -34.80)
>DroEre_CAF1 53679 103 - 1
GCCAUCUAUUAUUCGC---CGCUGGCCAGCUGAGCUGUGGGCCAACUUUUGAUUGACUUGGCCCCUUGUCGCCCUUUUUGGCCAAAAGGCGAG--------------AGCUGCGAACAAA
...........(((((---.((((((((((...)))).(((((((.((......)).)))))))......)))....((.(((....))).))--------------))).))))).... ( -34.10)
>DroYak_CAF1 53698 117 - 1
UCCAUCUAUUAUUCGC---CGCUGGCCAGCUGAGCUGUGGGCCAACUUUUGAUUGACUUGGCCCCUUGUCGCCCUUUUUGGCCAAAAGCCGAAAGCCGAAAGCAGAAAGCUGCGAACAAA
...........(((((---.((((((((((...)))).(((((((.((......)).)))))))......)))..(((((((.....)))))))(.(....))....))).))))).... ( -37.10)
>consensus
UCCAUCUAUUAUUCGC___CGCUGGCCAGCUGAGCUGUGGGCCAACUUUUGAUUGACUUGGCCCCUUGUCGCCCUUUUUGGCCAAAAGCCGAA______________AGCUGCGAACAAA
...........(((((....((((((((((...)))).(((((((.((......)).)))))))......)))...((((((.....))))))..............))).))))).... (-30.28 = -30.32 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:21 2006