Locus 1992

Sequence ID	3R_DroMel_CAF1
Location	5,639,102 – 5,639,261
Length	159
Max. P	0.974936

overview

Window 4

Location	5,639,102 – 5,639,222
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.42
Mean single sequence MFE	-43.80
Consensus MFE	-36.56
Energy contribution	-37.32
Covariance contribution	0.76
Combinations/Pair	1.17
Mean z-score	-2.00
Structure conservation index	0.83
SVM decision value	1.74
SVM RNA-class probability	0.974936
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5639102 120 - 27905053
AUGGGAACAGAGUGCCUCCAUAGCCGUUGAAGGUAAUGUGCAGGUAUCCGCCAAAGGACAUCACCAGGUGGUGGAAGACGUGCAGGAAGGAUAUCUGGCGAUCCUUCUUGCGCAGCACAA
.((....))...(((((.((.......)).))))).(((((..((.(((((((..((......))...)))))))..))(((((((((((((........))))))))))))).))))). ( -48.50)
>DroSec_CAF1 12705 120 - 1
AUGGGAAGAGAGUGCCUCCAUAGCCGUUGAAGGUGAUGUGCAGGUAACCGCCGAAGGACAUCACCAGGUGGUGGAAGACGUGCAGGAAGGAUAUCUGGCGAUGCUUCUUGCGCAGCACAA
...........((((.(((((.(((......((((((((.(.(((....)))...).)))))))).))).)))))....((((((((((.((........)).)))))))))).)))).. ( -48.00)
>DroSim_CAF1 13427 120 - 1
AUGGGAACAGAGUGCCUCCGUAGCCGUUGAAGGUGAUGUGCAGGUAUCCGCCGAAGGACAUCACCAGGUGGUGGAAGACGUGCAGGAAGGAUAUCUGGCGAUGCUUCUUGCGCAGCACAA
.((....))..((((.((((..(((......((((((((.(.(((....)))...).)))))))).)))..))))....((((((((((.((........)).)))))))))).)))).. ( -47.50)
>DroEre_CAF1 13798 120 - 1
AUGGGAAGAAAACGCCUCCAUAGCCGUUGAAGGUGAUGUUCACGUAGCCGCCAAAGGACAUCGCCAGGUGGUGAAAGACGUGCAGGACGGAUAUCUGGCGGUCCUUCUUUCGCAGCACAA
.(((((((((..(((((((...(((......)))...((((((((.((((((...((......)).)))))).....)))))...)))))).....))))....))))))).))...... ( -36.20)
>DroYak_CAF1 13589 120 - 1
AUGGGAAGAGAAUGCCGCCAUAGCCGCUGUAGGUGAUGUGCAUGUAACCACCGAAGGACAUGACCAGGUGGUGGAAGACGUGCAGGACGGAUAUCUGGCGAUCCUUCUUUCGCAGCACAA
..((((((.((.((((..(((.(((......))).)))(((((((..((((((..((......))...))))))...)))))))............)))).))))))))........... ( -38.80)
>consensus
AUGGGAAGAGAGUGCCUCCAUAGCCGUUGAAGGUGAUGUGCAGGUAACCGCCGAAGGACAUCACCAGGUGGUGGAAGACGUGCAGGAAGGAUAUCUGGCGAUCCUUCUUGCGCAGCACAA
............(((((.((.......)).))))).(((((..((..((((((..((......))...))))))...))(((((((((((((........))))))))))))).))))). (-36.56 = -37.32 +   0.76)

alignment

secondary structure

dotplot

Window 5

Location	5,639,142 – 5,639,261
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	90.67
Mean single sequence MFE	-42.01
Consensus MFE	-35.78
Energy contribution	-36.38
Covariance contribution	0.60
Combinations/Pair	1.13
Mean z-score	-1.75
Structure conservation index	0.85
SVM decision value	1.32
SVM RNA-class probability	0.942202
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5639142 119 - 27905053
CGUACAUGAUCACAUGGACCGCCACAUUGAGCAGGCAUAAUGGGAACAGAGUGCCUCCAUAGCCGUUGAAGGUAAUGUGCAGGUAUCCGCCAAAGGACAUCACCAGGUGGUGGAAGACG
(((.((((....))))..(((((((.(((.((((((((..((....))..)))))..(((.(((......))).)))))).(((.(((......))).)))..))))))))))...))) ( -41.80)
>DroSec_CAF1 12745 119 - 1
CGUACAUGAUCACAUGGACCGCCACAUUGAGCAGGCACAAUGGGAAGAGAGUGCCUCCAUAGCCGUUGAAGGUGAUGUGCAGGUAACCGCCGAAGGACAUCACCAGGUGGUGGAAGACG
(((.((((....))))..(((((((.((.(((.(((...(((((...........))))).)))))).))((((((((.(.(((....)))...).))))))))..)))))))...))) ( -42.70)
>DroSim_CAF1 13467 119 - 1
CGUACAUGAUCACAUGGACCGCCACAUUGAGCAGGCACAAUGGGAACAGAGUGCCUCCGUAGCCGUUGAAGGUGAUGUGCAGGUAUCCGCCGAAGGACAUCACCAGGUGGUGGAAGACG
(((.((((....))))..(((((((.....(.((((((..((....))..)))))).)............((((((((.(.(((....)))...).))))))))..)))))))...))) ( -47.40)
>DroEre_CAF1 13838 119 - 1
UGUACAUGAUCACAUGGACCGCCACGUUGAGCAGGCAGGAUGGGAAGAAAACGCCUCCAUAGCCGUUGAAGGUGAUGUUCACGUAGCCGCCAAAGGACAUCGCCAGGUGGUGAAAGACG
....((((....)))).((((((...((.(((.(((...(((((...........))))).)))))).))((((((((((..............)))))))))).))))))........ ( -37.34)
>DroYak_CAF1 13629 119 - 1
AGUACAUGAUCACGUGGACCGCCACGUUGAGCAGGCACGAUGGGAAGAGAAUGCCGCCAUAGCCGCUGUAGGUGAUGUGCAUGUAACCACCGAAGGACAUGACCAGGUGGUGGAAGACG
.((((((.(((((((((....))))))..(((.(((...((((.............)))).))))))...))).))))))..((..((((((..((......))...))))))...)). ( -40.82)
>consensus
CGUACAUGAUCACAUGGACCGCCACAUUGAGCAGGCACAAUGGGAAGAGAGUGCCUCCAUAGCCGUUGAAGGUGAUGUGCAGGUAACCGCCGAAGGACAUCACCAGGUGGUGGAAGACG
.((.((((....))))..(((((((.((.(((.(((...(((((...........))))).)))))).))((((((((.(.(((....)))...).))))))))..)))))))...)). (-35.78 = -36.38 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:31 2006