Locus 8016

Sequence ID	3L_DroMel_CAF1
Location	21,127,382 – 21,127,475
Length	93
Max. P	0.984528

overview

Window 4

Location	21,127,382 – 21,127,475
Length	93
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	95.81
Mean single sequence MFE	-29.18
Consensus MFE	-27.52
Energy contribution	-27.04
Covariance contribution	-0.48
Combinations/Pair	1.14
Mean z-score	-1.61
Structure conservation index	0.94
SVM decision value	1.98
SVM RNA-class probability	0.984528
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21127382 93 + 23771897
UCGAUGGGCAACCUGCCCACAUGCGCGAGCGAGCUUUUCCUUU------UCGCCAUUUUCGAGGGCGGAAAAUGCGCUGCACUUUGCUCUUCUCCUCUC
..(.(((((.....))))))..((....))((((......(((------(((((.........)))))))).(((...)))....)))).......... ( -28.10)
>DroSec_CAF1 178094 93 + 1
UCGAUGGGCAACCUGCCCACAUGCGCGAGCGAGCUUUUCCUUU------UCGCCAUUUUCGAGGGCGGAAAAUGCGCUGCACUUUGCUCUCCCCCUCUC
..(.(((((.....))))))(((.(((((.(((......))))------)))))))....(((((.(((....(((........)))..)))))))).. ( -29.70)
>DroSim_CAF1 89786 93 + 1
UCGAUGGGCAACCUGCCCACAUGCGCGAGCGAGCUUUUCCUUU------UCGCCAUUUUCGAGGGCGGAAAAUGCGCUGCACUUUGCUCUCCCCCUCUC
..(.(((((.....))))))(((.(((((.(((......))))------)))))))....(((((.(((....(((........)))..)))))))).. ( -29.70)
>DroEre_CAF1 100492 93 + 1
UCGAUGGGCAACCUGCCCACAUGCGCGAGCGAGCUUUUCCUUU------UCGCCAUUUUUGAGGGCGGAAAAUGCGCUGCACUUUGCUCUCCCCCUCUC
..(.(((((.....))))))(((.(((((.(((......))))------)))))))....(((((.(((....(((........)))..)))))))).. ( -29.40)
>DroYak_CAF1 71439 99 + 1
UCGAUGGGCAACCUGCCCACAUGCGCGAGCGAGCUUUUCCUUUUCAAUUUCGCCAUUUUCGAGGGCGGAAAAUGCACUGCACUUUGCUCUCCCCCUCUC
.((((((((.....)))))..(((....)))..................)))........(((((.(((....(((........)))..)))))))).. ( -29.00)
>consensus
UCGAUGGGCAACCUGCCCACAUGCGCGAGCGAGCUUUUCCUUU______UCGCCAUUUUCGAGGGCGGAAAAUGCGCUGCACUUUGCUCUCCCCCUCUC
.((((((((.....)))))..(((....)))..................)))........(((((.(((....(((........)))..)))))))).. (-27.52 = -27.04 +  -0.48)

alignment

secondary structure

dotplot

Window 5

Location	21,127,382 – 21,127,475
Length	93
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	95.81
Mean single sequence MFE	-31.48
Consensus MFE	-29.98
Energy contribution	-30.02
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.23
Structure conservation index	0.95
SVM decision value	0.67
SVM RNA-class probability	0.818689
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21127382 93 - 23771897
GAGAGGAGAAGAGCAAAGUGCAGCGCAUUUUCCGCCCUCGAAAAUGGCGA------AAAGGAAAAGCUCGCUCGCGCAUGUGGGCAGGUUGCCCAUCGA
.................((((((((..((((((.(((........)).).------...))))))...)))).))))..((((((.....))))))... ( -29.50)
>DroSec_CAF1 178094 93 - 1
GAGAGGGGGAGAGCAAAGUGCAGCGCAUUUUCCGCCCUCGAAAAUGGCGA------AAAGGAAAAGCUCGCUCGCGCAUGUGGGCAGGUUGCCCAUCGA
..((((((((((.....((((...))))))))).)))))........(((------...((...(((..((((((....))))))..))).))..))). ( -32.10)
>DroSim_CAF1 89786 93 - 1
GAGAGGGGGAGAGCAAAGUGCAGCGCAUUUUCCGCCCUCGAAAAUGGCGA------AAAGGAAAAGCUCGCUCGCGCAUGUGGGCAGGUUGCCCAUCGA
..((((((((((.....((((...))))))))).)))))........(((------...((...(((..((((((....))))))..))).))..))). ( -32.10)
>DroEre_CAF1 100492 93 - 1
GAGAGGGGGAGAGCAAAGUGCAGCGCAUUUUCCGCCCUCAAAAAUGGCGA------AAAGGAAAAGCUCGCUCGCGCAUGUGGGCAGGUUGCCCAUCGA
..((((((((((.....((((...))))))))).)))))........(((------...((...(((..((((((....))))))..))).))..))). ( -32.10)
>DroYak_CAF1 71439 99 - 1
GAGAGGGGGAGAGCAAAGUGCAGUGCAUUUUCCGCCCUCGAAAAUGGCGAAAUUGAAAAGGAAAAGCUCGCUCGCGCAUGUGGGCAGGUUGCCCAUCGA
..(((((((((((((........)))..))))).))))).............((((...((...(((..((((((....))))))..))).))..)))) ( -31.60)
>consensus
GAGAGGGGGAGAGCAAAGUGCAGCGCAUUUUCCGCCCUCGAAAAUGGCGA______AAAGGAAAAGCUCGCUCGCGCAUGUGGGCAGGUUGCCCAUCGA
..(((((.(((((((((((((...))))))).((((.........))))................))))((((((....))))))...)).))).)).. (-29.98 = -30.02 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:57 2006