Locus 6793

Sequence ID	3R_DroMel_CAF1
Location	17,944,056 – 17,944,176
Length	120
Max. P	0.732816

overview

Window 7

Location	17,944,056 – 17,944,176
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.19
Mean single sequence MFE	-36.20
Consensus MFE	-27.70
Energy contribution	-28.58
Covariance contribution	0.87
Combinations/Pair	1.12
Mean z-score	-1.74
Structure conservation index	0.77
SVM decision value	0.43
SVM RNA-class probability	0.732816
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17944056 120 + 27905053
UUAUGACCAAAAAGAGUUGUCGCAGUGAAAUGCUCGAUCUGCGAAACUCCGGAAAUGGCAGACCUAAAAUGCCUCGAAAGGCUCGAGGAUUUAGCAGUUGAUUUAAGCUGGUCAGACGAA
.............(((((.(((((((((.....)))..)))))))))))((....((((....(((((...((((((.....)))))).)))))(((((......)))))))))..)).. ( -34.90)
>DroSec_CAF1 24173 120 + 1
UUAUGACCAGAAAGAGUUGGCGUAGUGAAAUGCUCGAUCUGCGAAACUCCGGAAAUGGCAGUCCUAAAAUGCCUCGAAAGGCUCGAGGAUUCAACAGUGGAUUUAAGCUGGUCAGACAAA
...(((((((...(((((.((....((((.((((...((((.(.....)))))...)))).((((.....((((....))))...))))))))...)).)))))...)))))))...... ( -36.90)
>DroEre_CAF1 21485 120 + 1
UUAUGACCAGAAAGAGUUGGCGAAGUGAAACGCUCGAUCUGCGAAACUCCGGAAAUGGUAGGCCUAAGAUGCCUCGAAAGGCACGAGGAUUUAGUAGUGGACUUAAGCUGGUCAGGCGGC
...(((((((...(((((.((..(.((((.(.((((((((......(((((....))).)).....))))((((....)))).))))).)))).).)).)))))...)))))))...... ( -37.50)
>DroYak_CAF1 20554 120 + 1
UGAUGACCAGAAAGAGUUGGCGCAGUGAAAUGCUGGAUCUGCGUAACUCCGGAAAUGGUAGACCCAAAAUGCCACGAAAGGCACGAGGAUUCAGCAGAGGACUCAAGCAGGUCAGGCGGA
...(((((.(...(((((..(.........((((((((((.(((..(((((....))).)).........(((......)))))).)))))))))))..)))))...).)))))...... ( -35.50)
>consensus
UUAUGACCAGAAAGAGUUGGCGCAGUGAAAUGCUCGAUCUGCGAAACUCCGGAAAUGGCAGACCUAAAAUGCCUCGAAAGGCACGAGGAUUCAGCAGUGGACUUAAGCUGGUCAGACGAA
...(((((((...(((((.((.........((((.(((((.(((..(((((....))).)).........(((......)))))).))))).)))))).)))))...)))))))...... (-27.70 = -28.58 +   0.87)

alignment

secondary structure

dotplot

Window 8

Location	17,944,056 – 17,944,176
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.19
Mean single sequence MFE	-31.28
Consensus MFE	-24.08
Energy contribution	-24.52
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-1.65
Structure conservation index	0.77
SVM decision value	0.32
SVM RNA-class probability	0.689058
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17944056 120 - 27905053
UUCGUCUGACCAGCUUAAAUCAACUGCUAAAUCCUCGAGCCUUUCGAGGCAUUUUAGGUCUGCCAUUUCCGGAGUUUCGCAGAUCGAGCAUUUCACUGCGACAACUCUUUUUGGUCAUAA
.......(((((((...........)))(((((((((((...))))))).))))..)))).((((.....((((((((((((.............)))))).))))))...))))..... ( -33.32)
>DroSec_CAF1 24173 120 - 1
UUUGUCUGACCAGCUUAAAUCCACUGUUGAAUCCUCGAGCCUUUCGAGGCAUUUUAGGACUGCCAUUUCCGGAGUUUCGCAGAUCGAGCAUUUCACUACGCCAACUCUUUCUGGUCAUAA
......(((((((............((.((((.(((((((((....))))......(((((.((......)))))))......))))).)))).))..............)))))))... ( -28.17)
>DroEre_CAF1 21485 120 - 1
GCCGCCUGACCAGCUUAAGUCCACUACUAAAUCCUCGUGCCUUUCGAGGCAUCUUAGGCCUACCAUUUCCGGAGUUUCGCAGAUCGAGCGUUUCACUUCGCCAACUCUUUCUGGUCAUAA
......(((((((((((((.................((((((....)))))))))))))..........((((((..(((.......)))....))))))...........))))))... ( -29.32)
>DroYak_CAF1 20554 120 - 1
UCCGCCUGACCUGCUUGAGUCCUCUGCUGAAUCCUCGUGCCUUUCGUGGCAUUUUGGGUCUACCAUUUCCGGAGUUACGCAGAUCCAGCAUUUCACUGCGCCAACUCUUUCUGGUCAUCA
......(((((.....((((..((((((((.(((..(((((......)))))..(((.....))).....))).))).)))))....(((......)))....)))).....)))))... ( -34.30)
>consensus
UCCGCCUGACCAGCUUAAAUCCACUGCUAAAUCCUCGAGCCUUUCGAGGCAUUUUAGGUCUACCAUUUCCGGAGUUUCGCAGAUCGAGCAUUUCACUGCGCCAACUCUUUCUGGUCAUAA
......(((((((.............(((((.(((((.......)))))...))))).............((((((.(((((.............)))))..))))))..)))))))... (-24.08 = -24.52 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:05 2006