Locus 4970

Sequence ID	2L_DroMel_CAF1
Location	14,309,668 – 14,309,786
Length	118
Max. P	0.954578

overview

Window 2

Location	14,309,668 – 14,309,786
Length	118
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	91.47
Mean single sequence MFE	-16.29
Consensus MFE	-13.37
Energy contribution	-13.25
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.33
Structure conservation index	0.82
SVM decision value	0.04
SVM RNA-class probability	0.554580
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14309668 118 + 22407834
UUU-UCCCCAUUAAUUUCUCAUCACUUGCCAUCAACGGCUGUUUAGCCUGAUACGCAACCAUUAAUGAAUCCCAUUAAGAAAAUACAAUCAACAGCUUGUCGAUCAUUUGCUCUUAUCA
...-..........((((.......((((.((((..((((....))))))))..))))...((((((.....))))))))))...........(((.((.....))...)))....... ( -15.00)
>DroSec_CAF1 144353 118 + 1
UUU-UUCCCAUUAAUUUUUCAUCACUUGCCAUCAACGGCUACUUAGUCUGAUACGCAACCAUUAAUGAAUUCCAUUAAGAAAAUACAAUCAACGACUUGUCGAACAUUUGCUCUUAUCA
...-...........(((((.....((((.((((..((((....))))))))..))))...((((((.....))))))))))).........(((....)))................. ( -14.60)
>DroSim_CAF1 135099 118 + 1
UUU-UUCCCAUUAAUUUUUCAUCACUUGCCAUCAACGGCUACUUAGCCUGAUACGCAACCAUUAAUGAAUUCCAUUAAGAAAAUACAAUCAACGGCUUGUCGAACAUUUGCUCUUAUCA
...-.................((((..(((......((((....))))((((.........((((((.....)))))).........))))..)))..)).))................ ( -17.97)
>DroEre_CAF1 143831 118 + 1
UUU-UUCCCAUUAAUUUCACAUCAGUUCCCAUCAACGGCUGCCGAGCCUGAUACGCAACCAUUAAUGAAUCCCAUUAAGAAAAUACUAUCAACGGCUUGUCGAACAUUUCUUCUUAUCA
...-....................((((((......))..(.(((((((((((........((((((.....))))))........)))))..)))))).))))).............. ( -19.29)
>DroYak_CAF1 133393 119 + 1
UUUUUUUUCAUUUAUUUCUCAUCACUUUCCAUCAACGGCUGCUUAGCCUGAUACGCAAACAUUAAUGAAUCCCAUUAAGAAAAUACAAUCAACGGCUUGUCGAACAUUUCUUCUUAUCA
...................................((((.....((((((((.........((((((.....)))))).........))))..)))).))))................. ( -14.57)
>consensus
UUU_UUCCCAUUAAUUUCUCAUCACUUGCCAUCAACGGCUGCUUAGCCUGAUACGCAACCAUUAAUGAAUCCCAUUAAGAAAAUACAAUCAACGGCUUGUCGAACAUUUGCUCUUAUCA
...................................((((.....((((((((.........((((((.....)))))).........))))..)))).))))................. (-13.37 = -13.25 +  -0.12)

alignment

secondary structure

dotplot

Window 3

Location	14,309,668 – 14,309,786
Length	118
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	91.47
Mean single sequence MFE	-28.94
Consensus MFE	-22.92
Energy contribution	-23.60
Covariance contribution	0.68
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.79
SVM decision value	1.45
SVM RNA-class probability	0.954578
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14309668 118 - 22407834
UGAUAAGAGCAAAUGAUCGACAAGCUGUUGAUUGUAUUUUCUUAAUGGGAUUCAUUAAUGGUUGCGUAUCAGGCUAAACAGCCGUUGAUGGCAAGUGAUGAGAAAUUAAUGGGGA-AAA
............(..((((((.....))))))..).((((((((.(((..(((((((....((((.(((((((((....))))..))))))))).)))))))...))).))))))-)). ( -30.00)
>DroSec_CAF1 144353 118 - 1
UGAUAAGAGCAAAUGUUCGACAAGUCGUUGAUUGUAUUUUCUUAAUGGAAUUCAUUAAUGGUUGCGUAUCAGACUAAGUAGCCGUUGAUGGCAAGUGAUGAAAAAUUAAUGGGAA-AAA
......((((....))))......(((((((((.((((((((....)))).((((((((((((((............)))))))))))))).....))))...)))))))))...-... ( -27.50)
>DroSim_CAF1 135099 118 - 1
UGAUAAGAGCAAAUGUUCGACAAGCCGUUGAUUGUAUUUUCUUAAUGGAAUUCAUUAAUGGUUGCGUAUCAGGCUAAGUAGCCGUUGAUGGCAAGUGAUGAAAAAUUAAUGGGAA-AAA
......((((....))))......(((((((((.....((((....))))(((((((....((((.(((((((((....))))..))))))))).))))))).)))))))))...-... ( -30.70)
>DroEre_CAF1 143831 118 - 1
UGAUAAGAAGAAAUGUUCGACAAGCCGUUGAUAGUAUUUUCUUAAUGGGAUUCAUUAAUGGUUGCGUAUCAGGCUCGGCAGCCGUUGAUGGGAACUGAUGUGAAAUUAAUGGGAA-AAA
...((((((((.((..(((((.....)))))..)).))))))))..((..(((((((((((((((............)))))))))))))))..))...................-... ( -31.00)
>DroYak_CAF1 133393 119 - 1
UGAUAAGAAGAAAUGUUCGACAAGCCGUUGAUUGUAUUUUCUUAAUGGGAUUCAUUAAUGUUUGCGUAUCAGGCUAAGCAGCCGUUGAUGGAAAGUGAUGAGAAAUAAAUGAAAAAAAA
...((((((((.((..(((((.....)))))..)).))))))))......(((((((...(((.(((....((((....))))....))).))).)))))))................. ( -25.50)
>consensus
UGAUAAGAGCAAAUGUUCGACAAGCCGUUGAUUGUAUUUUCUUAAUGGGAUUCAUUAAUGGUUGCGUAUCAGGCUAAGCAGCCGUUGAUGGCAAGUGAUGAGAAAUUAAUGGGAA_AAA
......((((....))))......(((((((((.((((((((....)))).((((((((((((((............)))))))))))))).....))))...)))))))))....... (-22.92 = -23.60 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:16 2006