Locus 644

Sequence ID	3R_DroMel_CAF1
Location	2,385,957 – 2,386,051
Length	94
Max. P	0.978531

overview

Window 9

Location	2,385,957 – 2,386,051
Length	94
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	81.69
Mean single sequence MFE	-21.96
Consensus MFE	-15.14
Energy contribution	-15.42
Covariance contribution	0.28
Combinations/Pair	1.15
Mean z-score	-2.60
Structure conservation index	0.69
SVM decision value	1.82
SVM RNA-class probability	0.978531
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2385957 94 + 27905053
GUGGUUUUUAAAUAGUCUUUUGUGAAUAAUUCAUUUAUUUUU-------UUUUCUGAUUAAGGUGCUGCGAAAGCAGCCUUUACUGUAAAGAGCUUGUUUU
..(((((((..((((........((((((.....))))))..-------.........(((((.(((((....)))))))))))))).)))))))...... ( -20.90)
>DroSec_CAF1 98519 93 + 1
UUGGUUUUUAAGUAGUCUUUUGUAAAUUAUUCAUUUAUUUUU-------UUU-UGGAUUAAGAUGCUGCGAAAGCAGCGUUUACUGAAAAAAGCUUGUUUU
..(((((((...((((((.....(((.((......)).))).-------...-.))))))(((((((((....)))))))))......)))))))...... ( -22.80)
>DroSim_CAF1 91242 92 + 1
UUGGUUUUUAAGUAGUCUUUUGUGAAUUAUUCAUUUAUUUU--------UUA-UGGAUUAAGCUGCUGCGAAAGCAGCGUUUACUGAAAAAAGCUUGUUUU
..(((((((...(((...((..((((..((......))..)--------)))-..)).(((((.(((((....)))))))))))))..)))))))...... ( -22.40)
>DroEre_CAF1 92851 97 + 1
---GGUUUCAAAUAGUCCUCAGUGAAUUAUUCAUUUAUUAGUAUAUUUUUUU-UUGAUUAAGGUGCUGCGAAAGCAGCCUUUACUGCAAAGAGCUUGUUUU
---......((((((..((((((((((.....)))))))............(-(((..(((((.(((((....))))))))))...))))))).)))))). ( -22.60)
>DroYak_CAF1 87038 100 + 1
UUGGUUUUUGAAUAGUCUUCUGUGAAUUAUUCAUUUAUUUUUAUUUUUUUGC-UGGCUUAAGUUGCUGCAAAAGCAGCCUUUACUAUAAAGAGCUGGUUUU
........(((((((((......).))))))))............(((((((-.(((.......))))))))))(((((((((...))))).))))..... ( -21.10)
>consensus
UUGGUUUUUAAAUAGUCUUUUGUGAAUUAUUCAUUUAUUUUU_______UUU_UGGAUUAAGGUGCUGCGAAAGCAGCCUUUACUGAAAAGAGCUUGUUUU
..(((((((...(((......((((((.....))))))....................(((((.(((((....)))))))))))))..)))))))...... (-15.14 = -15.42 +   0.28)

alignment

secondary structure

dotplot

Window 0

Location	2,385,957 – 2,386,051
Length	94
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	81.69
Mean single sequence MFE	-13.26
Consensus MFE	-10.60
Energy contribution	-9.80
Covariance contribution	-0.80
Combinations/Pair	1.27
Mean z-score	-2.37
Structure conservation index	0.80
SVM decision value	1.79
SVM RNA-class probability	0.977541
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2385957 94 - 27905053
AAAACAAGCUCUUUACAGUAAAGGCUGCUUUCGCAGCACCUUAAUCAGAAAA-------AAAAAUAAAUGAAUUAUUCACAAAAGACUAUUUAAAAACCAC
......((.(((((.........(((((....)))))...............-------.........(((.....)))..)))))))............. ( -11.20)
>DroSec_CAF1 98519 93 - 1
AAAACAAGCUUUUUUCAGUAAACGCUGCUUUCGCAGCAUCUUAAUCCA-AAA-------AAAAAUAAAUGAAUAAUUUACAAAAGACUACUUAAAAACCAA
..........(((((.((((...(((((....)))))...........-...-------.....(((((.....)))))........)))).))))).... ( -12.60)
>DroSim_CAF1 91242 92 - 1
AAAACAAGCUUUUUUCAGUAAACGCUGCUUUCGCAGCAGCUUAAUCCA-UAA--------AAAAUAAAUGAAUAAUUCACAAAAGACUACUUAAAAACCAA
..........(((((.((((...((((((.....))))))........-...--------........(((.....)))........)))).))))).... ( -12.10)
>DroEre_CAF1 92851 97 - 1
AAAACAAGCUCUUUGCAGUAAAGGCUGCUUUCGCAGCACCUUAAUCAA-AAAAAAAUAUACUAAUAAAUGAAUAAUUCACUGAGGACUAUUUGAAACC---
....(((((.....))(((....(((((....))))).(((((.....-.......(((....)))..(((.....))).))))))))..))).....--- ( -14.00)
>DroYak_CAF1 87038 100 - 1
AAAACCAGCUCUUUAUAGUAAAGGCUGCUUUUGCAGCAACUUAAGCCA-GCAAAAAAAUAAAAAUAAAUGAAUAAUUCACAGAAGACUAUUCAAAAACCAA
.......((((((...(((....(((((....))))).))).)))..)-)).................((((((..((......)).))))))........ ( -16.40)
>consensus
AAAACAAGCUCUUUACAGUAAAGGCUGCUUUCGCAGCACCUUAAUCCA_AAA_______AAAAAUAAAUGAAUAAUUCACAAAAGACUAUUUAAAAACCAA
......((.(((((.........(((((....)))))...............................(((.....)))..)))))))............. (-10.60 =  -9.80 +  -0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:12 2006