Locus 3971

Sequence ID	X_DroMel_CAF1
Location	10,527,116 – 10,527,247
Length	131
Max. P	0.917532

overview

Window 9

Location	10,527,116 – 10,527,209
Length	93
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	81.16
Mean single sequence MFE	-26.01
Consensus MFE	-14.04
Energy contribution	-14.72
Covariance contribution	0.69
Combinations/Pair	1.12
Mean z-score	-2.64
Structure conservation index	0.54
SVM decision value	0.82
SVM RNA-class probability	0.859983
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10527116 93 - 22224390
CAGGACCAAGAUGACAUCUAAUCUCGAGAAAUCCAAGGGAUGUUCUU---------------------GAAACUGGAUGGUUAUAUUAAUAUGAAAUAUGAAAACCCUACCAAC
.(((..........((((((.(.(((((((((((...)))).)))))---------------------)).).)))))).(((((((.......)))))))....)))...... ( -20.30)
>DroSec_CAF1 58250 93 - 1
CAGGACCAAGAUGACAUCUAAUCUGGAGAAAUCCAGGGGAUGUUCUU---------------------GGAACUGAACGGUUAUAUUAAUAUGAAAUAUGAAAACCCUACCAAC
(((..((((((..((((((..((((((....))))))))))))))))---------------------))..)))...(((((((((.......))))))...)))........ ( -30.20)
>DroSim_CAF1 61942 93 - 1
GAGGACCAAGAUGACAUCUAAUCUGGAGAAAUCCAGGGGAUGUUCUU---------------------GGAACUGAACGGUUAUAUUAAUAUGAAAUAUGAAAACCCUACCAAC
.(((.((((((..((((((..((((((....))))))))))))))))---------------------))..........(((((((.......)))))))....)))...... ( -28.20)
>DroEre_CAF1 60188 113 - 1
CAGGGCCAAGAUGACGUCUAAUCUCGGGGAAUCCAGGGGAUGUUCUUGUUAUUAUUGUCGGCGGGAGUGGAACUGGUUGGGUAUAUUAAUAUCAAAUAUGAAAACUCCACAAA-
....(((.....((((..((((..((((((((((...)))).))))))..)))).))))))).(((((.......(((.(((((....))))).)))......))))).....- ( -25.32)
>consensus
CAGGACCAAGAUGACAUCUAAUCUCGAGAAAUCCAGGGGAUGUUCUU_____________________GGAACUGAACGGUUAUAUUAAUAUGAAAUAUGAAAACCCUACCAAC
.(((...((((..((((((...(((((....))))).)))))))))).................................(((((((.......)))))))....)))...... (-14.04 = -14.72 +   0.69)

alignment

secondary structure

dotplot

Window 0

Location	10,527,156 – 10,527,247
Length	91
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	80.00
Mean single sequence MFE	-26.34
Consensus MFE	-14.34
Energy contribution	-14.30
Covariance contribution	-0.04
Combinations/Pair	1.14
Mean z-score	-1.86
Structure conservation index	0.54
SVM decision value	0.03
SVM RNA-class probability	0.550423
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10527156 91 + 22224390
AGUUUC---------------------AAGAACAUCCCUUGGAUUUCUCGAGAUUAGAUGUCAUCUUGGUCCUGUGUUAUUUGCCGGCCAGUCGGGCACUGCAAACAGCCCA
((..((---------------------(((((((((.(((((.....)))))....)))))..))))))..))(.(((.(((((.((((.....))).).))))).))).). ( -24.90)
>DroSec_CAF1 58290 89 + 1
AGUUCC---------------------AAGAACAUCCCCUGGAUUUCUCCAGAUUAGAUGUCAUCUUGGUCCUG--UUAUUUGCCGGCCAGUCGGGCUUUGCAAACAGUCCA
((..((---------------------(((((((((..(((((....)))))....)))))..))))))..)).--...(((((.((((.....))))..)))))....... ( -28.60)
>DroSim_CAF1 61982 89 + 1
AGUUCC---------------------AAGAACAUCCCCUGGAUUUCUCCAGAUUAGAUGUCAUCUUGGUCCUC--UUAUUUGCCGGCCAGUCGGGCUUUGCAAACAGUCCA
((..((---------------------(((((((((..(((((....)))))....)))))..))))))..)).--...(((((.((((.....))))..)))))....... ( -28.00)
>DroEre_CAF1 60227 110 + 1
AGUUCCACUCCCGCCGACAAUAAUAACAAGAACAUCCCCUGGAUUCCCCGAGAUUAGACGUCAUCUUGGCCCUG--UUAUUUGCCGGCCAGUUGGGCUCUACAAACAGCCCA
............((((.(((..((((((.....((((...))))...(((((((........)))))))...))--))))))).))))....((((((........)))))) ( -28.60)
>DroYak_CAF1 60840 110 + 1
AGUUCCACUCCCGCCGAUAAUAAUUGCAAGAACAUCCCCUGGAUUCCUCGAGAUUAGAUGUCAUCUUGGCCCUG--UUAUUUGCCGGCCACUCGAGCUCUACAAACAGCCCA
(((((....((.((.(((((((....((((((((((..((.((....)).))....)))))..)))))....))--))))).)).))......))))).............. ( -21.60)
>consensus
AGUUCC_____________________AAGAACAUCCCCUGGAUUUCUCGAGAUUAGAUGUCAUCUUGGUCCUG__UUAUUUGCCGGCCAGUCGGGCUCUGCAAACAGCCCA
...........................(((((((((..((.(......).))....)))))..))))((((..............))))....(((((........))))). (-14.34 = -14.30 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	10,527,156 – 10,527,247
Length	91
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	80.00
Mean single sequence MFE	-32.62
Consensus MFE	-19.62
Energy contribution	-19.10
Covariance contribution	-0.52
Combinations/Pair	1.16
Mean z-score	-2.24
Structure conservation index	0.60
SVM decision value	1.12
SVM RNA-class probability	0.917532
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10527156 91 - 22224390
UGGGCUGUUUGCAGUGCCCGACUGGCCGGCAAAUAACACAGGACCAAGAUGACAUCUAAUCUCGAGAAAUCCAAGGGAUGUUCUU---------------------GAAACU
(((.((((((((.(.(((.....)))).)))).....))))..))).(((........)))(((((((((((...)))).)))))---------------------)).... ( -23.50)
>DroSec_CAF1 58290 89 - 1
UGGACUGUUUGCAAAGCCCGACUGGCCGGCAAAUAA--CAGGACCAAGAUGACAUCUAAUCUGGAGAAAUCCAGGGGAUGUUCUU---------------------GGAACU
.....(((((((...(((.....)))..))))))).--.((..((((((..((((((..((((((....))))))))))))))))---------------------))..)) ( -35.20)
>DroSim_CAF1 61982 89 - 1
UGGACUGUUUGCAAAGCCCGACUGGCCGGCAAAUAA--GAGGACCAAGAUGACAUCUAAUCUGGAGAAAUCCAGGGGAUGUUCUU---------------------GGAACU
.....(((((((...(((.....)))..))))))).--.((..((((((..((((((..((((((....))))))))))))))))---------------------))..)) ( -35.30)
>DroEre_CAF1 60227 110 - 1
UGGGCUGUUUGUAGAGCCCAACUGGCCGGCAAAUAA--CAGGGCCAAGAUGACGUCUAAUCUCGGGGAAUCCAGGGGAUGUUCUUGUUAUUAUUGUCGGCGGGAGUGGAACU
((((((.(....).)))))).((.((((((((((((--((((..(.((((...)))).(((((.((....))..))))))..))))))))..)))))))).))......... ( -41.90)
>DroYak_CAF1 60840 110 - 1
UGGGCUGUUUGUAGAGCUCGAGUGGCCGGCAAAUAA--CAGGGCCAAGAUGACAUCUAAUCUCGAGGAAUCCAGGGGAUGUUCUUGCAAUUAUUAUCGGCGGGAGUGGAACU
..(((..((((.......))))..)))(((......--....)))((((..((((((..(((.((....)).)))))))))))))..........((.((....)).))... ( -27.20)
>consensus
UGGGCUGUUUGCAGAGCCCGACUGGCCGGCAAAUAA__CAGGACCAAGAUGACAUCUAAUCUCGAGAAAUCCAGGGGAUGUUCUU_____________________GGAACU
(((.((((((((...(((.....)))..))))))......)).)))....(((((((...((.((....)).)).))))))).............................. (-19.62 = -19.10 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:14 2006